ORCID Profile
0000-0001-9596-3552
Current Organisations
School of Medical & Health Sciences, University of Economics and Human Sciences in Warsaw: Warsaw, PL
,
School of Medical & Health Sciences, University of Economics and Human Sciences in Warsaw
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Slovak University of Agriculture
,
University of Sydney
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Virology | Microbiology | Host-Parasite Interactions | Genomics | Infectious Agents | Microbial Ecology | Genome Structure and Regulation | Ecology | Crop and Pasture Protection (Pests, Diseases and Weeds) | Invasive Species Ecology | Genetics | Evolutionary Biology | Population, Ecological and Evolutionary Genetics | Ecological Physiology | Biological Adaptation
ANZSRC Socio-Economic Objective (SEO)
Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Expanding Knowledge in the Biological Sciences | Disease Distribution and Transmission (incl. Surveillance and Response) | Control of Pests, Diseases and Exotic Species at Regional or Larger Scales | Flora, Fauna and Biodiversity of environments not elsewhere classified | Control of Pests, Diseases and Exotic Species not elsewhere classified | Aquaculture Fin Fish (excl. Tuna) |
Related Links
Publications
Bioinformatics resources for SARS-CoV-2 discovery and surveillance
Publisher: Oxford University Press (OUP)
Date: 08-01-2021
DOI: 10.1093/BIB/BBAA386
Abstract: In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In addition to virus discovery, these NGS technologies and bioinformatics resources are currently being employed for ongoing genomic surveillance of SARS-CoV-2 worldwide, tracking its spread, evolution and patterns of variation on a global scale. In this review, we summarize the bioinformatics resources used for the discovery and surveillance of SARS-CoV-2. We also discuss the advantages and disadvantages of these bioinformatics resources and highlight areas where additional technical developments are urgently needed. Solutions to these problems will be beneficial not only to the prevention and control of the current COVID-19 pandemic but also to infectious disease outbreaks of the future.
Molecular epidemiology of an outbreak of infection with hepatitis C virus in recipients of anti-D immunoglobulin
Publisher: Elsevier BV
Date: 05-1995
DOI: 10.1016/S0140-6736(95)91993-7
Abstract: In a retrospective investigation of possible transmission of hepatitis C virus (HCV) by anti-rhesus D immunoglobulin (anti-D) in 1977, we compared variants infecting anti-D recipients in Ireland of one of the implicated batches with those of epidemiologically unrelated HCV-infected in iduals. All 100 of the recipients of the batch investigated to date were infected with a single genotype (type 1), consistent with a single-source outbreak, whereas a wider range of genotypes (1, 2, and 3) were found in anti-HCV positive in iduals from Ireland infected by different routes. Nucleotide sequences from a 222 base fragment from the NS-5 region of the genome lified from stored aliquots of the implicated batch closely matched those detected in anti-D recipients 17 years after the transmission event. This study shows the value of molecular epidemiological techniques for identifying distant sources of infection, and for the epidemiological investigation of the current distribution and transmission of HCV in different populations.
A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease
Publisher: Elsevier BV
Date: 02-2023
Self-reported confidence in patient safety knowledge among Australian undergraduate nursing students: A multi-site cross-sectional survey study
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.IJNURSTU.2017.03.006
Abstract: Patient safety is critical to the provision of quality health care and thus is an essential component of nurse education. To describe first, second and third year Australian undergraduate nursing students' confidence in patient safety knowledge acquired in the classroom and clinical settings across the three years of the undergraduate nursing program. A cross-sectional online survey conducted in 2015. Seven Australian universities with c uses across three states (Queensland, New South Wales, South Australia). A total of 1319 Australian undergraduate nursing students. Participants were surveyed using the 31-item Health Professional Education in Patient Safety Survey (H-PEPSS). Descriptive statistics summarised the s le and survey responses. Paired t-tests, ANOVA and generalized-estimating-equations models were used to compare responses across learning settings (classroom and clinical), and year of nursing course. Participants were most confident in their learning of clinical safety skills and least confident in learning about the sociocultural dimensions of working in teams with other health professionals, managing safety risks and understanding human and environmental factors. Only 59% of students felt confident they could approach someone engaging in unsafe practice, 75% of students agreed it was difficult to question the decisions or actions of those with more authority, and 78% were concerned they would face disciplinary action if they made a serious error. One patient safety subscale, Recognising and responding to remove immediate safety risks, was rated significantly higher by third year nursing students than by first and second year students. Two broader aspects of patient safety scales, Consistency in how patient safety issues are dealt with by different preceptors, and System aspects of patient safety are well covered in our program, were rated significantly higher by first year nursing students than by second and third year students. One scale, Understanding that reporting adverse events and close calls can lead to change and can reduce recurrence of events, was rated significantly higher by third year students than first and second year students. In order are to achieve meaningful improvements in patient safety, and create harm free environments for patients, it is crucial that nursing students develop confidence communicating with others to improve patient safety, particularly in the areas of challenging poor practice, and recognising, responding to and disclosing adverse events, including errors and near misses.
Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression
Publisher: Elsevier BV
Date: 09-2016
The Evolutionary and Epidemiological Dynamics of the Paramyxoviridae
Publisher: Springer Science and Business Media LLC
Date: 24-01-2008
The Biological Object Notation (BON): a structured file format for biological data.
Publisher: Springer Science and Business Media LLC
Date: 25-06-2018
DOI: 10.1038/S41598-018-28016-6
Abstract: The large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between computers and applications. There has also been a substantial increase in the amount of metadata associated with biological data sets, which is being increasingly incorporated into existing data formats. Despite the existence of structured formats based on XML, biological data sets are mainly formatted using unstructured file formats, and the incorporation of metadata results in increasingly complex parsing routines such that they become more error prone. To overcome these problems, we present the “biological object notation” (BON) format, a new way to exchange and parse nearly all biological data sets more efficiently and with less error than other currently available formats. Based on JavaScript Object Notation (JSON), BON simplifies parsing by clearly separating the biological data from its metadata and reduces complexity compared to XML based formats. The ability to selectively compress data up to 87% compared to other file formats and the reduced complexity results in improved transfer times and less error prone applications.
The impact of host genetic diversity on virus evolution and emergence
Publisher: Wiley
Date: 05-12-2017
DOI: 10.1111/ELE.12890
Abstract: Accumulating evidence indicates that bio ersity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the ersity of species within an environment as an overall measure of bio ersity, overlooking the role of genetic ersity within a particular host species. Although theoretical models propose that host genetic ersity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic ersity increases both parasite genetic ersity and the likelihood of a host being a donor in RABV cross-species transmission events. We conclude that host genetic ersity may be an important determinant of parasite evolution and emergence.
A molecular epidemiology study of Australian bat lyssavirus
Publisher: Microbiology Society
Date: 02-2003
Abstract: The genetic ersity of Australian bat lyssavirus (ABL) was investigated by comparing 24 ABL isolate glycoprotein (G) gene nucleotide sequences with those of 37 lyssaviruses representing Lyssavirus genotypes 1-6. Phylogenetic analyses indicated that ABL forms a monophyletic group separate from other lyssaviruses. This group differentiates into two clades: one associated with Pteropus (flying fox) species, the other with the insectivorous bat Saccolaimus flaviventris. Calculation of percentage nucleotide identities between isolates of the two clades revealed up to 18.7 % nucleotide sequence ergence between the two ABL variants. These observations suggest that ABL is a separate lyssavirus species with a similar epidemiology to chiropteran rabies virus (RV), where two distinct ABL variants co-exist in Australia in bat species with dissimilar ecology. Analyses of selection pressures in ABL G gene sequences provided some evidence of weak positive selection within the endodomain at amino acids 499 and 501, although in general the dominant evolutionary process observed was purifying selection. This intimates that, in nature, isolates of ABL, like those of RV, are subject to relatively strong selective constraints, suggesting a stability of host species, cell tropisms and ecological conditions.
The introduction of fox rabies into Italy (2008–2011) was due to two viral genetic groups with distinct phylogeographic patterns
Publisher: Elsevier BV
Date: 07-2013
DOI: 10.1016/J.MEEGID.2013.03.051
Abstract: Fox rabies re-emerged in north-eastern Italy at the end of 2008 and circulated until early 2011. As with previous rabies epidemics, the Italian cases were linked to the epidemiological situation in adjacent regions. To obtain a comprehensive picture of the dynamics of the recent Italian epidemic, we performed a detailed evolutionary analysis of RABVs circulating in north-eastern Italy. Sequences were obtained for the hyper-variable region of the nucleoprotein gene, the complete glycoprotein gene, and the intergenic region G-L from 113 selected fox rabies cases. We identified two viral genetic groups, here referred to as Italy-1 and Italy-2. Phylogenetic and phylogeographic analyses revealed that both groups had been circulating in the Western Balkans and Slovenia in previous years and were only later introduced into Italy (into the Friuli Venezia Giulia region-FVG), occupying different areas of the Italian territories. Notably, viruses belonging to the Italy-1 group remained confined to the region of introduction and their spread was minimised by the implementation of oral fox vaccination c aigns. In contrast, Italy-2 viruses spread westward over a territory of 100 km from their first identification in FVG, likely crossing the northern territories where surveillance was inadequate. A genetic sub-group (Italy-2A), characterised by a unique amino acid mutation (D106A) in the N gene, was also observed to occupy a distinct geographic cluster. This molecular epidemiological analysis of the 2008-2011 fox rabies epidemic will contribute to future control programmes both at national and regional levels. In particular, our findings highlight the weaknesses of the national surveillance strategy in the period preceding rabies re-emergence, and of control plans implemented immediately after rabies notification, and underline the need of a coordinated approach at the regional level for both the surveillance and control of wildlife rabies.
Virome composition in marine fish revealed by meta-transcriptomics
Publisher: Oxford University Press (OUP)
Date: 2021
DOI: 10.1093/VE/VEAB005
Abstract: Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify ergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, positive-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae, and Flaviviridae, and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition—viral richness, abundance, and ersity—can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish s led here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community ersity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi, and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
RNA Viruses in Hymenopteran Pollinators: Evidence of Inter-Taxa Virus Transmission via Pollen and Potential Impact on Non-Apis Hymenopteran Species
Publisher: Public Library of Science (PLoS)
Date: 22-12-2010
Analysis of flavivirus envelope proteins reveals variable domains that reflect their antigenicity and may determine their pathogenesis
Publisher: Elsevier BV
Date: 03-1995
DOI: 10.1016/0168-1702(94)00090-Y
Abstract: Studies on the molecular basis of flavivirus neutralisation, attenuation and tropism indicate that amino acid substitutions, in different parts of the envelope gene, may be responsible for the altered phenotypes. However, the association of particular substitutions with in idual characteristics has proven difficult. Comparative analysis of all known tick-borne flavivirus envelope proteins through sequence alignment and a sliding window, reveals clusters of amino acid variation distributed throughout the envelope protein coding region. Further comparison with mosquito-borne flaviviruses reveals essentially the same profile of variability throughout the envelope protein sequence although there is a major difference within the postulated B domain of these viruses which may reflect their different evolutionary development. Most phenotypically variant properties, such as serotypic differences, variants characteristic of vaccine strains, altered tropisms and neutralisation escape mutants, map within the variable clusters. Thus, we propose that natural mutagenesis and selection may occur at specific sites that do not destroy the secondary and tertiary E protein structure and that the variable clusters represent the exposed surface amino acids of the envelope protein defining antigenicity, tropicity and pathogenesis.
Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.VIROL.2014.11.026
Abstract: To determine the bio ersity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses.
The RNA Virus Quasispecies: Fact or Fiction?
Publisher: Elsevier BV
Date: 07-2010
Dengue Virus Type 3, Cuba, 2000–2002
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 05-2005
High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection
Publisher: Springer Science and Business Media LLC
Date: 03-03-2020
DOI: 10.1038/S41598-020-60992-6
Abstract: The ersity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing (“meta-transcriptomics”) to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. S les were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species ersity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease.
Presence of Oseltamivir-Resistant Pandemic A/H1N1 Minor Variants Before Drug Therapy With Subsequent Selection and Transmission
Publisher: Oxford University Press (OUP)
Date: 10-09-2012
Global transmission of influenza viruses from humans to swine
Publisher: Microbiology Society
Date: 10-2012
Abstract: To determine the extent to which influenza viruses jump between human and swine hosts, we undertook a large-scale phylogenetic analysis of pandemic A/H1N1/09 (H1N1pdm09) influenza virus genome sequence data. From this, we identified at least 49 human-to-swine transmission events that occurred globally during 2009–2011, thereby highlighting the ability of the H1N1pdm09 virus to transmit repeatedly from humans to swine, even following adaptive evolution in humans. Similarly, we identified at least 23 separate introductions of human seasonal (non-pandemic) H1 and H3 influenza viruses into swine globally since 1990. Overall, these results reveal the frequency with which swine are exposed to human influenza viruses, indicate that humans make a substantial contribution to the genetic ersity of influenza viruses in swine, and emphasize the need to improve biosecurity measures at the human–swine interface, including influenza vaccination of swine workers.
Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions
Publisher: Cold Spring Harbor Laboratory
Date: 21-10-2022
DOI: 10.1101/2022.10.20.513122
Abstract: More than 70 bat species are found in mainland Australia, including five species of megabat from a single genus (family Pteropodidae) and more than 65 species representing six families of microbats. The conservation status of these animals varies from least concern to endangered. Research directed at evaluating the impact of microorganisms on bat health has been generally restricted to surveillance for specific pathogens. While most of the current bat virome studies focus on s ling apparently healthy in iduals, little is known about the infectome of diseased bats. We performed traditional diagnostic techniques and metatranscriptomic sequencing on tissue s les from 43 in idual bats, comprising three flying fox and two microbat species experiencing a range of disease syndromes, including mass mortality, neurological signs, pneumonia and skin lesions. We identified reads from four pathogenic bacteria and two pathogenic fungi, including Pseudomonas aeruginosa in lung s les from flying foxes with peracute pneumonia, and with dermatitis. Of note, we identified the recently discovered Hervey pteropid gammaretrovirus, with evidence of replication consistent with an exogenous virus, in a bat with lymphoid leukemia. In addition, one novel picornavirus, at least three novel astroviruses and bat pegiviruses were identified. We suggest that the most likely cause of peracute lung disease was Pseudomonas aeruginosa , while we suspect Hervey pteropid gammaretrovirus was associated with lymphoid leukemia. It is possible that any of the novel astroviruses could have contributed to the presentation of skin lesions in in idual microbats. This study highlights the importance of studying the role of microorganisms in bat health and conservation. Bats have been implicated as reservoir hosts for zoonotic disease of concern, however, the burden of microorganism including viruses on bat health and disease is understudied. Here we incorporated veterinary diagnostics and RNA sequencing to identify the presence of microbes and viruses with possible pathogenic status in Australian bats with varying disease presentations. These techniques were able to effectively identify and describe several pathogenic species of bacteria and fungi in addition to known and novel viruses. This study emphasises the importance of screening pathogens in cases of bat mortality for the conservation of this erse order.
Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.MEEGID.2004.06.011
Abstract: The human immunodeficiency virus (HIV) pandemic continues to grow at an alarming rate, with a further 5 million new infections in 2003. Some 3.5 million of these were in sub-Saharan Africa, where approximately 70% of the world's HIV-positive population resides. In contrast, the spread of HIV in high-income countries has slowed since its discovery in the 1980s, and in regions such as Western Europe prevalence has decreased. Here, we employ coalescent methods to compare the epidemic growth rates of two subtypes of HIV-1 with differing epidemiological profiles: subtype C, which is dominant in sub-Saharan Africa and associated with heterosexual transmission, and subtype B, the main cause of AIDS in Western Europe and North America, and which was primarily transmitted through homosexual sex and injecting drug use. We show that although both subtypes emerged at approximately the same time ( approximately 1960), they have widely differing patterns of exponential population growth. At its current growth rate the epidemic of subtype C in sub-Saharan Africa is doubling every 2.4 years, which is approximately half the rate observed during the early stages of the subtype B epidemic in Western Europe and North America. However, the subtype C growth rate is still 5-10 times greater than that estimated for the blood-borne hepatitis C virus, supporting the hypothesis that sexual transmission has been primarily responsible for the HIV epidemic in sub-Saharan Africa.
Genomics and evolution of Aedes-borne flaviviruses
Publisher: Microbiology Society
Date: 09-09-2009
Abstract: We analysed the complete coding sequences of all recognized species of Aedes-borne flavivirus, including previously uncharacterized viruses within the yellow fever virus (YFV), Spondweni virus (SPOV) and dengue virus (DENV) groups. Two major phylogenetic lineages were revealed: one included the YFV and Entebbe bat virus groups, and the other included the DENV, SPOV and Culex-borne flavivirus groups. This analysis supported previous evidence that Culex-borne flaviviruses have evolved from ancestral Aedes-borne viruses. However, the topology at the junction between these lineages remains complex and may be refined by the discovery of viruses related to the Kedougou virus. Additionally, viral evolution was found to be associated with the appearance of new biological characteristics mutations that may modify the envelope protein structure were identified for seven viruses within the YFV group, and an expansion of host-vector range was identified in the two major evolutionary lineages, which in turn may facilitate the emergence of mosquito-borne flaviviruses.
Partial immunity and SARS-CoV-2 mutations—Response
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-04-2021
Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses
Publisher: American Society for Microbiology
Date: 09-2016
DOI: 10.1128/JVI.00832-16
Abstract: Hepadnaviruses (hepatitis B viruses [HBVs]) are the only animal viruses that replicate their DNA by reverse transcription of an RNA intermediate. Until recently, the known host range of hepadnaviruses was limited to mammals and birds. We obtained and analyzed the first hibian HBV genome, as well as several prototype fish HBVs, which allow the first comprehensive comparative genomic analysis of hepadnaviruses from four classes of vertebrates. Bluegill hepadnavirus (BGHBV) was characterized from in-house viral metagenomic sequencing. The African cichlid hepadnavirus (ACHBV) and the Tibetan frog hepadnavirus (TFHBV) were discovered using in silico analyses of the whole-genome shotgun and transcriptome shotgun assembly databases. Residues in the hydrophobic base of the capsid (core) proteins, designated motifs I, II, and III, are highly conserved, suggesting that structural constraints for proper capsid folding are key to capsid protein evolution. Surface proteins in all vertebrate HBVs contain similar predicted membrane topologies, characterized by three transmembrane domains. Most striking was the fact that BGHBV, ACHBV, and the previously described white sucker hepadnavirus did not form a fish-specific monophyletic group in the phylogenetic analysis of all three hepadnaviral genes. Notably, BGHBV was more closely related to the mammalian hepadnaviruses, indicating that cross-species transmission events have played a major role in viral evolution. Evidence of cross-species transmission was also observed with TFHBV. Hence, these data indicate that the evolutionary history of the hepadnaviruses is more complex than previously realized and combines both virus-host co ergence over millions of years and host species jumping. IMPORTANCE Hepadnaviruses are responsible for significant disease in humans (hepatitis B virus) and have been reported from a erse range of vertebrates as both exogenous and endogenous viruses. We report the full-length genome of a novel hepadnavirus from a fish and the first hepadnavirus genome from an hibian. The novel fish hepadnavirus, s led from bluegills, was more closely related to mammalian hepadnaviruses than to other fish viruses. This phylogenetic pattern reveals that, although hepadnaviruses have likely been associated with vertebrates for hundreds of millions of years, they have also been characterized by species jumping across wide phylogenetic distances.
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
Publisher: Springer Science and Business Media LLC
Date: 18-08-2022
DOI: 10.1038/S41564-022-01191-Z
Abstract: The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes s led from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.
Viral Evolution in the Genomic Age
Publisher: Public Library of Science (PLoS)
Date: 02-10-2007
The Current Health and Wellbeing of the Survivors of the Rana Plaza Building Collapse in Bangladesh: A Qualitative Study
Publisher: MDPI AG
Date: 02-07-2019
Abstract: This study aims to identify the ongoing physical and psychological health vulnerabilities of the readymade garment (RMG) factory workers involved in the Rana Plaza building collapse in 2013, along with their experiences within the current socioeconomic and political contexts of Bangladesh. Seventeen Rana Plaza survivors participated in unstructured, face-to-face, in-depth interviews. Interviews were thematically analyzed using Haddon’s matrix to examine pre-event, event, and post-event injury experiences. The collapse of the Rana Plaza building resulted in significant physical and emotional trauma for those who survived the event. The majority of the participants were forced to attend work on the day of the collapse. Participants reported physical health complaints related to bone injuries/fractures and utation, severe headache, kidney problems, and functional difficulties. In addition to the reported physical health issues, the participants revealed psychological health issues including trauma, depression and suicidal ideation, sleep disorders, anxiety, and sudden anger. Participants described barriers to their potential for re-employment in the RMG sector and outlined their limited access to free healthcare for follow-up treatment. Those who survived the collapse of the Rana Plaza building continue to experience significant adverse physical and emotional outcomes related to the disaster. Yet, they have little recourse to ensure the availability of adequate health care and rehabilitation. Given the international reliance on the Bangladeshi RMG industry, continued pressure to ensure care is provided for these survivors, and to reduce the risk of future disasters, is necessary.
HIV evolution: CTL escape mutation and reversion after transmission
Publisher: Springer Science and Business Media LLC
Date: 08-02-2004
DOI: 10.1038/NM992
Virological Sampling of Inaccessible Wildlife with Drones
Publisher: MDPI AG
Date: 02-06-2018
DOI: 10.3390/V10060300
Transgenic Virus Resistance in Crop-WildCucurbita pepoDoes Not Prevent Vertical Transmission ofZucchini yellow mosaic virus
Publisher: Scientific Societies
Date: 11-2015
DOI: 10.1094/PDIS-10-14-1062-RE
Abstract: Zucchini yellow mosaic virus (ZYMV) is an economically important pathogen of cucurbits that is transmitted both horizontally and vertically. Although ZYMV is seed-transmitted in Cucurbita pepo, the potential for seed transmission in virus-resistant transgenic cultivars is not known. We crossed and backcrossed a transgenic squash cultivar with wild C. pepo, and determined whether seed-to-seedling transmission of ZYMV was possible in seeds harvested from transgenic backcrossed C. pepo. We then compared these transmission rates to those of non-transgenic (backcrossed and wild) C. pepo. The overall seed-to-seedling transmission rate in ZYMV was similar to those found in previous studies (1.37%), with no significant difference between transgenic backcrossed (2.48%) and non-transgenic (1.03%) backcrossed and wild squash. Fewer transgenic backcrossed plants had symptom development (7%) in comparison with all non-transgenic plants (26%) and may be instrumental in preventing yield reduction due to ZYMV. Our study shows that ZYMV is seed transmitted in transgenic backcrossed squash, which may affect the spread of ZYMV via the movement of ZYMV-infected seeds. Deep genome sequencing of the seed-transmitted viral populations revealed that 23% of the variants found in this study were present in other vertically transmitted ZYMV populations, suggesting that these variants may be necessary for seed transmission or are distributed geographically via seeds.
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
Publisher: Springer Science and Business Media LLC
Date: 08-03-2017
DOI: 10.1038/NATURE21674
Abstract: Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this in idual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
Publisher: The Royal Society
Date: 07-07-2014
Abstract: Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among erse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.
A molecular portrait of maternal sepsis from Byzantine Troy
Publisher: eLife Sciences Publications, Ltd
Date: 10-01-2017
DOI: 10.7554/ELIFE.20983
Abstract: Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic ersity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.
The Ecology of Viral Emergence
Publisher: Annual Reviews
Date: 29-09-2022
DOI: 10.1146/ANNUREV-VIROLOGY-100120-015057
Abstract: The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component.
Experiences of Health Professionals Caring for People Presenting to the Emergency Department After Taking Crystal Methamphetamine (“ICE”)
Publisher: Informa UK Limited
Date: 09-12-2016
DOI: 10.1080/01612840.2016.1251516
Abstract: Globally, addiction to "ICE" (crystal meth hetamine) is increasing and presents emergency health care services personnel with a number of challenges. This paper reports the first of two major themes arising from a qualitative study investigating health professionals' experiences' managing people presenting to the Emergency Department (ED) after taking "ICE." The theme "Caring for people who use 'ICE' when presenting to EDs" comprises five subthemes. These are: (a) expecting the unexpected: "they're just off their heads" (b) complexity of care: "underlying trauma and emotional dysregulation"
Heading Off an Influenza Pandemic
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-08-2005
A Divergent Hepatitis D-Like Agent in Birds
Publisher: MDPI AG
Date: 17-12-2018
DOI: 10.3390/V10120720
Abstract: Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a ergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.
Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia.
Publisher: Public Library of Science (PLoS)
Date: 20-11-2014
Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene
Publisher: Microbiology Society
Date: 10-2005
Abstract: RNA viruses of the family Rhabdoviridae include arthropod-borne agents that infect plants, fish and mammals, and also include a variety of non-vector-borne mammalian viruses. Herein is presented a molecular phylogenetic analysis, the largest undertaken to date, of 56 rhabdoviruses, including 20 viruses which are currently unassigned or assigned as tentative species within the Rhabdoviridae . Degenerate primers targeting a region of block III of the L polymerase gene were defined and used for RT-PCR lification and sequencing. A maximum-likelihood phylogenetic analysis of a 158-residue L polymerase amino acid sequence produced an evolutionary tree containing the six recognized genera of the Rhabdoviridae and also enabled us to identify four more monophyletic groups of currently unclassified rhabdoviruses that we refer to as the ‘Hart Park’, ‘Almpiwar’, ‘Le Dantec’ and ‘Tibrogargan’ groups. The broad phylogenetic relationships among these groups and genera also indicate that the evolutionary history of rhabdoviruses was strongly influenced by mode of transmission, host species (plant, fish or mammal) and vector (orthopteran, homopteran or dipteran).
Pandemics–Keep Calm and Carry On
Publisher: Public Library of Science (PLoS)
Date: 04-02-2014
EVOLUTIONARY BIOLOGY OF HUMAN IMMUNODEFICIENCY VIRUS
Publisher: Annual Reviews
Date: 11-1994
The spread of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: A phylogeographic approach
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.VIROL.2013.08.028
Abstract: The emergence and spread of Type 2 Porcine Reproductive and Respiratory Syndrome virus (Type 2 PRRSV) in North America is heavily influenced by the multiple site production system used in the hog industry. However, it is unclear how anthropogenic factors such has this have shaped the current spatial distribution of PRRSV genotypes. We employed Bayesian phylogeographic analyses of 7040 ORF5 sequences to reveal the recent geographical spread of Type 2 PRRSV in North America. The directions and intensities in our inferred virus traffic network closely mirror the hog transportation. Most notably, we reveal multiple viral introductions from Canada into the United States causing a major shift in virus genetic composition in the Midwest USA that went unnoticed by the regular surveillance and field epidemiological studies. Overall, these findings provide important insights into the dynamics of Type 2 PRRSV evolution and spread that will facilitate programs for control and prevention.
Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone
Publisher: Elsevier BV
Date: 06-2015
Virome composition in marine fish revealed by meta-transcriptomics
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2021
DOI: 10.1101/2020.05.06.081505
Abstract: Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterised the viromes of 19 wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify ergent viruses that often evade characterisation. From this, we identified 25 new vertebrate-associated viruses and a further 22 viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, negative-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae and Flaviviridae and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition – viral richness, abundance and ersity – can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish s led here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community ersity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
Segmental configuration and putative origin of the reassortant orbivirus, epizootic hemorrhagic disease virus serotype 6, strain Indiana
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.VIROL.2011.12.004
Abstract: In 2006, an exotic reassortant orbivirus, epizootic hemorrhagic disease virus serotype 6 (EHDV-6) [strain (Indiana)], was first detected in the United States. To characterize the reassortment configuration of this virus and to conclusively determine the parental virus of each RNA segment, the complete genome of EHDV-6 (Indiana) was sequenced, in addition to the genomes of representative EHDV-6 and EHDV-2 isolates. Based on genomic comparisons to all other EHDV serotypes, we determined that EHDV-6 (Indiana) originated from a reassortment event between the Australian prototype strain of EHDV-6 (CSIRO 753) and the North American topotype of EHDV-2 (Alberta). Additionally, phylogenetic analysis of all EHDV-6 (Indiana) isolates detected in the United States from 2006 to 2010 suggests that the virus may be undergoing continual reassortment with EHDV-2 (Alberta). In 2010, EHDV-6 (CSIRO 753) was detected in Guadeloupe, demonstrating that the parental virus of the reassortment event is circulating in the Caribbean.
Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia.
Publisher: Springer Science and Business Media LLC
Date: 05-09-2020
DOI: 10.1186/S13071-020-04325-6
Abstract: Wildlife species carry a remarkable ersity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their ersity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites. We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) s led from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus southern brown bandicoot, Isoodon obesulus sw wallaby, Wallabia bicolor bare-nosed wombat, Vombatus ursinus ), one bird (regent honeyeater, Anthochaera phrygia ) and one hibian (eastern dwarf tree frog, Litoria fallax ). S les corresponded to both clinically healthy and diseased in iduals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences. We detected trypanosome sequences in all six species of vertebrates s led, with positive s les in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other hibians. To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic ersity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from erse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are ergent in genome sequence.
Identification of a Novel Papillomavirus Associated with Squamous Cell Carcinoma in a Domestic Cat
Publisher: MDPI AG
Date: 20-01-2020
DOI: 10.3390/V12010124
Abstract: Papillomaviruses infect the skin and mucosal surfaces of erse animal hosts with consequences ranging from asymptomatic colonization to highly malignant epithelial cancers. Increasing evidence suggests a role for papillomaviruses in the most common cutaneous malignancy of domestic cats, squamous cell carcinoma (SCC). Using total DNA sequencing we identified a novel feline papillomavirus in a nasal biopsy taken from a cat presenting with both nasal cavity lymphoma and recurrent squamous cell carcinoma affecting the nasal planum. We designate this novel virus as Felis catus papillomavirus 6 (FcaPV6). The complete FcaPV6 7453 bp genome was similar to those of other feline papillomaviruses and phylogenetic analysis revealed that it was most closely related to FcaPV3, although was distinct enough to represent a new viral type. Classification of FcaPV6 in a new genus alongside FcaPVs 3, 4 and 5 is supported. Archived excisional biopsy of the SCC, taken 20 months prior to presentation, was intensely positive on p16 immunostaining. FcaPV6, lified using virus-specific, but not consensus, PCR, was the only papillomavirus detected in DNA extracted from the SCC. Conversely, renal lymphoma, s led at necropsy two months after presentation, tested negative on FcaPV6-specific PCR. In sum, using metagenomics we demonstrate the presence of a novel feline papillomavirus in association with cutaneous squamous cell carcinoma.
Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna (Acridotheres tristis) in Australia
Publisher: Elsevier BV
Date: 12-2021
Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition
Publisher: MDPI AG
Date: 27-01-2022
DOI: 10.3390/V14020257
Abstract: Viruses that infect fish are understudied, yet they provide important evolutionary context to the viruses that infect terrestrial vertebrates. We surveyed gill tissue meta-transcriptomes collected from two species of native freshwater fish from Aotearoa New Zealand—Retropinna retropinna and Gobiomorphus cotidianus. A total of 64 fish were used for gill tissue meta-transcriptomic sequencing, from populations with contrasting life histories—landlocked (i.e., lacustrine) and diadromous—on the South Island and Chatham Islands. We observed that both viral richness and taxonomic ersity were significantly associated with life history and host species, with lacustrine R. retropinna characterised by higher viral alpha ersity than diadromous R. retropinna. Additionally, we observed transcripts of fish viruses from 12 vertebrate host-associated virus families, and phylogenetically placed eight novel RNA viruses and three novel DNA viruses in the Astroviridae, Paramyxoviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, Poxviridae, Alloherpesviridae, and Adintoviridae in their evolutionary contexts. These results represent an important survey of the viruses that infect two widespread native fish species in New Zealand, and provide insight useful for future fish virus surveys.
Human land-use impacts viral diversity and abundance in a New Zealand river
Publisher: Cold Spring Harbor Laboratory
Date: 04-01-2022
DOI: 10.1101/2022.01.04.474996
Abstract: Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land-use on viral ersity and evolution in water systems such as rivers. We used metagenomic next-generation sequencing to compare the ersity and abundance of viruses at s ling sites along a single river in New Zealand that differed in human land use impact, ranging from pristine to urban. From this we identified 504 putative virus species, of which 97% were novel. Many of the novel viruses were highly ergent, and likely included a new subfamily within the Parvoviridae . We identified at least 63 virus species that may infect vertebrates – most likely fish and water birds – from the Astroviridae, Birnaviridae, Parvoviridae and Picornaviridae . No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land-use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher ersity (327 virus species) than the farming (n=150) and pristine sites (n=119), and more viruses were shared between the urban and farming sites (n=76) than between the pristine and farming or urban sites (n=24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants and fungi. We also identified viruses linked to agriculture and human impact at the river s ling sites in farming and urban areas that were not present at the native forest sites. Overall, our study shows that human land-use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanization on water systems.
Genes, trees and infections: Molecular evidence in epidemiology
Publisher: Elsevier BV
Date: 07-1994
DOI: 10.1016/0169-5347(94)90291-7
Abstract: Molecular phylogenies constitute an important new way of tracking the progress of viral epidemics. The phylogenetic analysis of viral sequence data provides information on the origin, spread and maintenance of infections and can be used to reconstruct contact networks of infected in iduals. Analysis of the branching structure of phylogenetic trees also allows inferences to be made about the rate of transmission and the distinction between endemic and epidemic infections, and provides estimates of the numbers of infected in iduals.
High Resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 22-11-2021
Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China
Publisher: Springer Science and Business Media LLC
Date: 11-01-2023
DOI: 10.1186/S40168-022-01446-1
Abstract: The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the ersity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. We report the meta-transcriptomic sequencing of nearly 2000 s les of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016–2019. We document the natural ersity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within in idual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. Our data show that honeybee viruses are more widespread, prevalent, and genetically erse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale.
Eco-Anxiety: How thinking about climate change-related environmental decline is affecting our mental health
Publisher: Wiley
Date: 14-11-2019
DOI: 10.1111/INM.12673
Evolutionary History of MHC Class I Genes in the Mammalian Order Perissodactyla
Publisher: Springer Science and Business Media LLC
Date: 09-1999
DOI: 10.1007/PL00006554
Abstract: We carried out an analysis of partial sequences from expressed major histocompatibility complex (MHC) class I genes isolated from a range of equid species and more distantly related members of the mammalian order Perissodactyla. Phylogenetic analysis revealed a minimum of six groups, five of which contained genes and alleles that are found in equid species and one group specific to the rhinoceros. Four of the groups contained only one, or very few sequences, indicating the presence of relatively nonpolymorphic loci, while another group contained the majority of the equid sequences identified. These data suggest that a ersification of MHC genes took place after the split between the Equidae and the Rhinocerotidae yet before the speciation events within the genus Equus.
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient
Publisher: Microbiology Society
Date: 12-2007
Abstract: Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of DENV-1 from 12 patients infected on the island of New Caledonia were obtained, five of which carried genotype I viruses and six, genotype II viruses. One patient harboured a mixed infection, containing viruses assigned to both genotypes I and II, as well as a number of inter-genotypic recombinants. This is the first report of a population of dengue viruses isolated from a patient containing both parental and recombinant viruses.
Author response: A molecular portrait of maternal sepsis from Byzantine Troy
Publisher: eLife Sciences Publications, Ltd
Date: 21-11-2016
Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine
Publisher: Elsevier BV
Date: 10-2014
The role of pathogen genomics in assessing disease transmission
Publisher: BMJ
Date: 11-05-2015
DOI: 10.1136/BMJ.H1314
Abstract: Whole genome sequencing (WGS) of pathogens enables the sources and patterns of transmission to be identified during specific disease outbreaks and promises to transform epidemiological research on communicable diseases. This review discusses new insights into disease spread and transmission that have come from the use of WGS, particularly when combined with genomic scale phylogenetic analyses. These include elucidation of the mechanisms of cross species transmission, the potential modes of pathogen transmission, and which people in the population contribute most to transmission. Particular attention is paid to the ability of WGS to resolve in idual patient to patient transmission events. Importantly, WGS data seem to be sufficiently discriminatory to target cases linked to community or hospital contacts and hence prevent further spread, and to investigate genetically related cases without a clear epidemiological link. Approaches to combine evidence from epidemiological with genomic sequencing observations are summarised. Ongoing genomic surveillance can identify determinants of transmission, monitor pathogen evolution and adaptation, ensure the accurate and timely diagnosis of infections with epidemic potential, and refine strategies for their control.
Epidemiological Dynamics and Phylogeography of Influenza Virus in Southern China
Publisher: Oxford University Press (OUP)
Date: 28-08-2012
Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 12-2016
The Evolutionary Genetics of Viral Emergence
Publisher: Springer Berlin Heidelberg
Date: 2007
When HIV spread afar
Publisher: Proceedings of the National Academy of Sciences
Date: 20-11-2007
The evolution of Ebola virus: Insights from the 2013–2016 epidemic
Publisher: Springer Science and Business Media LLC
Date: 10-2016
DOI: 10.1038/NATURE19790
RNA virome diversity and Wolbachia infection in individual Drosophila simulans flies
Publisher: Microbiology Society
Date: 27-10-2021
DOI: 10.1099/JGV.0.001639
Abstract: The endosymbiont bacteria of the genus Wolbachia are associated with multiple mutualistic effects on insect biology, including nutritional and antiviral properties. Members of the genus Wolbachia naturally occur in fly species of the genus Drosophila , providing an operational model host for studying how virome composition may be affected by its presence. Drosophila simulans populations can carry a variety of strains of members of the genus Wolbachia , with the w Au strain associated with strong antiviral protection under experimental conditions. We used D. simulans s led from the Perth Hills, Western Australia, to investigate the potential virus protective effect of the w Au strain of Wolbachia on in idual wild-caught flies. Our data revealed no appreciable variation in virus composition and abundance between in iduals infected or uninfected with Wolbachia associated with the presence or absence of w Au. However, it remains unclear whether w Au might affect viral infection and host survival by increasing tolerance rather than inducing complete resistance. These data also provide new insights into the natural virome ersity of D. simulans . Despite the small number of in iduals s led, we identified a repertoire of RNA viruses, including nora virus, galbut virus, thika virus and La Jolla virus, that have been identified in other species of the genus Drosophila . Chaq virus-like sequences associated with galbut virus were also detected. In addition, we identified five novel viruses from the families Reoviridae , Tombusviridae , Mitoviridae and Bunyaviridae . Overall, this study highlights the complex interaction between Wolbachia and RNA virus infections and provides a baseline description of the natural virome of D. simulans .
Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish
Publisher: MDPI AG
Date: 04-11-2020
DOI: 10.3390/V12111254
Abstract: Tilapia lake virus (TiLV) has caused mass mortalities in farmed and wild tilapia with serious economic and ecological consequences. Until recently, this virus was the sole member of the Amnoonviridae, a family within the order Articulavirales comprising segmented negative-sense RNA viruses. We sought to identify additional viruses within the Amnoonviridae through total RNA sequencing (meta-transcriptomics) and data mining of published transcriptomes. Accordingly, we s led marine fish species from both Australia and China and discovered several segments of two new viruses within the Amnoonviridae, tentatively called Flavolineata virus and Piscibus virus, respectively. In addition, by mining vertebrate transcriptome data, we identified nine additional virus transcripts matching to multiple genomic segments of TiLV in both marine and freshwater fish. These new viruses retained sequence conservation with the distantly related Orthomyxoviridae in the RdRp subunit PB1, but formed a distinct and erse phylogenetic group. These data suggest that the Amnoonviridae have a broad host range within fish and that greater animal s ling will identify additional ergent members of the Articulavirales.
The factors influencing burnout and job satisfaction among critical care nurses: a study of Saudi critical care nurses
Publisher: Hindawi Limited
Date: 18-05-2016
DOI: 10.1111/JONM.12386
Abstract: The aim of the study was to explore the prevalence of burnout and job satisfaction among Saudi national critical care nurses. Burnout is caused by a number of factors, including personal, organisational and professional issues. Previous literature reports a strong relationship between burnout and job satisfaction among critical care nurses. Little is known about this phenomenon among Saudi national critical care nurses. A convenience s le of 150 Saudi national critical care nurses from three hospitals in Hail, Saudi Arabia were included in a cross-sectional survey. Saudi national critical care registered nurses reported moderate to high levels of burnout in the areas of emotional exhaustion and depersonalisation. Participants also reported a feeling of ambivalence and dissatisfaction with their jobs but were satisfied with the nature of their work. Saudi national critical care nurses experience moderate to high levels of burnout and low levels of job satisfaction. Burnout is a predictor of job satisfaction for Saudi national critical care nurses. These results provide clear evidence of the need for nurse managers and policy makers to devise strategies to help nurses better cope with a stressful work environment, thereby also improving job satisfaction among Saudi national critical care nurses.
Facemask against viral respiratory infections among Hajj pilgrims: A challenging clusterrandomized trial
Publisher: Public Library of Science (PLoS)
Date: 13-10-2020
What can we predict about viral evolution and emergence?
Publisher: Elsevier BV
Date: 04-2013
Co-circulation of Hantaan, Kenkeme, and Khabarovsk Hantaviruses in Bolshoy Ussuriysky Island, China
Publisher: Elsevier BV
Date: 10-2014
DOI: 10.1016/J.VIRUSRES.2014.07.021
Abstract: Hemorrhagic fever with renal syndrome (HFRS) was first recognized in far eastern Asia in the 1930s, and has been highly prevalent in this region ever since. To reveal the molecular epidemiology of hantaviruses in this region, a total of 374 small mammals (eight species of rodents and one species of shrew) were captured in the Chinese part of the Bolshoy Ussuriysky Island (Heilongjiang Province). Hantavirus sequences were recovered from three striped field mice (Apodemus agrarius), 11 Maximowicz's voles (Microtus maximowiczii), and one flat-skulled shrew (Sorex roboratus). Genetic and phylogenetic analysis revealed the presence of three viruses: Hantaan virus (HTNV), Khabarovsk virus (KHAV), and Kenkeme virus (KKMV). HTNV sequences recovered from A. agrarius were closely related to those identified in Apodemus mice from the surrounding areas, while a new lineage of KHAV was present in M. maximowiczii. Additionally, while the viral sequences recovered from one flat-skulled shrew were most closely related to KKMV, their ergence to the prototype strain suggests that they represent a new viral subtype. Overall, these results suggest that Bolshoy Ussuriysky Island harbors considerable hantavirus ersity.
Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses
Publisher: eLife Sciences Publications, Ltd
Date: 29-01-2015
DOI: 10.7554/ELIFE.05378
Abstract: Although arthropods are important viral vectors, the bio ersity of arthropod viruses, as well as the role that arthropods have played in viral origins and evolution, is unclear. Through RNA sequencing of 70 arthropod species we discovered 112 novel viruses that appear to be ancestral to much of the documented genetic ersity of negative-sense RNA viruses, a number of which are also present as endogenous genomic copies. With this greatly enriched ersity we revealed that arthropods contain viruses that fall basal to major virus groups, including the vertebrate-specific arenaviruses, filoviruses, hantaviruses, influenza viruses, lyssaviruses, and paramyxoviruses. We similarly documented a remarkable ersity of genome structures in arthropod viruses, including a putative circular form, that sheds new light on the evolution of genome organization. Hence, arthropods are a major reservoir of viral genetic ersity and have likely been central to viral evolution.
Patterns and features of methamphetamine‐related presentations to emergency departments in QLD from 2005 to 2017
Publisher: Wiley
Date: 09-06-2019
DOI: 10.1111/INM.12618
Abstract: This study explores the patterns and features of meth hetamine-related presentations to emergency departments (EDs) in Queensland. Despite an overall decrease in the use of meth hetamine in Australian, an increase in the use of the crystalized form of meth hetamine has been noted over recent years. A descriptive observational study was utilized to analyse emergency department (ED) injury surveillance data sourced from Queensland Injury Surveillance Unit (QISU) from 2005 to 2017. Data were analysed for presentations related to stimulants (n = 564) with meth hetamine (n = 250) included as a subcategory. Descriptive statistics were used to identify patterns and features of presentations related to meth hetamines. The relationship between demographic variables, service type variables, and drug type was assessed using chi-square and z-tests. Results included the following: 84.4% of meth hetamine-related presentations were allocated a triage score of 1, 2, or 3 14.8% of all meth hetamine-related presentations required police involvement 18% were brought in by ambulance and 15.6% exhibited behaviour that was either, agitated, aggressive, or violent in nature. Meth hetamine-related presentations more frequently required police or ambulance services and more often included aggression or agitation. Meth hetamine-related presentations to ED have a high acuity and often require other emergency resources (police and ambulance). There is a need to develop policy for managing aggressive and agitated people presenting to EDs as a result of meth hetamine use and to further explore the experience of personnel (police and ambulance) managing persons under the influence of meth hetamine.
Microevolution of Dengue Viruses Circulating among Primary School Children in Kamphaeng Phet, Thailand
Publisher: American Society for Microbiology
Date: 06-2008
DOI: 10.1128/JVI.02728-07
Abstract: To determine the extent and structure of genetic variation in dengue viruses (DENV) on a restricted spatial and temporal scale, we sequenced the E (envelope) genes of DENV-1, -2, and -3 isolates collected in 2001 from children enrolled in a prospective school-based study in K haeng Phet, Thailand, and diagnosed with dengue disease. Our analysis revealed substantial viral genetic variation in both time and space, with multiple viral lineages circulating within in idual schools, suggesting the frequent gene flow of DENV into this microenvironment. More-detailed analyses of DENV-2 s les revealed strong clustering of viral isolates within in idual schools and evidence of more-frequent viral gene flow among schools closely related in space. Conversely, we observed little evolutionary change in those viral isolates s led over multiple time points within in idual schools, indicating a low rate of mutation fixation. These results suggest that frequent viral migration into K haeng Phet, coupled with population (school) sub ision, shapes the genetic ersity of DENV on a local scale, more so than in situ evolution within school catchment areas.
Predicting virus emergence amid evolutionary noise
Publisher: The Royal Society
Date: 10-2017
DOI: 10.1098/RSOB.170189
Abstract: The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of uns led viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence. Truly understanding disease emergence therefore requires a new mechanistic and integrated view of the factors that allow or prevent viruses spreading in novel hosts. We present such a view, suggesting that both ecological and genetic aspects of virus emergence can be placed within a simple population genetic framework, which in turn highlights the importance of host population size and density in determining whether emergence will be successful. Despite this framework, we conclude that a more practical solution to preventing and containing the successful emergence of new diseases entails ongoing virological surveillance at the human–animal interface and regions of ecological disturbance.
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil
Publisher: American Association for the Advancement of Science (AAAS)
Date: 09-2023
Comparative analysis reveals frequent recombination in the parvoviruses
Publisher: Microbiology Society
Date: 12-2007
Abstract: Parvoviruses are small single-stranded DNA viruses that are ubiquitous in nature. Infections with both autonomous and helper-virus dependent parvoviruses are common in both human and animal populations, and many animals are host to a number of different parvoviral species. Despite the epidemiological importance of parvoviruses, the presence and role of genome recombination within or among parvoviral species has not been well characterized. Here we show that natural recombination may be widespread in these viruses. Different genome regions of both porcine parvoviruses and Aleutian mink disease viruses have conflicting phylogenetic histories, providing evidence for recombination within each of these two species. Further, the rodent parvoviruses show complex evolutionary histories for separate genomic regions, suggesting recombination at the interspecies level.
SWAN: sliding window analysis of nucleotide sequence variability.
Publisher: Oxford University Press (OUP)
Date: 06-1998
DOI: 10.1093/BIOINFORMATICS/14.5.467
Abstract: RESULTS: This paper describes a new program which reveals, analyses and graphically represents patterns of variability along nucleotide sequences. AVAILABILITY: The program, 'SWAN', is available from the WWW at evolve.zoo.ox.ac.uk/ or from the authors upon request. CONTACT: Vitali.Proutski@zoology.oxford.ac.uk
Living with diabetes and disadvantage: A qualitative, geographical case study
Publisher: Wiley
Date: 07-05-2020
DOI: 10.1111/JOCN.15295
Persistence of Multiple Genetic Lineages within Intrahost Populations of Ross River Virus
Publisher: American Society for Microbiology
Date: 06-2011
DOI: 10.1128/JVI.02622-10
Abstract: We examined the structure and extent of genetic ersity in intrahost populations of Ross River virus (RRV) in s les from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the s les were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six in iduals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances.
The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance
Publisher: Oxford University Press (OUP)
Date: 18-04-2007
Abstract: A dramatic rise in the frequency of resistance to adamantane drugs by influenza A (H3N2) viruses has occurred in recent years -- from approximately 2% to approximately 90% in multiple countries worldwide-and associated with a single S31N amino acid replacement in the viral matrix M2 protein. To explore the emergence and spread of these adamantane resistant viruses we performed a phylogenetic analysis of recently s led complete A/H3N2 genome sequences. Strikingly, all adamantane resistant viruses belonged to a single lineage (the "N-lineage") characterized by 17 amino acid replacements across the viral genome. Further, our analysis revealed that the genesis of the N-lineage was due to a 4+4 segment reassortment event involving 2 distinct lineages of influenza A/H3N2 virus. A subsequent study of hemagglutinin HA1 sequences suggested that the N-lineage was circulating widely in Asia during 2005, and then dominated the Northern hemisphere 2005-2006 season in Japan and the USA. Given the infrequent use of adamantane drugs in many countries, as well as the decades of use in the US associated with little drug resistance, we propose that the globally increasing frequency of adamantane resistance is more likely attributable to its interaction with fitness-enhancing mutations at other genomic sites rather than to direct drug selection pressure. This implies that adamantanes may not be useful for treatment and prophylaxis against influenza viruses in the long term. More generally, these findings illustrate that drug selection pressure is not the sole factor determining the evolution and maintenance of drug resistance in human pathogens.
Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient.
Publisher: Proceedings of the National Academy of Sciences
Date: 06-1992
Abstract: In an investigation of the evolution of the third hypervariable loop of gp120 (V3), the principal neutralization determinant of human immunodeficiency virus type 1, we have analyzed 89 V3 sequences of plasma viral RNA purified from peripheral blood s les donated over 7 years by an infected hemophiliac. Considerable sequence ersity in the V3 region was found at all time points after seroconversion. Phylogenetic analysis revealed that an important ersification had occurred by 3 years postinfection and that, subsequently, most sequences could be allocated to either one of two major lineages that persisted throughout the remainder of the infection. Rapid changes in frequency of the most common sequences and the observation that the same hexapeptide motif (GPGSAV) at the crown of the V3 loop has evolved convergently provide strong evidence that selective processes determine the evolutionary fate of sequence variants in this region.
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae
Publisher: Oxford University Press (OUP)
Date: 31-05-2021
DOI: 10.1093/VE/VEAB050
Abstract: The Nidovirales comprise a genetically erse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, hibians, and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of ergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish—the pouched l rey. By mining fish transcriptome data, we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae but formed a distinct and erse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationship of viruses within the Letovirinae does not mirror that of their hosts. For ex le, the coronavirus found in the pouched l rey fell within the phylogenetic ersity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
Multiple Introductions of the Old World Begomovirus Tomato yellow leaf curl virus into the New World
Publisher: American Society for Microbiology
Date: 11-2007
DOI: 10.1128/AEM.01150-07
Abstract: A phylogenetic analysis of three genomic regions revealed that Tomato yellow leaf curl virus (TYLCV) from western North America is distinct from TYLCV isolated in eastern North America and the Caribbean. This analysis supports a second introduction of this Old World begomovirus into the New World, most likely from Asia.
Surface adhesins and exopolymers of selected foodborne pathogens
Publisher: Microbiology Society
Date: 12-2014
Abstract: The ability of bacteria to bind different compounds and to adhere to biotic and abiotic surfaces provides them with a range of advantages, such as colonization of various tissues, internalization, avoidance of an immune response, and survival and persistence in the environment. A variety of bacterial surface structures are involved in this process and these promote bacterial adhesion in a more or less specific manner. In this review, we will focus on those surface adhesins and exopolymers in selected foodborne pathogens that are involved mainly in primary adhesion. Their role in biofilm development will also be considered when appropriate. Both the clinical impact and the implications for food safety of such adhesion will be discussed.
Extremely Rapid Spread of Human Immunodeficiency Virus Type 1 BF Recombinants in Argentina
Publisher: American Society for Microbiology
Date: 2007
DOI: 10.1128/JVI.01403-06
Abstract: The epidemic of human immunodeficiency virus type 1 (HIV-1) in Argentina is distinctive in that many infections are caused by subtype BF recombinant viruses. To determine their demographic history, we estimated the evolutionary rate, mode of population growth, and age of genetic ersity among 40 BF vpu sequences. This revealed one of the highest substitution rates reported for HIV-1, at 10.793 × 10 −3 substitutions per site per year, and a very rapid rate of population growth, with an initial mean epidemic doubling time of 3.72 months. This rapid population growth is compatible with an elevated fitness for subtype BF compared to that for “pure” B and F viruses.
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021
Publisher: MDPI AG
Date: 21-12-2022
DOI: 10.3390/V15010016
Abstract: Epizootic haemorrhagic disease (EHD) is a Culicoides-borne viral disease caused by the epizootic haemorrhagic disease virus (EHDV) associated with clinical manifestations in domestic and wild ruminants, primarily white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus). In late September 2021, EHDV was reported in cattle farms in central/western Tunisia. It rapidly spread throughout the country with more than 200 confirmed outbreaks. We applied a combination of classical and molecular techniques to characterize the causative virus as a member of the serotype EHDV-8. This is the first evidence of EHDV- 8 circulation since 1982 when the prototype EHDV-8 strain was isolated in Australia. This work highlights the urgent need for vaccines for a range of EHDV serotypes.
Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.VIROL.2017.02.009
Abstract: Live poultry markets (LPMs) are an important source of novel avian influenza viruses (AIV). During 2015-2016 we surveyed AIV ersity in ten LPMs in Hubei, Zhejiang and Jiangxi provinces, China. A high ersity and prevalence of AIVs (totaling 12 subtypes) was observed in LPMs in these provinces. Strikingly, however, the subtypes discovered during 2015-2016 were markedly different to those reported by us in these same localities one year previously, suggesting a dynamic shift in viral genetic ersity over the course of a single year. Phylogenetic analyses revealed frequent reassortment, including between high and low pathogenic AIV subtypes and among those that circulate in domestic and wild birds. Notably, the novel H5N6 reassortant virus, which contains a set of H9N2-like internal genes, was prevalent in all three regions surveyed. Overall, these data highlight the profound changes in genetic ersity and in patterns of reassortment in those AIVs that circulate in LPMs.
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
Publisher: Oxford University Press (OUP)
Date: 10-07-2015
Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and a novel hepacivirus in Australian brushtail possums
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S42522-019-0006-X
Abstract: Australian brushtail possums ( Trichosurus vulpecula ) are an introduced pest species in New Zealand, but native to Australia where they are protected for bio ersity conservation. Wobbly possum disease (WPD) is a fatal neurological disease of Australian brushtail possums described in New Zealand populations that has been associated with infection by the arterivirus ( Arteriviridae ) wobbly possum disease virus (WPDV-NZ). Clinically, WPD-infected possums present with chronic meningoencephalitis, choroiditis and multifocal neurological symptoms including ataxia, incoordination, and abnormal gait. We conducted a retrospective investigation to characterise WPD in native Australian brushtail possums, and used a bulk meta-transcriptomic approach (i.e. total RNA-sequencing) to investigate its potential viral aetiology. PCR assays were developed for case diagnosis and full genome recovery in the face of extensive genetic variation. We identified genetically distinct lineages of arteriviruses from archival tissues of WPD-infected possums in Australia, termed wobbly possum disease virus AU1 and AU2. Phylogenetically, WPDV-AU1 and WPDV-AU2 shared only ~ 70% nucleotide similarity to each other and the WPDV-NZ strain, suggestive of a relatively ancient ergence. Notably, we also identified a novel and ergent hepacivirus ( Flaviviridae ) - the first in a marsupial - in both WPD-infected and uninfected possums, indicative of virus co-infection. We have identified marsupial-specific lineages of arteriviruses in mainland Australia that are genetically distinct from that in New Zealand, in some cases co-infecting animals with a novel hepacivirus. Our study provides new insight into the hidden genetic ersity of arteriviruses, the capacity for virus co-infection, and highlights the utility of meta-transcriptomics for disease investigation in a One Health context.
Global Distribution of Novel Rhinovirus Genotype
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 06-2008
A systematic review of the prevalence and risk factors of smoking among Saudi adolescents
Publisher: Saudi Medical Journal
Date: 09-2019
A single positively selected West Nile viral mutation confers increased virogenesis in American crows
Publisher: Springer Science and Business Media LLC
Date: 12-08-2007
DOI: 10.1038/NG2097
Creating walking tracks to success: A narrative analysis of Australian Aboriginal and Torres Strait Islander nursing students’ stories of success
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.COLEGN.2016.08.001
Abstract: Australian Aboriginal and Torres Strait Islander people have higher rates of morbidity and mortality thanother Australians. One proposed strategy to improve this situation is to increase the participation ofAboriginal and Torres Strait Islander people, including Aboriginal and Torres Strait Islander nurses, inthe health workforce. Although the numbers of Aboriginal and Torres Strait Islander students under-taking tertiary nursing courses have increased, completion rates have not kept pace. The study aimedto describe Aboriginal and Torres Strait Islander nursing students’ experiences of enablers for successfulcourse completion and to develop a narrative of student experience. A qualitative study using a strengths-based approach with a narrative analysis of semi-structured interview data was conducted across fourschools of Nursing in Queensland, Australia. Eight final-year Aboriginal and Torres Strait Islander nursingstudents volunteered to participate in the study. A collective story with the overarching plotline Creatingwalking tracks to success was developed. Six threads of experience emerged: Making a difference, Valu-ing Indigeneity, Healing strength of connections, Resisting racism, Embracing support, and perseveringtowards completion. Key success factors included resilient attributes, building supportive connectionsand having positive expectations of the future, along with sustained institutional support from Aboriginaland Torres Strait Islander nurse academics and clinicians. Development of tailored resilience-buildingtraining for Aboriginal and Torres Strait Islander nursing students and appointment of Aboriginal andTorres Strait Islander academics in Schools of Nursing that include such students may facilitate futuresuccessful completions in other programs.
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance.
Publisher: Springer Science and Business Media LLC
Date: 18-05-2022
DOI: 10.1038/S41467-022-30518-X
Abstract: Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on licon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory s les. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data.
Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses
Publisher: Microbiology Society
Date: 06-2009
Abstract: Whitefly-transmitted geminiviruses are major pathogens of the important crop cassava in Africa. The intensive s ling and sequencing of cassava mosaic disease-causing viruses that occurred in the wake of a severe outbreak in Central Africa (1997–2002) allowed us to estimate the rate of evolution of this virus. East African cassava mosaic virus and related species are obligately bipartite (DNA-A and DNA-B segments), and these two genome segments have different evolutionary histories. Despite these phylogenetic differences, we inferred high rates of nucleotide substitution in both segments: mean rates of 1.60×10 −3 and 1.33×10 −4 substitutions site −1 year −1 for DNA-A and DNA-B, respectively. While similarly high substitution rates were found in datasets free of detectable recombination, only that estimated for the coat protein gene ( AV1 ), for which an additional DNA-A sequence isolated in 1995 was available, was statistically robust. These high substitution rates also confirm that those previously estimated for the monopartite tomato yellow leaf curl virus (TYLCV) are representative of multiple begomoviruses. We also validated our rate estimates by comparing them with those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses.
Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus
Publisher: Public Library of Science (PLoS)
Date: 08-05-2009
Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 06-2020
Origin of the São Paulo Yellow Fever epidemic of 2017–2018 revealed through molecular epidemiological analysis of fatal cases
Publisher: Springer Science and Business Media LLC
Date: 31-12-2019
DOI: 10.1038/S41598-019-56650-1
Abstract: The largest outbreak of yellow fever of the 21 st century in the Americas began in 2016, with intense circulation in the southeastern states of Brazil, particularly in sylvatic environments near densely populated areas including the metropolitan region of São Paulo city (MRSP) during 2017–2018. Herein, we describe the origin and molecular epidemiology of yellow fever virus (YFV) during this outbreak inferred from 36 full genome sequences taken from in iduals who died following infection with zoonotic YFV. Our analysis revealed that these deaths were due to three genetic variants of sylvatic YFV that belong the South American I genotype and that were related to viruses previously isolated in 2017 from other locations in Brazil (Minas Gerais, Espírito Santo, Bahia and Rio de Janeiro states). Each variant represented an independent virus introduction into the MRSP. Phylogeographic and geopositioning analyses suggested that the virus moved around the peri-urban area without detectable human-to-human transmission, and towards the Atlantic rain forest causing human spill-over in nearby cities, yet in the absence of sustained viral transmission in the urban environment.
Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species
Publisher: Springer Science and Business Media LLC
Date: 09-12-2016
DOI: 10.1038/SREP38770
Abstract: Rickettsiales are important zoonotic pathogens, causing severe disease in humans globally. Although mosquitoes are an important vector for erse pathogens, with the exception of members of the genus Wolbachia little is known about their role in the transmission of Rickettsiales. Herein, Rickettsiales were identified by PCR in five species of mosquitoes ( Anopheles sinensis, Armigeres subalbatus, Aedes albopictus, Culex quinquefasciatus and Cu. tritaeniorhynchus ) collected from three Chinese provinces during 2014–2015. Subsequent phylogenetic analyses of the rrs, groEL and gltA genes revealed the presence of Anaplasma, Ehrlichia, Candidatus Neoehrlichia, and Rickettsia bacteria in mosquitoes, comprising nine documented and five tentative species bacteria, as well as three symbionts/endosybionts. In addition, bacteria were identified in mosquito eggs, larvae, and pupae s led from aquatic environments. Hence, these data suggest that Rickettsiales circulate widely in mosquitoes in nature. Also of note was that Ehrlichia and Rickettsia bacteria were detected in each life stage of laboratory cultured mosquitoes, suggesting that Rickettsiales may be maintained in mosquitoes through both transstadial and transovarial transmission. In sum, these data indicate that mosquitoes may have played an important role in the transmission and evolution of Rickettsiales in nature.
Publisher Correction: Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China
Publisher: Springer Science and Business Media LLC
Date: 10-05-2018
DOI: 10.1038/S41598-018-25257-3
Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses
Publisher: Cold Spring Harbor Laboratory
Date: 23-11-2022
DOI: 10.1101/2022.11.23.517609
Abstract: Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the ersity and abundance of viruses within bats at the level of in idual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 in idual bats s led from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.
Rates of evolutionary change in viruses: patterns and determinants
Publisher: Springer Science and Business Media LLC
Date: 04-03-2008
DOI: 10.1038/NRG2323
Abstract: Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by erse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
Identification of a Novel Papillomavirus Associated with Squamous Cell Carcinoma in a Domestic Cat
Publisher: MDPI AG
Date: 23-12-2019
DOI: 10.20944/PREPRINTS201912.0302.V1
Abstract: Papillomaviruses infect the skin and mucosal surfaces of erse animal hosts with consequences ranging from asymptomatic colonization to highly malignant epithelial cancers. Increasing evidence suggests a role for papillomaviruses in the most common cutaneous malignancy of domestic cats, squamous cell carcinoma (SCC). Using total DNA sequencing we identified a novel feline papillomavirus in a nasal biopsy taken from a cat presenting with both nasal cavity lymphoma and recurrent squamous cell carcinoma affecting the nasal planum. We designate this novel virus as Felis catus papillomavirus 6 (FcaPV6). The complete FcaPV6 7453 bp genome was similar to those of other feline papillomaviruses and phylogenetic analysis revealed that it was most closely related to FcaPV3, although was distinct enough to represent a new viral species within the genus Taupapillomavirus. Archived excisional biopsy of the SCC, taken 20 months prior to presentation, was intensely positive on p16 immunostaining. FcaPV6, lified using virus-specific, but not consensus, PCR was the only papillomavirus detected in DNA extracted from the SCC. Conversely, renal lymphoma, s led at necropsy two months after presentation, tested negative on FcaPV6-specific PCR. In sum, using metagenomics we demonstrate the presence of a novel feline papillomavirus in association with cutaneous squamous cell carcinoma.
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia
Publisher: Oxford University Press (OUP)
Date: 2021
DOI: 10.1093/VE/VEAB034
Abstract: Biological invasions are among the biggest threats to freshwater bio ersity. This is increasingly relevant in the Murray–Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray–Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and ersity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray–Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish s led here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large ersity of viruses with often deep evolutionary histories.
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians
Publisher: Oxford University Press (OUP)
Date: 26-12-2022
DOI: 10.1093/VE/VEAC124
Abstract: The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the ersity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include hibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus–host co- ergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750–800 million years ago.
Molecular Clocks and the Puzzle of RNA Virus Origins
Publisher: American Society for Microbiology
Date: 04-2003
Reply to ‘Reconciling disparate estimates of viral genetic diversity during human influenza infections’
Publisher: Springer Science and Business Media LLC
Date: 12-08-2019
A DivergentArticulavirusin an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons
Publisher: MDPI AG
Date: 04-06-2020
DOI: 10.3390/V12060613
Abstract: The discovery of highly ergent RNA viruses is compromised by their limited sequence similarity to known viruses. Evolutionary information obtained from protein structural modelling offers a powerful approach to detect distantly related viruses based on the conservation of tertiary structures in key proteins such as the RNA-dependent RNA polymerase (RdRp). We utilised a template-based approach for protein structure prediction from amino acid sequences to identify distant evolutionary relationships among viruses detected in meta-transcriptomic sequencing data from Australian wildlife. The best predicted protein structural model was compared with the results of similarity searches against protein databases. Using this combination of meta-transcriptomics and protein structure prediction we identified the RdRp (PB1) gene segment of a ergent negative-sense RNA virus, denoted Lauta virus (LTAV), in a native Australian gecko (Gehyra lauta). The presence of this virus was confirmed by PCR and Sanger sequencing. Phylogenetic analysis revealed that Lauta virus likely represents a newly described genus within the family Amnoonviridae, order Articulavirales, that is most closely related to the fish virus Tilapia tilapinevirus (TiLV). These findings provide important insights into the evolution of negative-sense RNA viruses and structural conservation of the viral replicase among members of the order Articulavirales.
Blood molecular markers associated with COVID‐19 immunopathology and multi‐organ damage
Publisher: EMBO
Date: 14-12-2020
Virology: Pathogenic passengers
Publisher: Springer Science and Business Media LLC
Date: 10-2011
DOI: 10.1038/478319A
Comparative Phylodynamics of Rabbit Hemorrhagic Disease Virus in Australia and New Zealand
Publisher: American Society for Microbiology
Date: 15-09-2015
DOI: 10.1128/JVI.01100-15
Abstract: The introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand during the 1990s as a means of controlling feral rabbits is an important case study in viral emergence. Both epidemics are exceptional in that the founder viruses share an origin and the timing of their release is known, providing a unique opportunity to compare the evolution of a single virus in distinct naive populations. We examined the evolution and spread of RHDV in Australia and New Zealand through a genome-wide evolutionary analysis, including data from 28 newly sequenced RHDV field isolates. Following the release of the Australian inoculum strain into New Zealand, no subsequent mixing of the populations occurred, with viruses from both countries forming distinct groups. Strikingly, the rate of evolution in the capsid gene was higher in the Australian viruses than in those from New Zealand, most likely due to the presence of transient deleterious mutations in the former. However, estimates of both substitution rates and population dynamics were strongly s le dependent, such that small changes in s le composition had an important impact on evolutionary parameters. Phylogeographic analysis revealed a clear spatial structure in the Australian RHDV strains, with a major ision between those viruses from western and eastern states. Importantly, RHDV sequences from the state where the virus was first released, South Australia, had the greatest ersity and were diffuse throughout both geographic lineages, such that this region was likely a source population for the subsequent spread of the virus across the country. IMPORTANCE Most studies of viral emergence lack detailed knowledge about which strains were founders for the outbreak or when these events occurred. Hence, the human-mediated introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand from known starting stocks provides a unique opportunity to understand viral evolution and emergence. Within Australia, we revealed a major phylogenetic ision between viruses s led from the east and west of the country, with both regions likely seeded by viruses from South Australia. Despite their common origins, marked differences in evolutionary rates were observed between the Australian and New Zealand RHDV, which led to conflicting conclusions about population growth rates. An analysis of mutational patterns suggested that evolutionary rates have been elevated in the Australian viruses, at least in part due to the presence of low-fitness (deleterious) variants that have yet to be selectively purged.
Extinction and Rapid Emergence of Strains of Dengue 3 Virus during an Interepidemic Period
Publisher: Elsevier BV
Date: 09-2002
Abstract: Strains of dengue 3 (DEN-3) virus circulating in Thailand prior to 1992 appear to have disappeared from that location and to have been replaced by two new lineages which have evolved locally, rather than being introduced. Similar DEN-3 virus extinctions may have occurred previously in Thailand in 1962 and 1973. Although no causal relationship could be shown, this strain replacement event was accompanied by DEN-3 replacing DEN-2 as the serotype recovered most frequently from patients in Thailand. Although this implies a change in selection pressure, we found no evidence for positive natural selection at the level of either the E protein or the E protein gene. Further, the extinction of the pre-1992 strains and the appearance of the new lineages occurred during an interepidemic period, suggesting that a genetic bottleneck, rather than selection, might have been important in the emergence of these two new strains of virus. The pre-1992 DEN-3 virus lineage could still be found in 1998, to the west, in Myanmar. The ratio of nonsynonymous-to-synonymous nucleotide changes within a DEN-3 virus population from a single patient was less than the ratio among the consensus sequences of DEN-3 viruses from different patients, suggesting that many of the nonsynonymous nucleotide changes which occurred naturally in the E protein were deleterious and removed by purifying selection.
Comparative population dynamics of mosquito-borne flaviviruses
Publisher: Elsevier BV
Date: 07-2003
DOI: 10.1016/S1567-1348(02)00153-3
Abstract: Among the members of the genus Flavivirus are several important human pathogens, including the dengue (DEN) and Japanese encephalitis (JE) viruses. From the analysis of gene sequence data of s les of these virus populations it is possible to infer phylogenetic relationships, which in turn can yield important epidemiological information, including their demographic history in humans. In this study, we use a recently developed method, based on coalescent theory, to infer the population dynamics of a variety of mosquito-borne flaviviruses. Our study involves the testing of alternative hypotheses, the estimation of confidence intervals around demographic model parameter values, and the placing of the maximum likelihood (ML) demographic model into a "real time" epidemiological history. We reveal that all the Flavivirus populations studied are growing at an exponential rate, with the rates of population growth of dengue virus serotypes 2 and 3 increasing rapidly in the recent past, and that of Japanese encephalitis virus changing from constant population size to exponential growth within the last century. We therefore demonstrate that the use of these coalescent methods may be extremely valuable in monitoring responses to interventions such as vaccination or vector control.
The Transferrin Receptor Genes of Trypanosoma equiperdum Are Less Diverse in Their Transferrin Binding Site than Those of the Broad-Host Range Trypanosoma brucei
Publisher: Springer Science and Business Media LLC
Date: 04-2003
DOI: 10.1007/S00239-002-2408-Z
Abstract: Trypanosoma brucei and T. equiperdum infect the mammalian bloodstream and tissues. T. brucei is transmitted by tsetse flies between an extremely large range of mammals in sub-Saharan Africa. In contrast, T. equiperdum is restricted to equines, where it is transmitted as a venereal disease. Both species evade immune destruction by changing their variant surface glycoprotein (VSG), encoded in a telomeric VSG expression site. T. brucei has about 20 VSG expression sites, and it has been proposed that their genetic ersity plays a role in host adaptation. Two expression site-associated genes ESAG6 and ESAG7, encode variable transferrin receptor subunits allowing trypanosomes to internalize polymorphic transferrin molecules from different mammals. We investigated if there was a correlation between the size of the trypanosome host range and the degree of ESAG6 genetic ersity. Both T. equiperdum and T. brucei appear to have approximately similar numbers of ESAG6, however, the genetic ersity of the ESAG6 family varies in the two species. We sequenced 114 T. equiperdum ESAG6 genomic clones, resulting in the isolation of 10 T. equiperdum ESAG6 variants. The T. equiperdum ESAG6 genes were less genetically erse than those of T. brucei in regions known to play a role in transferrin binding. This indicates that ESAG6 genetic ersity playing a role in host adaptation could have been lost in the absence of selection pressure. There was also evidence of positive selection ( d(N) /d(S) = approximately 5) acting on other ESAG6 regions not involved in transferrin binding, perhaps due to antigenic variation of these surface molecules.
HIV clearance in an infant?
Publisher: Springer Science and Business Media LLC
Date: 06-1995
DOI: 10.1038/375637A0
Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions
Publisher: American Society for Microbiology
Date: 29-08-2017
DOI: 10.1128/MSYSTEMS.00050-17
Abstract: Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.
Invasion and Maintenance of Dengue Virus Type 2 and Type 4 in the Americas
Publisher: American Society for Microbiology
Date: 15-12-2005
DOI: 10.1128/JVI.79.23.14680-14687.2005
Abstract: Dengue virus type 4 (DENV-4) was first reported in the Americas in 1981, where it caused epidemics of dengue fever throughout the region. In the same year, the region's first epidemic of dengue hemorrhagic fever was reported, caused by an Asian strain of dengue virus type 2 (DENV-2) that was distinct from the American subtype circulating previously. Despite the importance of these epidemics, little is known about the rates or determinants of viral spread among island and mainland populations or their directions of movement. We employed a Bayesian coalescent approach to investigate the transmission histories of DENV-2 and DENV-4 since their introduction in 1981 and a parsimony method to assess patterns of strain migration. For both viruses there was an initial invasion phase characterized by an exponential increase in the number of DENV lineages, after which levels of genetic ersity remained constant despite reported fluctuations in DENV-2 and DENV-4 activity. Strikingly, viral lineage numbers increased far more rapidly for DENV-4 than DENV-2, indicative of a more rapid rate of exponential population growth in DENV-4 or a higher rate of geographic dispersal, allowing this virus to move more effectively among localities. We propose that these contrasting dynamics may reflect underlying differences in patterns of host immunity. Despite continued gene flow along particular transmission routes, the overall extent of viral traffic was less than expected under panmixis. Hence, DENV in the Americas has a clear geographic structure that maintains viral ersity between outbreaks.
Red fox viromes across an urban-rural gradient
Publisher: Cold Spring Harbor Laboratory
Date: 16-06-2020
DOI: 10.1101/2020.06.15.153858
Abstract: The Red fox ( Vulpes vulpes ) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. Foxes’ cryptic and highly adaptable nature allows them to invade cities and live among humans while remaining largely unnoticed. Urban living and access to anthropogenic food resources also influences fox ecology. Urban foxes grow larger, live at higher densities and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To assess this possibility, we used a meta-transcriptomic approach to characterise the viromes of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. In contrast, urban fox viromes comprised a greater ersity of viruses compared to rural foxes. We identified nine potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae and Picornaviridae as well as rabbit haemorrhagic disease virus-2 (RHDV2). This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human-wildlife interface. Urbanisation of wild environments is increasing as human populations continue to expand. Remnant pockets of natural environments and other green spaces in urban landscapes provide invasive wildlife such as red foxes with refuges within urban areas, where they thrive on the food resources provisioned by humans. Close contact between humans, domestic species and foxes likely increases the risk of novel pathogen emergence. Indeed, the vast majority of emerging infectious diseases in humans originate in wild animals. Here, we explored potential differences in viromes between urban fox invaders and their rural counterparts. Viromes of foxes and their ectoparasites comprise a ersity of viruses including those from the Astroviridae, Picobirnaviridae, Hepeviridae, Caliciviridae and Picornaviridae . Microbial surveillance in foxes and other urban wildlife is vital for monitoring viral emergence and for the prevention of infectious diseases.
Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia
Publisher: MDPI AG
Date: 18-08-2018
DOI: 10.20944/PREPRINTS201808.0318.V1
Abstract: There is an ongoing global pandemic of human respiratory syncytial virus (RSV) infection that results in substantial annual morbidity and mortality. In Australia, RSV is the major cause of acute lower respiratory tract infections (ALRI). Nevertheless, little is known about the extent and origins of genetic ersity of RSV in Australia, nor the factors that shape this ersity. We conducted a genome-scale analysis of RSV infections in New South Wales (NSW). RSV genomes were successfully sequenced for 144 specimens collected between 2010-2016. Of these, 64 belonged to the RSVA and 80 to the RSVB subtype. Phylogenetic analysis revealed a wide ersity of RSV lineages within NSW and that both subtypes evolved rapidly in a strongly clock-like manner, with mean rates of approximately 6-8 x 10-4 nucleotide substitutions per site per year. There was only weak evidence for geographic clustering of sequences, indicative of fluid patterns of transmission within the infected population, and no evidence of any clustering by patient age such that viruses in the same lineages circulate through the entire host population. Importantly, we show that both subtypes circulated concurrently in NSW with multiple introductions into the Australian population in each year, and only limited evidence for multi-year persistence.
The causes and consequences of HIV evolution
Publisher: Springer Science and Business Media LLC
Date: 2004
DOI: 10.1038/NRG1246
Correction: Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain
Publisher: Life Science Alliance, LLC
Date: 29-04-2020
Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States
Publisher: American Society for Microbiology
Date: 07-2008
DOI: 10.1128/JVI.00251-08
Abstract: Israel acute paralysis virus (IAPV) is associated with colony collapse disorder of honey bees. Nonetheless, its role in the pathogenesis of the disorder and its geographic distribution are unclear. Here, we report phylogenetic analysis of IAPV obtained from bees in the United States, Canada, Australia, and Israel and the establishment of diagnostic real-time PCR assays for IAPV detection. Our data indicate the existence of at least three distinct IAPV lineages, two of them circulating in the United States. Analysis of representatives from each proposed lineage suggested the possibility of recombination events and revealed differences in coding sequences that may have implications for virulence.
COVID-19—lessons for zoonotic disease
Publisher: American Association for the Advancement of Science (AAAS)
Date: 11-03-2022
Abstract: Disease emergence is driven by human–animal contact in a global viral ecosystem
A cluster-randomised controlled trial to test the efficacy of facemasks in preventing respiratory viral infection among Hajj pilgrims
Publisher: Springer Science and Business Media LLC
Date: 2015
Phylogenetic evidence for recombination in dengue virus
Publisher: Oxford University Press (OUP)
Date: 03-1999
DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A026121
Abstract: A split decomposition analysis of dengue (DEN) virus gene sequences revealed extensive networked evolution, indicative of recombination, among DEN-1 strains but not within serotypes DEN-2, DEN-3, or DEN-4. Within DEN-1, two viruses s led from South America in the last 10 years were identified as recombinants. To map the breakpoints and test their statistical support, we developed a novel maximum likelihood method. In both recombinants, the breakpoints were found to be in similar positions, within the fusion peptide of the envelope protein, demonstrating that a single recombination event occurred prior to the ergence of these two strains. This is the first report of recombination in natural populations of dengue virus.
Experimental Verification of Seed Transmission of Zucchini yellow mosaic virus
Publisher: Scientific Societies
Date: 06-2011
Abstract: Within two decades of its discovery, Zucchini yellow mosaic virus (ZYMV) achieved a global distribution. However, whether or not seed transmission occurs in this economically significant crop pathogen is controversial, and the relative impact of seed transmission on the epidemiology of ZYMV remains unclear. Using reverse transcription–polymerase chain reaction, we observed a seed transmission rate of 1.6% in Cucurbita pepo subsp. texana and show that seed-infected C. pepo plants are capable of initiating horizontal ZYMV infections, both mechanically and via an aphid vector (Myzus persicae). We also provide evidence that ZYMV-infected seeds may act as effective viral reservoirs, partially accounting for the current geographic distribution of ZYMV. Finally, the observation that ZYMV infection of C. pepo seeds results in virtually symptomless infection, coupled with our finding that an antibody test failed to detect vertically transmitted ZYMV in infected seed, highlights the urgent need to standardize current detection methods for seed infection.
Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques
Publisher: Frontiers Media SA
Date: 24-01-2022
DOI: 10.3389/FVETS.2021.778556
Abstract: Rhesus macaques ( Macaca mulatta ) are the most widely distributed species of Old World monkey and are frequently used as animal models to study human health and disease. Their gastrointestinal microbial community likely plays a major role in their physiology, ecology and evolution. Herein, we compared the fecal microbiome and antibiotic resistance genes in 15 free-ranging and 81 zoo-captive rhesus macaques s led from two zoos in China, using both 16S licon sequencing and whole genome shotgun DNA sequencing approaches. Our data revealed similar levels of microbial ersity/richness among the three groups, although the composition of each group differed significantly and were particularly marked between the two zoo-captive and one wild groups. Zoo-captive animals also demonstrated a greater abundance and ersity of antibiotic genes. Through whole genome shotgun sequencing we also identified a mammalian (simian) associated adenovirus. Overall, this study provides a comprehensive analysis of resistomes and microbiomes in zoo-captive and free-ranging monkeys, revealing that semi-captive wildlife might harbor a higher ersity of antimicrobial resistant genes.
The hepatitis C virus epidemic among injecting drug users
Publisher: Elsevier BV
Date: 03-2005
DOI: 10.1016/J.MEEGID.2004.08.001
Abstract: Given the economic and health costs of hepatitis C virus (HCV) infection, and the ongoing transmission within the injecting drug user (IDU) population, there is a need for improved understanding of HCV epidemiology within this risk group. We employed a recently developed method based on phylogenetic analysis to infer HCV epidemic history and to provide the first estimates of the rate of spread of subtypes 1a and 3a circulating within injecting drug user populations. The data indicates that HCV subtype 1a entered the IDU population on at least three separate occasions. Both subtypes demonstrate exponential population growth during the 20th century, with a doubling time of 7-8 years. The results provide a baseline for prediction of the future course of the HCV epidemic, and its likely response to transmission control policies.
The origins and genomic diversity of American Civil War Era smallpox vaccine strains
Publisher: Springer Science and Business Media LLC
Date: 20-07-2020
DOI: 10.1186/S13059-020-02079-Z
Abstract: Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and ersity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive s ling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.
Virome heterogeneity and connectivity in waterfowl and shorebird communities
Publisher: Springer Science and Business Media LLC
Date: 25-06-2019
Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats
Publisher: Microbiology Society
Date: 09-2012
Abstract: A previous phylogenetic study suggested that mammalian gammaretroviruses may have originated in bats. Here we report the discovery of RNA transcripts from two putative endogenous gammaretroviruses in frugivorous ( Rousettus leschenaultii retrovirus, RlRV) and insectivorous ( Megaderma lyra retrovirus, MlRV) bat species. Both genomes possess a large deletion in pol , indicating that they are defective retroviruses. Phylogenetic analysis places RlRV and MlRV within the ersity of mammalian gammaretroviruses, with the former falling closer to porcine endogenous retroviruses and the latter to Mus dunni endogenous virus, koala retrovirus and gibbon ape leukemia virus. Additional genomic mining suggests that both microbat ( Myotis lucifugus ) and megabat ( Pteropus v yrus ) genomes harbour many copies of endogenous retroviral forms related to RlRV and MlRV. Furthermore, phylogenetic analysis reveals the presence of three genetically erse groups of endogenous gammaretroviruses in bat genomes, with M. lucifugus possessing members of all three groups. Taken together, this study indicates that bats harbour distinct gammaretroviruses and may have played an important role as reservoir hosts during the ersification of mammalian gammaretroviruses.
Frequent In-Migration and Highly Focal Transmission of Dengue Viruses among Children in Kamphaeng Phet, Thailand
Publisher: Public Library of Science (PLoS)
Date: 17-01-2013
Reconstructing the Complex Evolutionary History of Hepatitis B Virus
Publisher: Springer Science and Business Media LLC
Date: 07-1999
DOI: 10.1007/PL00006526
Abstract: A detailed analysis of the evolutionary history of hepatitis B virus (HBV) was undertaken using 39 mammalian hepadnaviruses for which complete genome sequences were available, including representatives of all six human genotypes, as well as a large s le of small S gene sequences. Phylogenetic trees of these data were ambiguous, supporting no single place of origin for HBV, and depended heavily on the underlying model of DNA substitution. In some instances genotype F, predominant in the Americas, was the first to erge, suggesting that the virus arose in the New World. In other trees, however, sequences from genotype B, prevalent in East Asia, were the most ergent. An attempt was also made to determine the rate of nucleotide substitution in the C open reading frame and then to date the origin of HBV. However, no relationship between time and number of substitutions was found in two independent data sets, indicating that a reliable molecular clock does not exist for these data. Both the pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct the past spread of this virus.
Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus
Publisher: American Society for Microbiology
Date: 15-07-2010
DOI: 10.1128/JVI.00112-10
Abstract: Determining the evolutionary basis of cross-species transmission and immune evasion is key to understanding the mechanisms that control the emergence of either new viruses or novel antigenic variants with pandemic potential. The hemagglutinin glycoprotein of influenza A viruses is a critical host range determinant and a major target of neutralizing antibodies. Equine influenza virus (EIV) is a significant pathogen of the horse that causes periodical outbreaks of disease even in populations with high vaccination coverage. EIV has also jumped the species barrier and emerged as a novel respiratory pathogen in dogs, canine influenza virus. We studied the dynamics of equine influenza virus evolution in horses at the intrahost level and how this evolutionary process is affected by interhost transmission in a natural setting. To this end, we performed clonal sequencing of the hemagglutinin 1 gene derived from in idual animals at different times postinfection. Our results show that despite the population consensus sequence remaining invariant, genetically distinct subpopulations persist during the course of infection and are also transmitted, with some variants likely to change antigenicity. We also detected a natural case of mixed infection in an animal infected during an outbreak of equine influenza, raising the possibility of reassortment between different strains of virus. In sum, our data suggest that transmission bottlenecks may not be as narrow as originally perceived and that the genetic ersity required to adapt to new host species may be partially present in the donor host and potentially transmitted to the recipient host.
Dengue Virus Serotype 2 from a Sylvatic Lineage Isolated from a Patient with Dengue Hemorrhagic Fever
Publisher: Public Library of Science (PLoS)
Date: 28-04-2009
The Ecology of Emergent Infectious Disease
Publisher: Oxford University Press (OUP)
Date: 02-1996
DOI: 10.2307/1312815
Inferring Phylogenies. By Joseph Felsenstein. Sunderland (Massachusetts): Sinauer Associates. $59.95. xx + 664 p; ill.; index. ISBN: 0–87893–177–5. 2004.
Publisher: University of Chicago Press
Date: 06-2004
DOI: 10.1086/423061
The link between improved mental health outcomes for Indigenous Australians and relationships: what is the role of mental health nurses?
Publisher: Wiley
Date: 20-09-2016
DOI: 10.1111/INM.12252
Molecular Monitoring of SARS-CoV-2 in Different Sewage Plants in Venice and the Implications for Genetic Surveillance
Publisher: American Chemical Society (ACS)
Date: 09-05-2022
Pandemics: spend on surveillance, not prediction
Publisher: Springer Science and Business Media LLC
Date: 06-2018
A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations
Publisher: American Society for Microbiology
Date: 15-08-2017
DOI: 10.1128/JVI.00158-17
Abstract: Understanding the ersity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees ( Apis mellifera ) has changed dramatically since the emergence of the parasitic mite Varroa destructor , which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral ersity. To capture the viral ersity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa . This analysis revealed seven novel viruses isolated from honey bees s led globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically erse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral ersity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales . Collapsing Varroa -infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral ersity in honey bees, we employed viral metatranscriptomics analyses on three geographically erse Varroa- resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of erse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and ersity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak
Publisher: MDPI AG
Date: 28-06-2022
DOI: 10.3390/V14071412
Abstract: Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterised the ersity of these Carnivore protoparvovirus 1 variants in 18 faecal s les collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of ,000 × coverage per site. All s les comprised FPV alone. Compared with the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were nonsynonymous, including 9 in nonstructural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit interhost ersity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intrahost ersity at all polymorphic positions was low, with subconsensus variant frequencies (SVF) of % except for two positions (2108 and 3208) in two s les with SVF of 1.1–1.3%. Intrahost nucleotide ersity was measured across the whole genome (0.7–1.5%) and for each gene and was highest in the NS2 gene of four s les (1.2–1.9%). Overall, intrahost viral genetic ersity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.
Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence.
Publisher: Oxford University Press (OUP)
Date: 06-10-2009
Abstract: Hantaviruses are considered one of the best ex les of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, approximately 100 million years ago. We tested this hypothesis of host-virus co ergence in two ways: 1) we used cophylogenetic reconciliation analysis to assess the fit of the virus tree onto that of the host and 2) we estimated the evolutionary rates and ergence times for the Hantavirus genus using a Bayesian Markov Chain Monte Carlo method and similarly compared these with those of their hosts. Our reconciliation analysis provided no evidence for a history of co ergence between hantaviruses and their hosts. Further, the ergence times for the Hantavirus genus were many orders of magnitude too recent to correspond with the timescale of their hosts' speciation. We therefore propose that apparent similarities between the phylogenies of hantaviruses and their mammalian hosts are the result of a more recent history of preferential host switching and local adaptation. Based on the presence of clade-defining amino acids in all genomic segments, we propose that the patterns of amino acid replacement in these viruses are also compatible with a history of host-specific adaptation.
DengueInfo: A web portal to dengue information resources
Publisher: Elsevier BV
Date: 07-2007
DOI: 10.1016/J.MEEGID.2007.02.002
Abstract: DengueInfo (www.dengueinfo.org) is a web portal and database that brings clarity to dengue research by integrating the growing number of complete genome sequences of dengue virus with relevant literature and curated epidemiological information. Additionally, it represents a repository of on-going prospective and retrospective studies of dengue disease severity. We intend the database to be a flagship resource for the dengue community, providing standardized and high quality information and facilitating research into key aspects of dengue biology and assisting in its control. To aid this process we also introduce a standard nomenclature for dengue isolates inspired by globally accepted system used for influenza virus.
Human Adaptation of Ebola Virus during the West African Outbreak
Publisher: Elsevier BV
Date: 11-2016
Detection of TT virus among chimpanzees in the wild using a noninvasive technique
Publisher: Wildlife Disease Association
Date: 04-2004
DOI: 10.7589/0090-3558-40.2.230
Abstract: Zoonotic transmission and emergence of pathogens are serious threats to endangered populations of free-ranging primate species. Recent discovery of a nonpathogenic yet highly prevalent virus in human populations, TT virus (TTV), has prompted studies into the presence of this virus among captive in iduals of other species of nonhuman primates. In this study, we screened captive primate species for TTV. In addition, we provide the first data on TTV infectionin free-ranging primates by noninvasive screening of three chimpanzee (Pan troglodytes sweinfurthii) commlunities. Phylogenetic relationships between virus isolates and those previously reported from hulman popullations, captive primates, and domesticated species are inferred. Our findings are discussed with respect to potential zoonotic events that may result from increased levels of human encroachlment into wild habitats.
Why do RNA viruses recombine?
Publisher: Springer Science and Business Media LLC
Date: 04-07-2011
DOI: 10.1038/NRMICRO2614
The Ecology and Evolution of Influenza Viruses
Publisher: Cold Spring Harbor Laboratory
Date: 23-12-2020
High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections
Publisher: American Society for Microbiology
Date: 15-01-2012
DOI: 10.1128/JVI.05985-11
Abstract: Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this ersity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of s ling and/or experimental methods that do not fully account for errors generated through lification and sequencing of viral RNAs. We investigated the extent and pattern of genetic ersity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma s les ( n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from lification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence ersities of viral populations were very low, with conservative estimates of the average levels of genetic ersity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some s les suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic ersity and disease severity, immune status, or level of viremia.
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
Publisher: Oxford University Press (OUP)
Date: 30-07-2021
DOI: 10.1093/VE/VEAB064
Abstract: The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the ‘real-time’ generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic’s transmission lineages.
Heterosexual transmission of hepatitis C virus
Publisher: Elsevier BV
Date: 10-1993
Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History
Publisher: American Society for Microbiology
Date: 03-2017
DOI: 10.1128/JVI.01953-16
Abstract: Bats harbor a large ersity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat s les collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5′ and 3′ ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination “hot spot” in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic ersity of bat CoVs is primarily structured by host species and subsequently by geographic distances. IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.
Molecular Surveillance for Lymphoproliferative Disease Virus in Wild Turkeys (Meleagris gallopavo) from the Eastern United States
Publisher: Public Library of Science (PLoS)
Date: 21-04-2015
Continental synchronicity of human influenza virus epidemics despite climactic variation
Publisher: Public Library of Science (PLoS)
Date: 11-01-2018
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses
Publisher: Oxford University Press (OUP)
Date: 16-09-2021
DOI: 10.1093/VE/VEAB080
Abstract: The ersity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants, we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within 3 years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and -4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.
A generic assay for whole-genome amplification and deep sequencing of enterovirus A71.
Publisher: Elsevier BV
Date: 04-2015
Extensive Geographical Mixing of 2009 Human H1N1 Influenza A Virus in a Single University Community
Publisher: American Society for Microbiology
Date: 15-07-2011
DOI: 10.1128/JVI.00438-11
Abstract: Despite growing interest in the molecular epidemiology of influenza virus, the pattern of viral spread within in idual communities remains poorly understood. To determine the phylogeography of influenza virus in a single population, we examined the spatial diffusion of H1N1/09 influenza A virus within the student body of the University of California, San Diego (UCSD), s ling for a 1-month period between October and November 2009. Despite the highly focused nature of our study, an analysis of complete viral genome sequences revealed between 24 and 33 independent introductions of H1N1/09 into the UCSD community, comprising much of the global genetic ersity in this virus. These data were also characterized by a relatively low level of on-c us transmission as well as extensive spatial mixing, such that there was little geographical clustering by either student residence or city ZIP code. Most notably, students experiencing illness on the same day and residing in the same dorm possessed phylogenetically distinct lineages. H1N1/09 influenza A virus is therefore characterized by a remarkable spatial fluidity, which is likely to impede community-based methods for its control, including class cancellations, quarantine, and chemoprophylaxis.
Identification of diverse full-length endogenous betaretroviruses in megabats and microbats
Publisher: Springer Science and Business Media LLC
Date: 27-03-2013
Abstract: Betaretroviruses infect a wide range of species including primates, rodents, ruminants, and marsupials. They exist in both endogenous and exogenous forms and are implicated in animal diseases such as lung cancer in sheep, and in human disease, with members of the human endogenous retrovirus-K (HERV-K) group of endogenous betaretroviruses (βERVs) associated with human cancers and autoimmune diseases. To improve our understanding of betaretroviruses in an evolutionarily distinct host species, we characterized βERVs present in the genomes and transcriptomes of mega- and microbats, which are an important reservoir of emerging viruses. A erse range of full-length βERVs were discovered in mega- and microbat genomes and transcriptomes including the first identified intact endogenous retrovirus in a bat. Our analysis revealed that the genus Betaretrovirus can be ided into eight distinct sub-groups with evidence of cross-species transmission. Betaretroviruses are revealed to be a complex retrovirus group, within which one sub-group has evolved from complex to simple genomic organization through the acquisition of an env gene from the genus Gammaretrovirus . Molecular dating suggests that bats have contended with betaretroviral infections for over 30 million years. Our study reveals that a erse range of betaretroviruses have circulated in bats for most of their evolutionary history, and cluster with extant betaretroviruses of ergent mammalian lineages suggesting that their distribution may be largely unrestricted by host species barriers. The presence of βERVs with the ability to transcribe active viral elements in a major animal reservoir for viral pathogens has potential implications for public health.
Comparative Studies of RNA Virus Evolution
Publisher: Elsevier
Date: 2008
Origin and Phylodynamics of Rabbit Hemorrhagic Disease Virus
Publisher: American Society for Microbiology
Date: 12-2009
DOI: 10.1128/JVI.01523-09
Abstract: To determine the origin, phylogenetic relationships, and evolutionary dynamics of rabbit hemorrhagic disease virus (RHDV), we examined 210 partial and complete capsid gene nucleotide sequences. Using a Bayesian Markov chain Monte Carlo approach, we estimated that these sequences evolved at a rate of 3.9 × 10 −4 to 11.9 × 10 −4 nucleotide substitutions per site per year. This rate was consistent across subsets of data, was robust in response to recombination, and casts doubt on the provenance of viral strains isolated from the 1950s to the 1970s, which share strong sequence similarity to modern isolates. Using the same analysis, we inferred that the time to the most recent common ancestor for a joint group of RHDV and rabbit calicivirus sequences was years ago and was years ago for the RHDV isolates that have spread around the world since 1984. Importantly, multiple lineages of RHDV were clearly circulating before the major Chinese outbreak of 1984, a finding indicative of an early evolution of RHDV virulence. Four phylogenetic groups within RHDV were defined and analyzed separately. Each group shared a common ancestor in the mid-1960s or earlier, and each showed an expansion of populations starting before 1984. Notably, the group characterized by the antigenic variant RHDVa harbors the greatest genetic ersity, compatible with an elevated fitness. Overall, we contend that the high virulence of RHDV likely evolved once in the early part of the 20th century, well before the documented emergence of rabbit hemorrhagic disease in 1984.
If you knew the end of a story would you still want to hear it? Using research poems to listen to Aboriginal stories
Publisher: Informa UK Limited
Date: 02-01-2016
Limited cross-species virus transmission in a spatially restricted coral reef fish community
Publisher: Oxford University Press (OUP)
Date: 2023
DOI: 10.1093/VE/VEAD011
Abstract: The Great Barrier Reef (GBR)—the largest coral reef ecosystem in the world—supports over 1,200 fish species with some of the highest population densities and ersities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community ersity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus ersity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space—a 100-m2 coral reef ecosystem—suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes—characterized by small body sizes and short life spans—exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.
Biodiversity and evolution of Imjin virus and Thottapalayam virus in Crocidurinae shrews in Zhejiang Province, China
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.VIRUSRES.2014.05.014
Abstract: The recent discovery of numerous hantaviruses in insectivores has provided a new view of hantavirus bio ersity and evolution. To determine the presence and genetic ersity of Imjin virus (MJNV) and Thottapalayam virus (TPMV) in insectivores in Zhejiang Province, China, we captured and performed virus screening of 32 Ussuri white-toothed shrews (Crocidura lasiura) and 105 Asian house shrews (Suncus murinus) in different coastal regions. Hantavirus genome (S, M, and L segments) sequences were successfully recovered from one Ussuri white-toothed shrew and seven Asian house shrews. Phylogenetic analysis revealed that the virus carried by the Ussuri white-toothed shrew was most closely related to MJNV, but with >15% nucleotide sequence difference, suggesting that it represents a new subtype. The hantaviruses carried by Asian house shrews were closely related to the TPMV variants found in the same geographic area, but more distantly related to those s led in India and Nepal. Additionally, the TPMV sequences obtained in this study, as well as those found previously in this area, could be ided into three lineages reflecting their geographic origins, indicative of largely allopatric evolution. Overall, our data highlights the high genetic ersity of insectivore-borne hantaviruses in China, suggesting that more may be discovered in the future.
A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution
Publisher: Oxford University Press (OUP)
Date: 14-06-2006
Abstract: RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide sites are commonplace in the genomes of these infectious agents. However, the role of epistasis in natural populations of RNA viruses remains unclear. To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co-occurring mutations along phylogenies of 177 RNA virus genes. This analysis revealed widespread evidence for positive epistatic interactions at both synonymous and nonsynonymous nucleotide sites and in both clonal and recombining viruses, with the majority of these interactions spanning very short sequence regions. These findings have important implications for understanding the key aspects of RNA virus evolution, including the dynamics of adaptation. Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid.
Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range
Publisher: American Society for Microbiology
Date: 15-01-2016
DOI: 10.1128/JVI.02636-15
Abstract: Sylvatic carnivores, such as raccoons, have recently been recognized as important hosts in the evolution of canine parvovirus (CPV), a pandemic pathogen of domestic dogs. Although viruses from raccoons do not efficiently bind the dog transferrin receptor (TfR) or infect dog cells, a single mutation changing an aspartic acid to a glycine at capsid (VP2) position 300 in the prototype raccoon CPV allows dog cell infection. Because VP2 position 300 exhibits extensive amino acid variation among the carnivore parvoviruses, we further investigated its role in determining host range by analyzing its ersity and evolution in nature and by creating a comprehensive set of VP2 position 300 mutants in infectious clones. Notably, some position 300 residues rendered CPV noninfectious for dog, but not cat or fox, cells. Changes of adjacent residues (residues 299 and 301) were also observed often after cell culture passage in different hosts, and some of the mutations mimicked changes seen in viruses recovered from natural infections of alternative hosts, suggesting that compensatory mutations were selected to accommodate the new residue at position 300. Analysis of the TfRs of carnivore hosts used in the experimental evolution studies demonstrated that their glycosylation patterns varied, including a glycan present only on the domestic dog TfR that dictates susceptibility to parvoviruses. Overall, there were significant differences in the abilities of viruses with alternative position 300 residues to bind TfRs and infect different carnivore hosts, demonstrating that the process of infection is highly host dependent and that VP2 position 300 is a key determinant of host range. IMPORTANCE Although the emergence and pandemic spread of canine parvovirus (CPV) are well documented, the carnivore hosts and evolutionary pathways involved in its emergence remain enigmatic. We recently demonstrated that a region in the capsid structure of CPV, centered around VP2 position 300, varies after transfer to alternative carnivore hosts and may allow infection of previously nonsusceptible hosts in vitro . Here we show that VP2 position 300 is the most variable residue in the parvovirus capsid in nature, suggesting that it is a critical determinant in the cross-species transfer of viruses between different carnivores due to its interactions with the transferrin receptor to mediate infection. To this end, we demonstrated that there are substantial differences in receptor binding and infectivity of various VP2 position 300 mutants for different carnivore species and that single mutations in this region can influence whether a host is susceptible or refractory to virus infection.
Meaningful Engagement With Aboriginal Communities Using Participatory Action Research to Develop Culturally Appropriate Health Resources
Publisher: SAGE Publications
Date: 16-01-2020
Abstract: Introduction: This article outlines the processes used to meaningfully and authentically engage Australian Aboriginal communities in Northern New South Wales, Australia, to develop culturally appropriate stroke health resources. Methodology: Participatory action research using the research topic yarning framework is a collaborative, culturally safe way to uncover vital information and concepts. There were two stages in the participatory action research project: community engagement and evaluation of the processes involved in developing the localised, culturally appropriate health resources. Results: Establishing relationships built on trust, mutual sharing of knowledge, and bringing together the wider community, enabled the health message to be embedded within the community, ensuring the message was culturally appropriate and sustainable. Discussion: The stroke education resource is a tangible outcome and a major achievement however, the process of authentic engagement to achieve the final product was the ultimate accomplishment.
Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849
Publisher: Massachusetts Medical Society
Date: 23-01-2014
Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments
Publisher: Elsevier BV
Date: 08-2013
DOI: 10.1016/J.MEEGID.2013.03.015
Abstract: Recombination plays an important role in shaping the genetic ersity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to ascertain whether these represent natural recombinants. To facilitate the future identification of recombinants, reference sets of non-recombinant sequences were selected for use in an automatic screening protocol for detecting mosaic sequences. Tests using real and simulated mosaic sequences indicate that our screening protocol is both sensitive (average >90%) and accurate (average >77%) enough to identify a range of different mosaic patterns. The relatively high prevalence of mosaic influenza virus sequences implies that efficient systematic screens, such as that proposed here, should be performed routinely to detect natural recombinant strains, potential laboratory artifacts, and sequencing contaminants either prior to sequences being deposited in GenBank or before they are used for phylogenetic analyses.
Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa
Publisher: Massachusetts Medical Society
Date: 13-04-2017
DOI: 10.1056/NEJMC1701600
Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark
Publisher: Elsevier BV
Date: 03-2023
JC Virus Evolution and Its Association with Human Populations
Publisher: American Society for Microbiology
Date: 15-10-2006
DOI: 10.1128/JVI.00441-06
Abstract: The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. There are at least 14 subtypes of the virus associated with different human populations. Because of its presumed co ergence with humans, JCV has been used as a genetic marker for human evolution and migration. Co ergence has also been used as a basis for estimating the rate of nucleotide substitution in JCV. We tested the hypothesis of host-virus co ergence by (i) performing a reconciliation analysis of phylogenetic trees of human and JCV populations and (ii) providing the first estimate of the evolutionary rate of JCV that is independent from the assumption of co ergence. Strikingly, our comparisons of JCV and human phylogenies provided no evidence for co ergence, suggesting that this virus should not be used as a marker for human population history. Further, while the estimated nucleotide substitution rate of JCV has large confidence intervals due to limited s ling, our analysis suggests that this virus may evolve nearly two orders of magnitude faster than predicted under the co ergence hypothesis.
Yersinia pestis and the three plague pandemics–Authors' reply
Publisher: Elsevier BV
Date: 10-2014
The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats
Publisher: Hindawi Limited
Date: 10-07-2022
DOI: 10.1111/TBED.14646
Abstract: Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.
Boosting Virology in Brazil
Publisher: Public Library of Science (PLoS)
Date: 11-03-2008
Evolution of Bovine Ephemeral Fever Virus in the Australian Episystem
Publisher: American Society for Microbiology
Date: 02-2013
DOI: 10.1128/JVI.02797-13
Abstract: Bovine ephemeral fever virus (BEFV) is an arthropod-borne rhabdovirus that causes a debilitating disease of cattle in Africa, Asia, and Australia however, its global geodynamics are poorly understood. An evolutionary analysis of G gene (envelope glycoprotein) ectodomain sequences of 97 BEFV isolates collected from Australia during 1956 to 2012 revealed that all have a single common ancestor and are phylogenetically distinct from BEFV s led in other geographical regions. The age of the Australian clade is estimated to be between 56 and 65 years, suggesting that BEFV has entered the continent on few occasions since it was first reported in 1936 and that the 1955-1956 epizootic was the source of all currently circulating viruses. Notably, the Australian clade has evolved as a single genetic lineage across the continent and at a high evolutionary rate of ∼10 −3 nucleotide substitutions/site/year. Screening of 66 isolates using monoclonal antibodies indicated that neutralizing antigenic sites G1, G2, and G4 have been relatively stable, although variations in site G3a/b defined four antigenic subtypes. A shift in an epitope at site G3a, which occurred in the mid-1970s, was strongly associated with a K218R substitution. Similarly, a shift at site G3b was associated primarily with substitutions at residues 215, 220, and 223, which map to the tip of the spike on the prefusion form of the G protein. Finally, we propose that positive selection on residue 215 was due to cross-reacting neutralizing antibody to Kimberley virus (KIMV). IMPORTANCE This is the first study of the evolution of BEFV in Australia, showing that the virus has entered the continent only once during the past 50 to 60 years, it is evolving at a relatively constant rate as a single genetic lineage, and although the virus is relatively stable antigenically, mutations have resulted in four antigenic subtypes. Furthermore, the study shows that the evolution of BEFV in Australia appears to be driven, at least in part, by cross-reactive antibodies to KIMV which has a similar distribution and ecology but has not been associated with disease. As BEFV and KIMV are each known to be present in Africa and Asia, this interaction may occur on a broader geographic scale.
Is the Quasispecies Concept Relevant to RNA Viruses?
Publisher: American Society for Microbiology
Date: 2002
The evolution of MHC class I genes in cattle
Publisher: Springer Japan
Date: 2000
Editorial: Patient safety in mental health services: Understanding the impact of emotional harm
Publisher: Wiley
Date: 20-05-2016
DOI: 10.1111/INM.12222
Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus
Publisher: American Society for Microbiology
Date: 15-05-2008
DOI: 10.1128/JVI.02683-07
Abstract: To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (∼2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length ( nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during lification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.
Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)
Publisher: Oxford University Press (OUP)
Date: 14-10-2023
DOI: 10.1093/VE/VEAD061
Population dynamics of flaviviruses revealed by molecular phylogenies.
Publisher: Proceedings of the National Academy of Sciences
Date: 23-01-1996
Abstract: The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly erse viral strains.
Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds
Publisher: Elsevier BV
Date: 2009
Circumpolar diversification of the Ixodes uriae tick virome
Publisher: Public Library of Science (PLoS)
Date: 03-08-2020
Evidence for an aquatic origin of influenza virus and the orderArticulavirales
Publisher: Cold Spring Harbor Laboratory
Date: 16-02-2023
DOI: 10.1101/2023.02.15.528772
Abstract: The emergence of novel disease-causing viruses in mammals is part of the long evolutionary history of viruses. Tracing these evolutionary histories contextualises virus spill over events and may help to elucidate how and why they occur. We used a combination of total RNA sequencing and transcriptome data mining to extend the ersity and evolutionary history of the order Articulavirales , which includes the influenza viruses. From this, we identified the first instance of Articulavirales in the Cnidaria (including corals), constituting a novel and ergent family that we tentatively named the Cnidenomoviridae . This may be the basal group within the Articulavirales . We also extended the known evolutionary history of the influenza virus lineage by identifying a highly ergent, sturgeon-associated influenza virus. This suggests that fish were among the first hosts of influenza viruses. Finally, we substantially expanded the known ersity of quaranjaviruses and proposed that this genus be reclassified as a family (the Quaranjaviridae ). We find evidence that vertebrate infecting Quaranjaviridae may have initially evolved in crustaceans before spilling into terrestrial Chelicerata (i.e., ticks). Together, our findings indicate that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of this order was not shaped by strict virus-host co ergence, but rather by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.
RNA Viruses, Evolution of
Publisher: Elsevier
Date: 2016
Distribution of Surface Protein Variants among Hyperinvasive Meningococci: Implications for Vaccine Design
Publisher: American Society for Microbiology
Date: 10-2004
DOI: 10.1128/IAI.72.10.5955-5962.2004
Abstract: The bacterium Neisseria meningitidis is a major cause of meningitis and septicemia worldwide. Outer membrane proteins (OMPs) are candidates in the search for comprehensive meningococcal vaccines however, the formulation of OMP vaccines is complicated by antigenic ersity, which is generated by high levels of genetic reassortment and strong positive selection in the meningococcal antigen genes. The genetic and antigenic ersity of three OMPs (FetA, PorA, and PorB) among a global collection of meningococcal isolates representative of the major hyperinvasive clonal complexes was determined. There was evidence for antigenic structuring among the three OMPs that could not be explained purely by descent. These observations violated the predictions of the clonal and epidemic clonal models of population structure but were in concordance with models of strain structure which propose that host immunity selects for nonoverlapping antigen combinations. The patterns of antigenic variant combinations suggested that an OMP-based vaccine with as few as six PorA and five FetA variant sequences could generate homologous immune responses against all 78 isolates examined.
Sexual Transmission of Single Human Immunodeficiency Virus Type 1 Virions Encoding Highly Polymorphic Multisite Cytotoxic T-Lymphocyte Escape Variants
Publisher: American Society for Microbiology
Date: 15-11-2005
DOI: 10.1128/JVI.79.22.13953-13962.2005
Abstract: Antigenic variation inherent in human immunodeficiency virus type 1 (HIV-1) virions that successfully instigate new infections transferred by sex has not been well defined. Yet this is the viral “challenge” which any vaccine-induced immunity must deal with. Closely timed comparisons of the virus circulating in the “donor” and that which initiates new infection are difficult to carry out rigorously, as suitable s les are very hard to get in the face of ethical hurdles. Here we investigate HIV-1 variation in four homosexual couples where we s led blood from both parties within several weeks of the estimated transmission event. We analyzed variation within highly immunogenic HIV-1 internal proteins encoding epitopes recognized by cytotoxic Tlymphocytes (CTLs). These responses are believed to be crucial as a means of containing viral replication. In the donors we detected virions capable of evading host CTL recognition at several linked epitopes of distinct HLA class I restriction. When a donor transmitted escape variants to a recipient with whom he had HLA class I molecules in common, the recipient's CTL response to those epitopes was prevented, thus impeding adequate viral control. In addition, we show that even when HLA class I alleles are disparate in the transmitting couple, a single polymorphism can abolish CTL recognition of an overlapping epitope of distinct restriction and so confer immune escape properties to the recipient's seroconversion virus. In donors who are themselves controlling an early, acute infection, the precise timing of onward transmission is a crucial determinant of the viral variants available to compose the inoculum.
Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission
Publisher: Microbiology Society
Date: 10-2004
Abstract: To determine the selection pressures faced by RNA viruses of plants, patterns of nonsynonymous ( d N ) and synonymous ( d S ) substitution in the capsid genes of 36 viruses with differing modes of transmission were analysed. This analysis provided strong evidence that the capsid proteins of vector-borne plant viruses are subject to greater purifying selection on amino acid change than those viruses transmitted by other routes and that virus–vector interactions impose greater selective constraints than those between virus and plant host. This could be explained by specific interactions between capsid proteins and cellular receptors in the insect vectors that are necessary for successful transmission. However, contrary to initial expectations based on phylogenetic relatedness, vector-borne plant viruses are subject to weaker selective constraints than vector-borne animal viruses. The results suggest that the greater complexity involved in the transmission of circulative animal viruses compared with non-circulative plant viruses results in more intense purifying selection.
Reported outcomes for young people who mentor their peers: a literature review
Publisher: RCN Publishing Ltd.
Date: 07-09-2018
Prescription drug diversion is becoming a lucrative business in regional and rural Australian communities and is escalating due to methamphetamine withdrawal
Publisher: Wiley
Date: 25-03-2018
DOI: 10.1111/INM.12458
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.
Publisher: Springer Science and Business Media LLC
Date: 24-07-2014
Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses
Publisher: American Society for Microbiology
Date: 09-2017
DOI: 10.1128/JVI.00764-17
Abstract: Although shrews are one of the largest groups of mammals, little is known about their role in the evolution and transmission of viral pathogens, including coronaviruses (CoVs). We captured 266 Asian house shrews ( Suncus murinus ) in Jiangxi and Zhejiang Provinces, China, during 2013 to 2015. CoV RNA was detected in 24 Asian house shrews, with an overall prevalence of 9.02%. Complete viral genome sequences were successfully recovered from the RNA-positive s les. The newly discovered shrew CoV fell into four lineages reflecting their geographic origins, indicative of largely allopatric evolution. Notably, these viruses were most closely related to alphacoronaviruses but sufficiently ergent that they should be considered a novel member of the genus Alphacoronavirus , which we denote Wénchéng shrew virus (WESV). Phylogenetic analysis revealed that WESV was a highly ergent member of the alphacoronaviruses and, more dramatically, that the S gene of WESV fell in a cluster that was genetically distinct from that of known coronaviruses. The ergent position of WESV suggests that coronaviruses have a long association with Asian house shrews. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to genes of any known viruses. Together, these data suggest that shrews are natural reservoirs for coronaviruses and may have played an important and long-term role in CoV evolution. IMPORTANCE The subfamily Coronavirinae contains several notorious human and animal pathogens, including severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus, and porcine epidemic diarrhea virus. Because of their genetic ersity and phylogenetic relationships, it has been proposed that the alphacoronaviruses likely have their ultimate ancestry in the viruses residing in bats. Here, we describe a novel alphacoronavirus (Wénchéng shrew virus [WESV]) that was s led from Asian house shrews in China. Notably, WESV is a highly ergent member of the alphacoronaviruses and possesses an S gene that is genetically distinct from those of all known coronaviruses. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to those of any known viruses. Together, these data suggest that shrews are important and longstanding hosts for coronaviruses that merit additional research and surveillance.
Living through a volcanic eruption: Understanding the experience of survivors as a phenomenological existential phenomenon
Publisher: Wiley
Date: 19-02-2016
DOI: 10.1111/INM.12212
Abstract: Mount Merapi in Indonesia is the most active volcano in the world with its 4-6-year eruption cycle. The mountain and surrounding areas are populated by hundreds of thousands of people who live near the volcano despite the danger posed to their wellbeing. The aim of this study was to explore the lived experience of people who survived the most recent eruption of Mount Merapi, which took place in 2010. Investigators conducted interviews with 20 participants to generate textual data that were coded and themed. Three themes linked to the phenomenological existential experience (temporality and relationality) of living through a volcanic eruption emerged from the data. These themes were: connectivity, disconnection and reconnection. Results indicate that the close relationship in iduals have with Mount Merapi and others in their neighbourhood outweighs the risk of living in the shadow of an active volcano. This is the first study to analyze the phenomenological existential elements of living through a volcanic eruption.
Speciation: Spinning the web of life
Publisher: Elsevier BV
Date: 09-1994
DOI: 10.1016/S0960-9822(00)00188-3
Abstract: Phylogenetic trees based on molecular and morphological data show that erse spider species found on the Hawaiian islands have evolved following multiple colonization events.
The evolution of base composition and phylogenetic inference
Publisher: Elsevier BV
Date: 09-2000
DOI: 10.1016/S0169-5347(00)01934-0
Abstract: Base composition varies at all levels of the phylogenetic hierarchy and throughout the genome, and can be caused by active selection or passive mutation pressure. This variation can make reconstructing trees difficult. However, recent tree-based analyses have shed light on the forces responsible for the evolution of base composition, forces that might be very general. More explicit tree-based work is encouraged.
Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China
Publisher: Microbiology Society
Date: 04-2016
DOI: 10.1099/JGV.0.000399
Abstract: The wide circulation of novel avian influenza viruses (AIVs) highlights the risk of pandemic influenza emergence in China. To investigate the prevalence and genetic ersity of AIVs in different ecological contexts, we surveyed AIVs in live poultry markets (LPMs), free-range poultry and the wetland habitats of wild birds in Zhejiang and Hubei provinces. Notably, LPMs contained the highest frequency of AIV infection, and the greatest number of subtypes (n = 9) and subtype co-infections (n = 14), as well as frequent reassortment, suggesting that they play an active role in fuelling AIV transmission. AIV-positive s les were also identified in wild birds in both provinces and free-range poultry in one s ling site close to a wetland region in Hubei. H9N2, H7N9 and H5N1 were the most commonly s led subtypes in the LPMs from Zhejiang, whilst H5N6 and H9N2 were the dominant subtypes in the LPMs from Hubei. Phylogenetic analyses of the whole-genome sequences of 43 AIVs revealed that three reassortant H5 subtypes were circulating in LMPs in both geographical regions. Notably, the viruses s led from the wetland regions and free-range poultry contained complex reassortants, for which the origins of some segments were unclear. Overall, our study highlights the extent of AIV genetic ersity in two highly populated parts of central and south-eastern China, particularly in LPMs, and emphasizes the need for continual surveillance.
Evidence for an ancient aquatic origin of the RNA viral order Articulavirales
Publisher: Proceedings of the National Academy of Sciences
Date: 31-10-2023
Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates
Publisher: American Society for Microbiology
Date: 07-2010
DOI: 10.1128/JVI.01603-09
Abstract: Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has traditionally circulated in Africa and Asia, causing human febrile illness accompanied by severe, chronic joint pain. In Africa, epidemic emergence of CHIKV involves the transition from an enzootic, sylvatic cycle involving arboreal mosquito vectors and nonhuman primates, into an urban cycle where peridomestic mosquitoes transmit among humans. In Asia, however, CHIKV appears to circulate only in the endemic, urban cycle. Recently, CHIKV emerged into the Indian Ocean and the Indian subcontinent to cause major epidemics. To examine patterns of CHIKV evolution and the origins of these outbreaks, as well as to examine whether evolutionary rates that vary between enzootic and epidemic transmission, we sequenced the genomes of 40 CHIKV strains and performed a phylogenetic analysis representing the most comprehensive study of its kind to date. We inferred that extant CHIKV strains evolved from an ancestor that existed within the last 500 years and that some geographic overlap exists between two main enzootic lineages previously thought to be geographically separated within Africa. We estimated that CHIKV was introduced from Africa into Asia 70 to 90 years ago. The recent Indian Ocean and Indian subcontinent epidemics appear to have emerged independently from the mainland of East Africa. This finding underscores the importance of surveillance to rapidly detect and control African outbreaks before exportation can occur. Significantly higher rates of nucleotide substitution appear to occur during urban than during enzootic transmission. These results suggest fundamental differences in transmission modes and/or dynamics in these two transmission cycles.
Evolution of dengue virus in Mexico is characterized by frequent lineage replacement
Publisher: Springer Science and Business Media LLC
Date: 15-06-2010
DOI: 10.1007/S00705-010-0721-1
Abstract: Both dengue fever and its more serious clinical manifestation, dengue hemorrhagic fever, represent major public health concerns in the Americas. To understand the patterns and dynamics of virus transmission in Mexico, a country characterized by a marked increase in dengue incidence in recent years, we undertook a molecular evolutionary analysis of the largest s le of Mexican strains of dengue virus compiled to date. Our E gene data set comprises sequences s led over a period of 27 years and representing all of the Mexican states that are endemic for dengue. Our phylogenetic analysis reveals that, for each of the four dengue viruses (DENV-1 to DENV-4), there have been multiple introductions of viral lineages in Mexico, with viruses similar to those observed throughout the Americas, but there has been strikingly little co-circulation. Rather, dengue virus evolution in Mexico is typified by frequent lineage replacement, such that only a single viral lineage dominates in a specific serotype at a specific time point. Most lineage replacement events involve members of the same viral genotype, although a replacement event involving different genotypes was observed with DENV-2, and viral lineages that are new to Mexico are described for DENV-1, DENV-3 and DENV-4.
Equine and Canine Influenza H3N8 Viruses Show Minimal Biological Differences Despite Phylogenetic Divergence
Publisher: American Society for Microbiology
Date: 07-2015
DOI: 10.1128/JVI.00521-15
Abstract: The A/H3N8 canine influenza virus (CIV) emerged from A/H3N8 equine influenza virus (EIV) around the year 2000 through the transfer of a single virus from horses to dogs. We defined and compared the biological properties of EIV and CIV by examining their genetic variation, infection, and growth in different cell cultures, receptor specificity, hemagglutinin (HA) cleavage, and infection and growth in horse and dog tracheal explant cultures. Comparison of sequences of viruses from horses and dogs revealed mutations that may be linked to host adaptation and tropism. We prepared infectious clones of representative EIV and CIV strains that were similar to the consensus sequences of viruses from each host. The rescued viruses, including HA and neuraminidase (NA) double reassortants, exhibited similar degrees of long-term growth in MDCK cells. Different host cells showed various levels of susceptibility to infection, but no differences in infectivity were seen when comparing viruses. All viruses preferred α2-3- over α2-6-linked sialic acids for infections, and glycan microarray analysis showed that EIV and CIV HA-Fc fusion proteins bound only to α2-3-linked sialic acids. Cleavage assays showed that EIV and CIV HA proteins required trypsin for efficient cleavage, and no differences in cleavage efficiency were seen. Inoculation of the viruses into tracheal explants revealed similar levels of infection and replication by each virus in dog trachea, although EIV was more infectious in horse trachea than CIV. IMPORTANCE Influenza A viruses can cross species barriers and cause severe disease in their new hosts. Infections with highly pathogenic avian H5N1 virus and, more recently, avian H7N9 virus have resulted in high rates of lethality in humans. Unfortunately, our current understanding of how influenza viruses jump species barriers is limited. Our aim was to provide an overview and biological characterization of H3N8 equine and canine influenza viruses using various experimental approaches, since the canine virus emerged from horses approximately 15 years ago. We showed that although there were numerous genetic differences between the equine and canine viruses, this variation did not result in dramatic biological differences between the viruses from the two hosts, and the viruses appeared phenotypically equivalent in most assays we conducted. These findings suggest that the cross-species transmission and adaptation of influenza viruses may be mediated by subtle changes in virus biology.
Declining Growth Rate of West Nile Virus in North America
Publisher: American Society for Microbiology
Date: 03-2007
DOI: 10.1128/JVI.02169-06
Abstract: To determine the demographic history of West Nile virus (WNV) in North America, we employed a coalescent method to envelope coding region data sets for the NY99 and WN02 genotypes. Although the observed genetic ersities in both genotypes were of approximately the same age, the mean rate of epidemiological growth of the WN02 population was approximately three times that of the NY99 population, a finding compatible with the recent dominance of the former genotype. However, there has also been a marked decrease in the recent growth rate of WN02, suggesting that WNV has reached its peak prevalence in North America.
A divergent Articulavirus in an Australian gecko identified using meta-transcriptomics and protein structure comparisons
Publisher: Cold Spring Harbor Laboratory
Date: 22-05-2020
DOI: 10.1101/2020.05.21.109603
Abstract: The discovery of highly ergent RNA viruses is compromised by their limited sequence similarity to known viruses. Evolutionary information obtained from protein structural modelling offers a powerful approach to detect distantly related viruses based on the conservation of tertiary structures in key proteins such as the viral RNA-dependent RNA polymerase (RdRp). We utilised a template-based approach for protein structure prediction from amino acid sequences to identify distant evolutionary relationships among viruses detected in meta-transcriptomic sequencing data from Australian wildlife. The best predicted protein structural model was compared with the results of similarity searches against protein databases based on amino acid sequence data. Using this combination of meta-transcriptomics and protein structure prediction we identified the RdRp (PB1) gene segment of a ergent negative-sense RNA virus in a native Australian gecko ( Geyra lauta ) that was confirmed by PCR and Sanger sequencing. Phylogenetic analysis identified the Gecko articulavirus (GECV) as a newly described genus within the family Amnoonviridae , order Articulavirales , that is most closely related to the fish virus Tilapia tilapinevirus (TiLV). These findings provide important insights into the evolution of negative-sense RNA viruses and structural conservation of the viral replicase among members of the order Articulavirales .
Infectious disease phylodynamics with occurrence data
Publisher: Wiley
Date: 27-05-2021
Abstract: Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance of pathogens, especially during the SARS‐CoV‐2 pandemic, new practical questions about their use are emerging. One such question focuses on the inclusion of un‐sequenced case occurrence data alongside sequenced data to improve phylodynamic analyses. This approach can be particularly valuable if sequencing efforts vary over time. Using simulations, we demonstrate that birth–death phylodynamic models can employ occurrence data to eliminate bias in estimates of the basic reproductive number due to misspecification of the s ling process. In contrast, the coalescent exponential model is robust to such s ling biases, but in the absence of a s ling model it cannot exploit occurrence data. Subsequent analysis of the SARS‐CoV‐2 epidemic in the northwest USA supports these results. We conclude that occurrence data are a valuable source of information in combination with birth–death models. These data should be used to bolster phylodynamic analyses of infectious diseases and other rapidly spreading species in the future.
The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution
Publisher: European Centre for Disease Control and Prevention (ECDC)
Date: 04-11-2021
DOI: 10.2807/1560-7917.ES.2021.26.44.2001996
Abstract: Many countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus. We aimed to assess the duration of chains of virus transmission within in idual countries and the extent to which countries exported viruses to their geographical neighbours. We analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, in countries of northern Europe. We examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the COVID-19 pandemic. The Nordic countries differed markedly in the invasiveness of control strategies, which we found reflected in transmission chain dynamics. For ex le, Sweden, which compared with the other Nordic countries relied more on recommendation-based rather than legislation-based mitigation interventions, had transmission chains that were more numerous and tended to have more cases. This trend increased over the first 8 months of 2020. Together with Denmark, Sweden was a net exporter of SARS-CoV-2. Norway and Finland implemented legislation-based interventions their transmission chain dynamics were in stark contrast to their neighbouring country Sweden. Sweden constituted an epidemiological and evolutionary refugium that enabled the virus to maintain active transmission and spread to other geographical locations. Our analysis reveals the utility of genomic surveillance where monitoring of active transmission chains is a key metric.
RNA virome abundance and diversity is associated with host age in a bird species.
Publisher: Elsevier BV
Date: 09-2021
DOI: 10.1016/J.VIROL.2021.06.007
Abstract: Despite the ongoing interest in virus discovery, little is known about the factors that shape communities of viruses within in idual hosts. Here, we address how virus communities might be impacted by the age of the hosts they infect, using total RNA sequencing to reveal the RNA viromes of different age groups of Ruddy Turnstones (Arenaria interpres). From oropharyngeal and cloacal swabs we identified 14 viruses likely infecting birds, 11 of which were novel, including members of the Reoviridae, Astroviridae, and Picornaviridae. Strikingly, 12 viruses identified were from juvenile birds s led in the first year of their life, compared to only two viruses in adult birds. Both viral abundance and alpha ersity were marginally higher in juvenile than adult birds. As well as informing studies of virus ecology, that host age might be associated with viral composition is an important consideration for the future surveillance of novel and emerging viruses.
Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and novel hepaciviruses in Australian brushtail possums
Publisher: Cold Spring Harbor Laboratory
Date: 07-10-2019
DOI: 10.1101/795336
Abstract: Australian brushtail possums ( Trichosurus vulpecula ) are an introduced pest species in New Zealand, but native to Australia where they are protected for bio ersity conservation. Wobbly possum disease (WPD) is a fatal neurological disease of Australian brushtail possums described in New Zealand populations that has been associated with infection by the arterivirus ( Arteriviridae ) wobbly possum disease virus (WPDV-NZ). Clinically, WPD-infected possums present with chronic meningoencephalitis, choroiditis and multifocal neurological symptoms including ataxia, incoordination, and abnormal gait. We conducted a retrospective investigation to characterise WPD in native Australian brushtail possums, and used a bulk meta-transcriptomic approach (i.e. total RNA-sequencing) to investigate its potential viral aetiology. PCR assays were developed for case diagnosis and full genome recovery in the face of extensive genetic variation. We identified a distinct lineage of arteriviruses from archival tissues of WPD-infected possums in Australia, termed wobbly possum disease virus AU1 and AU2. Phylogenetically, WPDV-AU1 and WPDV-AU2 shared only ∼70% nucleotide similarity to each other and the WPDV-NZ strain, suggestive of a relatively ancient ergence. Notably, we identified a novel and ergent hepacivirus ( Flaviviridae ) - the first in a marsupial - in both WPD-infected and uninfected possums, indicative of virus co-infection. We have identified a distinctive marsupial-specific lineage of arteriviruses in mainland Australia that is genetically distinct from that in New Zealand, in some cases co-infecting animals with a novel hepacivirus. Our study provides new insight into the hidden genetic ersity of arteriviruses, the capacity for virus co-infection, and highlights the utility of meta-transcriptomics for disease investigation and surveillance in a One Health context.
Recombination in Evolutionary Genomics
Publisher: Annual Reviews
Date: 12-2002
DOI: 10.1146/ANNUREV.GENET.36.040202.111115
Abstract: ▪ Abstract Recombination can be a dominant force in shaping genomes and associated phenotypes. To better understand the impact of recombination on genomic evolution, we need to be able to identify recombination in aligned sequences. We review bioinformatic approaches for detecting recombination and measuring recombination rates. We also examine the impact of recombination on the reconstruction of evolutionary histories and the estimation of population genetic parameters. Finally, we review the role of recombination in the evolutionary history of bacteria, viruses, and human mitochondria. We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution.
Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks
Publisher: Public Library of Science (PLoS)
Date: 20-12-2012
Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building
Publisher: Elsevier BV
Date: 03-2019
Phylogeography and Evolutionary History of Reassortant H9N2 Viruses with Potential Human Health Implications
Publisher: American Society for Microbiology
Date: 15-08-2011
DOI: 10.1128/JVI.00219-11
Abstract: Avian influenza viruses of the H9N2 subtype have seriously affected the poultry industry of the Far and Middle East since the mid-1990s and are considered one of the most likely candidates to cause a new influenza pandemic in humans. To understand the genesis and epidemiology of these viruses, we investigated the spatial and evolutionary dynamics of complete genome sequences of H9N2 viruses circulating in nine Middle Eastern and Central Asian countries from 1998 to 2010. We identified four distinct and cocirculating groups (A, B, C, and D), each of which has undergone widespread inter- and intrasubtype reassortments, leading to the generation of viruses with unknown biological properties. Our analysis also suggested that eastern Asia served as the major source for H9N2 gene segments in the Middle East and Central Asia and that in this geographic region within-country evolution played a more important role in shaping viral genetic ersity than migration between countries. The genetic variability identified among the H9N2 viruses was associated with specific amino acid substitutions that are believed to result in increased transmissibility in mammals, as well as resistance to antiviral drugs. Our study highlights the need to constantly monitor the evolution of H9N2 viruses in poultry to better understand the potential risk to human health posed by these viruses.
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
Publisher: Elsevier BV
Date: 02-2020
Transmission of hepatitis B virus infection in Gambian families revealed by phylogenetic analysis
Publisher: Elsevier BV
Date: 07-2001
DOI: 10.1016/S0168-8278(01)00064-2
Abstract: Transmission of hepatitis B virus (HBV) in Africa occurs horizontally, with most people becoming infected between the ages of 1 and 5 years. The index cases in such events have been assumed to come from within the family unit or from sources outside the immediate family, such as other families or inhabitants of the same compound or village. Here, we define these routes of transmission by phylogenetic tree analysis of sequences from the entire pre-core/core region of the virus, in Gambian chronic carriers. Amplification by polymerase chain reaction of serum extracted HBV-DNA was followed by direct sequencing of the target region. Following editing and alignment of these sequences, phylogenetic tree analysis was performed using the neighbour-joining and maximum-likelihood methods. Despite the overall conserved nature of the sequences of the pre-core/core region from 142 chronic carriers, distinct clusters were easily defined at the family and village level, but not on a wider geographical separation. Phylogenetic tree analysis of sequences obtained from family members provided strong evidence of intrafamilial transmission of HBV in at least two-thirds of the families studied from Gambia.
Insights into the evolutionary history of an emerging livestock pathogen: Porcine circovirus 2
Publisher: American Society for Microbiology
Date: 15-12-2009
DOI: 10.1128/JVI.01719-09
Abstract: Porcine circovirus 2 (PCV2) is the primary etiological agent of postweaning multisystemic wasting syndrome (PMWS), one of the most economically important emerging swine diseases worldwide. Virulent PCV2 was first identified following nearly simultaneous outbreaks of PMWS in North America and Europe in the 1990s and has since achieved global distribution. However, the processes responsible for the emergence and spread of PCV2 remain poorly understood. Here, phylogenetic and cophylogenetic inferences were utilized to address key questions on the time scale, processes, and geographic diffusion of emerging PCV2. The results of these analyses suggest that the two genotypes of PCV2 (PCV2a and PCV2b) are likely to have emerged from a common ancestor approximately 100 years ago and have been on independent evolutionary trajectories since that time, despite cocirculating in the same host species and geographic regions. The patterns of geographic movement of PCV2 that we recovered appear to mimic those of the global pig trade and suggest that the movement of asymptomatic animals is likely to have facilitated the rapid spread of virulent PCV2 around the globe. We further estimated the rate of nucleotide substitution for PCV2 to be on the order of 1.2 × 10 −3 substitutions/site/year, the highest yet recorded for a single-stranded DNA virus. This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide.
Stochastic models of molecular evolution and the estimation of phylogeny and rates of nucleotide substitution in the hominoid primates
Publisher: Elsevier BV
Date: 12-1989
Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease
Publisher: Cold Spring Harbor Laboratory
Date: 08-03-2020
DOI: 10.1101/2020.03.07.982207
Abstract: Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the ersity of viruses they carry and use this information to help understand the potential risks of spill-over to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased meta-transcriptomic approach, combined with careful clinical investigation and histopathology, we identified a number of novel viruses from the families Astroviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, Flaviviridae, and Circoviridae in common urban wild birds including Australian magpies, magpie lark, pied currawongs, Australian ravens, and rainbow lorikeets. In each case the presence of the virus was confirmed by RT-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular and neuropathology in birds of the Corvidae and Artamidae families, and neuropathology in members of the Psittaculidae . The existence of such a erse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock and human health. More broadly, our work shows how meta-transcriptomics brings a new utility to pathogen discovery in wildlife diseases. Wildlife naturally harbor a erse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing we identified highly erse viruses in native birds in Australian urban environments presenting with paresis. This investigation included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome, and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free ranging wildlife, and promotes further surveillance for specific potential pathogens of potential conservation and zoonotic concern.
Discovery of a highly divergent hepadnavirus in shrews from China
Publisher: Elsevier BV
Date: 05-2019
Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys
Publisher: Public Library of Science (PLoS)
Date: 10-10-2007
Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-08-2016
Abstract: Hoenen et al . (Reports, 3 April 2015, p. 117 published online 26 March) suggested that the Ebola virus Makona responsible for the West African epidemic evolved more slowly than previously reported. We show that this was based on corrupted data. An erratum provided a rate compatible with the initial and later, more precise, estimates but did not correctly state the nature of the error.
RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data
Publisher: Cold Spring Harbor Laboratory
Date: 03-2022
DOI: 10.1101/2022.02.28.482397
Abstract: Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly ergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental s les. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate ergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and ergent virus-like sequences into the known ersity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motif, as well as pre-built RdRp alignments. In parallel, our analysis of the sequence ersity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some sequences cluster into potential new orders of RNA viruses related to the Wolframvirales and Tolivirales . Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position, which might provide new insights into the structure, function and evolution of viral RdRps.
Evolutionary genetics and vector adaptation of recombinant viruses of the western equine encephalitis antigenic complex provides new insights into alphavirus diversity and host switching
Publisher: Elsevier BV
Date: 2015
Viral community composition of hypersaline lakes
Publisher: Oxford University Press (OUP)
Date: 07-2023
DOI: 10.1093/VE/VEAD057
Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype
Publisher: Oxford University Press (OUP)
Date: 07-2023
DOI: 10.1093/VE/VEAD051
The phylogeography of human viruses
Publisher: Wiley
Date: 09-12-2003
DOI: 10.1046/J.1365-294X.2003.02051.X
Abstract: Viruses, especially those with RNA genomes, represent ideal organisms to study the dynamics of microevolutionary change. In particular, their rapid rate of nucleotide substitution means that the epidemiological processes that shape their ersity act on the same time-scale as mutations are fixed in viral populations. Consequently, the branching structure of virus phylogenies provides a unique insight into spatial and temporal dynamics. Herein, I describe the key processes in virus phylogeography. These are generally associated with the relative rates of dispersal among populations and virus-host co ergence (vicariance), and the ision between acute (short-term) and persistent (long-term) infections. These processes will be illustrated by important human viruses - HIV, dengue, rabies, polyomavirus JC and human papillomavirus - which display varying spatial and temporal structures and virus-host relationships. Key research questions for the future will also be established.
Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses
Publisher: Oxford University Press (OUP)
Date: 07-2023
DOI: 10.1093/VE/VEAD052
The evolution of epidemic influenza
Publisher: Springer Science and Business Media LLC
Date: 30-01-2007
DOI: 10.1038/NRG2053
Abstract: Recent developments in complete-genome sequencing, antigenic mapping and epidemiological modelling are greatly improving our knowledge of the evolution of human influenza virus at the epidemiological scale. In particular, recent studies have revealed a more complex relationship between antigenic evolution, natural selection and reassortment than previously realized. Despite these advances, there is much that remains to be understood about the epidemiology of influenza virus, particularly the processes that determine the virus's strong seasonality. We argue that a complete understanding of the evolutionary biology of this important human pathogen will require a genomic view of genetic ersity, including the acquisition of polymorphism data from within in idual hosts and from geographical regions, particularly the tropics, which have been poorly surveyed to date.
Intrahost Evolutionary Dynamics of Canine Influenza Virus in Naïve and Partially Immune Dogs
Publisher: American Society for Microbiology
Date: 15-05-2010
DOI: 10.1128/JVI.02469-09
Abstract: The patterns and dynamics of evolution in acutely infecting viruses within in idual hosts are largely unknown. To this end, we investigated the intrahost variation of canine influenza virus (CIV) during the course of experimental infections in naïve and partially immune dogs and in naturally infected dogs. Tracing sequence ersity in the gene encoding domain 1 of the hemagglutinin (HA1) protein over the time course of infection provided information on the patterns and processes of intrahost viral evolution and revealed some of the effects of partial host immunity. Viral populations s led on any given day were generally characterized by mean pairwise genetic ersities between 0.1 and 0.2% and by mutational spectra that changed considerably on different days. Some observed mutations may have affected antigenicity or host range, including reversions of CIV host-associated mutations. Patterns of sequence ersity differed between naïve and vaccinated dogs, with some presumably antigenic mutations transiently reaching high frequency in the latter. CIV populations are therefore characterized by the rapid generation and clearance of genetic ersity. Potentially advantageous mutations arise readily during the course of single infections and may give rise to antigenic escape or host range variants.
The early diversification of influenza A/H1N1pdm
Publisher: Public Library of Science (PLoS)
Date: 03-11-2009
Dissemination, divergence and establishment of H7N9 influenza viruses in China
Publisher: Springer Science and Business Media LLC
Date: 11-03-2015
DOI: 10.1038/NATURE14348
Abstract: Since 2013 the occurrence of human infections by a novel avian H7N9 influenza virus in China has demonstrated the continuing threat posed by zoonotic pathogens. Although the first outbreak wave that was centred on eastern China was seemingly averted, human infections recurred in October 2013 (refs 3-7). It is unclear how the H7N9 virus re-emerged and how it will develop further potentially it may become a long-term threat to public health. Here we show that H7N9 viruses have spread from eastern to southern China and become persistent in chickens, which has led to the establishment of multiple regionally distinct lineages with different reassortant genotypes. Repeated introductions of viruses from Zhejiang to other provinces and the presence of H7N9 viruses at live poultry markets have fuelled the recurrence of human infections. This rapid expansion of the geographical distribution and genetic ersity of the H7N9 viruses poses a direct challenge to current disease control systems. Our results also suggest that H7N9 viruses have become enzootic in China and may spread beyond the region, following the pattern previously observed with H5N1 and H9N2 influenza viruses.
Meta-transcriptomics and the evolutionary biology of RNA viruses.
Publisher: Elsevier BV
Date: 2017
Phylogenetic Evidence for Frequent Positive Selection and Recombination in the Meningococcal Surface Antigen PorB
Publisher: Oxford University Press (OUP)
Date: 10-2002
DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A003991
Abstract: Previous estimates of rates of synonymous (d(S)) and nonsynonymous (d(N)) substitution among Neisseria meningitidis gene sequences suggested that the surface loops of the variable outer membrane protein PorB were under only weak selection pressure from the host immune response. These findings were consistent with studies indicating that PorB variants were not always protective in immunological and microbiological assays and questioned the suitability of this protein as a vaccine component. PorB, which is expressed at high levels on the surface of the meningococcus, has been implicated in mechanisms of pathogenesis and has also been used as a typing target in epidemiological investigations. In this work, using more precise estimates of selection pressures and recombination rates, we have shown that some residues in the surface loops of PorB are under very strong positive selection, as great as that observed in human immunodeficiency virus-1 surface glycoproteins, whereas amino acids within the loops and the membrane-spanning regions of the protein are under purifying selection, presumably because of structural constraints. Congruence tests showed that recombination occurred at a rate that was not sufficient to erase all phylogenetic similarity and did not greatly bias selection analysis. Homology models of PorB structure indicated that many strongly selected sites encoded residues that were predicted to be exposed to host immune responses, implying that this protein is under strong immune selection and requires further examination as a potential vaccine candidate. These data show that phylogenetic inference can be used to complement immunological and biochemical data in the choice of vaccine candidates.
A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1093/VE/VEY020
Evolution of structural proteins of feline immunodeficiency virus: molecular epidemiology and evidence of selection for change
Publisher: Microbiology Society
Date: 03-1993
DOI: 10.1099/0022-1317-74-3-425
Abstract: The DNA sequences of structural genes of several U.K. and European isolates of feline immunodeficiency virus (FIV) were determined and compared with those of other worldwide isolates. Phylogenetic analyses of both gag and env sequences demonstrate that a Japanese isolate represents a distinct sequence subgroup, with corrected amino acid distances to the other isolates averaging 23% in env and 8% in gag. Analysis also reveals that an evolutionary radiation of FIV occurred with many isolates erging at approximately the same time, and that although isolates from similar geographical sources often cluster together, there is evidence of more than one origin for FIV in the U.K., The Netherlands and Italy. Estimation of the numbers of silent and replacement nucleotide substitutions indicates the presence of constraints against amino acid changes in gag and conserved regions of env but suggests that positive selection for protein sequence changes operates in variable regions of env. The possible immunological forces underlying these changes are discussed.
Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2021
DOI: 10.1101/2021.02.17.21251943
Abstract: Australia’s early COVID-19 experience involved clusters in northern Sydney, including hospital and aged-care facility (ACF) outbreaks. We explore transmission dynamics, drivers and outcomes of a metropolitan hospital COVID-19 outbreak that occurred in the context of established local community transmission. A retrospective cohort analysis is presented, with integration of viral genome sequencing, clinical and epidemiological data. We demonstrate using genomic epidemiology that the hospital outbreak (n=23) was linked to a concurrent outbreak at a local aged care facility, but was phylogenetically distinct from other community clusters. Thirty day survival was 50% for hospitalised patients (an elderly cohort with significant comorbidities) and 100% for staff. Staff who acquired infection were unable to attend work for a median of 26.5 days (range 14-191) an additional 140 staff were furloughed for quarantine. Transmission from index cases showed a wide dispersion (mean 3.5 persons infected for every patient case and 0.6 persons infected for every staff case). One patient, who received regular nebulised medication prior to their diagnosis being known, acted as an apparent superspreader. No secondary transmissions occurred from isolated cases or contacts who were quarantined prior to becoming infectious. This analysis elaborates the wide-ranging impacts on patients and staff of nosocomial COVID-19 transmission and highlights the utility of genomic analysis as an adjunct to traditional epidemiological investigations. Delayed case recognition resulted in nosocomial transmission but once recognised, prompt action by the outbreak management team and isolation with contact and droplet (without airborne) precautions were sufficient to prevent transmission within this cohort. Our findings support current PPE recommendations in Australia but demonstrate the risk of administering nebulised medications when COVID-19 is circulating locally.
High-Resolution Phylogenetic Analysis of Hepatitis C Virus Adaptation and Its Relationship to Disease Progression
Publisher: American Society for Microbiology
Date: 04-2004
DOI: 10.1128/JVI.78.7.3447-3454.2004
Abstract: Hepatitis C virus (HCV) persists in the majority of those infected despite host immune responses. Evidence has accrued that selectively fixed mutations in the envelope genes (E1 and E2) are associated with viral persistence, particularly those that occur within the first hypervariable region of E2 (HVR1). However, the in idual amino acid residues under selection have not been identified, nor have their selection pressures been measured, despite the importance of this information for understanding disease pathogenesis and for vaccine design. We performed a high-resolution analysis of published gene sequence data from in iduals undergoing acute HCV infection, employing two phylogenetic methods to determine site-specific selection pressures. Strikingly, we found a statistically significant association between the number of sites selected and disease outcome, with the fewest selected sites in fulminant HCV cases and the greatest number of selected sites in rapid progressors, reflecting the duration and intensity of the arms race between host and virus. Moreover, sites outside the HVR1 appear to play a major role in viral evolution and pathogenesis, although there was no association between viral persistence and specific mutations in E1 and E2. Our analysis therefore allows fine dissection of immune selection pressures, which may be more erse than previously thought. Such analyses could play a similarly informative role in studies of other persistent virus infections, such as human immunodeficiency virus.
Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1093/VE/VEY019
Identification of a Novel Picorna-Like Virus, Burpengary Virus, That Is Negatively Associated with Chlamydial Disease in the Koala
Publisher: MDPI AG
Date: 15-02-2019
DOI: 10.20944/PREPRINTS201902.0140.V1
Abstract: Koalas (Phascolarctos cinereus) are native Australian marsupials whose populations are in decline from a range of threats. Infectious diseases caused by the bacterium Chlamydia pecorum and other pathogens are of particular concern. We analysed 26 poly-A selected RNA-sequencing libraries from a data set designed to study the immune response of koalas to ocular chlamydial infection. Using virus discovery techniques, we identified the coding-complete genome sequence of a novel picorna-like virus, denoted Burpengary virus, that was most common in south-east Queensland. Notably, abundance measurements of the virus across all 26 libraries revealed an inverse relationship in prevalence with ocular disease in Koalas, suggesting that co-infection between Burpengary virus and Chlamydia pecorum is inhibited.
The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations
Publisher: Public Library of Science (PLoS)
Date: 15-08-2013
Correction: Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus
Publisher: Public Library of Science (PLoS)
Date: 26-01-2011
DOI: 10.1371/ANNOTATION/66C3B26F-7B78-4412-96D0-C960B8D74B50
Phylogeography of the Spring and Fall Waves of the H1N1/09 Pandemic Influenza Virus in the United States
Publisher: American Society for Microbiology
Date: 15-01-2011
DOI: 10.1128/JVI.01762-10
Abstract: Spatial variation in the epidemiological patterns of successive waves of pandemic influenza virus in humans has been documented throughout the 20th century but never understood at a molecular level. However, the unprecedented intensity of s ling and whole-genome sequencing of the H1N1/09 pandemic virus now makes such an approach possible. To determine whether the spring and fall waves of the H1N1/09 influenza pandemic were associated with different epidemiological patterns, we undertook a large-scale phylogeographic analysis of viruses s led from three localities in the United States. Analysis of genomic and epidemiological data reveals distinct spatial heterogeneities associated with the first pandemic wave, March to July 2009, in Houston, TX, Milwaukee, WI, and New York State. In Houston, no specific H1N1/09 viral lineage dominated during the spring of 2009, a period when little epidemiological activity was observed in Texas. In contrast, major pandemic outbreaks occurred at this time in Milwaukee and New York State, each dominated by a different viral lineage and resulting from strong founder effects. During the second pandemic wave, beginning in August 2009, all three U.S. localities were dominated by a single viral lineage, that which had been dominant in New York during wave 1. Hence, during this second phase of the pandemic, extensive viral migration and mixing diffused the spatially defined population structure that had characterized wave 1, lifying the one viral lineage that had dominated early on in one of the world's largest international travel centers.
Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.
Publisher: Elsevier BV
Date: 04-2014
The origin and global emergence of adamantane resistant A/H3N2 influenza viruses
Publisher: Elsevier BV
Date: 06-2009
A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-10-2007
Abstract: In colony collapse disorder (CCD), honey bee colonies inexplicably lose their workers. CCD has resulted in a loss of 50 to 90% of colonies in beekeeping operations across the United States. The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD. We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by the examination of s les collected from several sites over a period of 3 years. One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD.
Hidden diversity and evolution of viruses in market fish
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1093/VE/VEY031
Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021
Publisher: Elsevier BV
Date: 11-2022
Embodying compassion: A systematic review of the views of nurses and patients
Publisher: Wiley
Date: 08-01-2019
DOI: 10.1111/JOCN.14722
Abstract: To provide a review of empirical research investigating how compassion is expressed by nurses and received by patients in hospital settings. Compassion is viewed as an important and fundamental part of a health professional practice. Universally, reports from both media and government agencies have addressed perceived deficits of compassion in healthcare with nurses accused of a lack of compassion. Research into compassion to date has largely focused on the problematic nature of compassion such as burnout, fatigue and other negative personal and work-related outcomes. A systematic literature review of empirical research guided by a meta-ethnographic approach supported the systematic comparison and translation of the included studies. Six online databases were searched from January 2006-December 2016. This review was carried out according to the PRISMA-P reporting guidelines. How compassion in healthcare was defined was extracted alongside findings on how compassion was expressed by nurses and received by patients. Synthesis of the research was completed resulting in new interpretations. Eleven papers met the inclusion criteria and were included in the review. Multiple differing definitions of compassion in healthcare were applied. Nurses embody and enact compassion through behaviours such as spending time with patients and communicating effectively with patients. Patients experience compassion through a sense of togetherness with nurses. Existing research demonstrated dissonance between the expression of compassion by nurses and how compassion is experienced by patients. The themes identified in this review should be considered by health professionals providing patient care. Health providers should acknowledge and account for the time that nurses need with patients to demonstrate compassion in practice. Nursing education relating to the expression of compassion should articulate both the subjectivity and ambiguity of the term and examine the relationship between compassion and suffering.
Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand
Publisher: Cold Spring Harbor Laboratory
Date: 22-04-2022
DOI: 10.1101/2022.04.21.489127
Abstract: New Zealand has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has received little research attention. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus and avastrovirus in the Eurasian blackbird ( Turdus merula , an introduced species), song thrush ( Turdus philomelos , introduced) and silvereye ( Zosterops lateralis , introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior unders ling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were found only in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance is needed in New Zealand avifauna, particularly in Turdus populations and endemic species.
No detectable effect of Wolbachia w Mel on the prevalence and abundance of the RNA virome of Drosophila melanogaster
Publisher: The Royal Society
Date: 25-07-2018
Abstract: Wolbachia is an endosymbiotic bacterium that can block viral infections in arthropods, generating interest in its potential to control the spread of mosquito-borne disease. Drosophila melanogaster is model organism for Wolbachia infection, and the w Mel strain of Wolbachia can improve host survival following viral infection. However, it is unclear whether w Mel induces anti-viral blocking against the broader native virome of D. melanogaster , or whether the major effect of Wolbachia is a reduction in viral abundance rather than viral clearance. We examined the effect of Wolbachia on viral abundance by comparing the total transcriptome of w Mel-positive and w Mel-negative D. melanogaster populations s led from six locations in Australia. In addition, we examined the impact of w Mel on in idual flies by obtaining transcriptome data from 20 w Mel-positive and 20 w Mel-negative D. melanogaster from the location (Melbourne) with highest density of w Mel. These data revealed high viral abundance in both Wolbachia -positive and -negative populations and in iduals. Notably, none of the viral species identified, representing RNA viruses from at least nine families/floating genera, showed evidence of protection by w Mel. Although the viral loads of picorna-like viruses are reduced by w Mel under experimental conditions, we observed no such effect here. These data show that D. melanogaster can harbour abundant RNA viruses regardless of its Wolbachia status and imply that the interaction between Wolbachia and viruses in nature is more complex than simple blocking.
Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae
Publisher: Microbiology Society
Date: 04-2013
Abstract: Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic ersity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co- ergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.
Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives
Publisher: American Society for Microbiology
Date: 15-07-2019
DOI: 10.1128/JVI.01212-16
Abstract: Two closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit ( Oryctolagus cuniculus ) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 s les isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic ersity, perhaps coincident with the emergence of myxoma virus. IMPORTANCE The comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two closely related RNA viruses that cocirculate in Australia, the highly virulent rabbit hemorrhagic disease virus (RHDV) and the nonpathogenic rabbit calicivirus Australia 1 (RCV-A1). Both viruses infect the European rabbit, but they differ in virulence, tissue tropism, and mechanisms of transmission. Surprisingly, and despite these fundamental differences, RCV-A1 and RHDV have evolved at very similar (high) rates and with strong purifying selection. Furthermore, candidate key mutations were identified that may play a role in virulence and/or tissue tropism and therefore warrant further investigation.
Exploring Host–Pathogen Interactions through Biological Control
Publisher: Public Library of Science (PLoS)
Date: 25-06-2015
Investigation of Potential HIV Transmission to the Patients of an HIV-Infected Surgeon
Publisher: American Medical Association (AMA)
Date: 14-04-1993
Malpais spring virus is a new species in the genus vesiculovirus
Publisher: Springer Science and Business Media LLC
Date: 04-03-2013
Virome heterogeneity and connectivity in waterfowl and shorebird communities
Publisher: Cold Spring Harbor Laboratory
Date: 29-01-2019
DOI: 10.1101/528174
Abstract: Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses ( Picobirnaviridae and Reoviridae ), single-stranded RNA viruses ( Astroviridae, Caliciviridae, Picornaviridae ), a retro-transcribing DNA virus ( Hepadnaviridae ), and a single-stranded DNA virus ( Parvoviridae ). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity and heterogeneity. Virome connectivity was apparent in two well described multi-host virus species (avian coronavirus and influenza A virus) and a novel Rotavirus species that were shared among some Anseriform species, while heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes. Notably, within avian host families there was no significant relationship between either host taxonomy or foraging ecology and virome composition, although Anseriform species positive for influenza A virus harboured more additional viruses than those negative for influenza virus. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
The genomic and epidemiological dynamics of human influenza A virus
Publisher: Springer Science and Business Media LLC
Date: 16-04-2008
DOI: 10.1038/NATURE06945
How accurately can we assess zoonotic risk?
Publisher: Public Library of Science (PLoS)
Date: 20-04-2021
DOI: 10.1371/JOURNAL.PBIO.3001135
Abstract: Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic “risk assessment.” Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human–animal interface may be more productive.
The use of taxon-specific reference databases compromises metagenomic classification
Publisher: Springer Science and Business Media LLC
Date: 27-02-2020
DOI: 10.1186/S12864-020-6592-2
Abstract: A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic s les. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of s les. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan’s fungal reference database with one containing genome sequences of hibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.
Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok
Publisher: Proceedings of the National Academy of Sciences
Date: 19-09-2006
Abstract: Dengue virus, the causative agent of dengue fever and its more serious manifestation dengue hemorrhagic fever, is widespread throughout tropical and subtropical regions. The virus exists as four distinct serotypes, all of which have cocirculated in Bangkok for several decades with epidemic outbreaks occurring every 8–10 years. We analyze time-series data of monthly infection incidence, revealing a distinctive pattern with epidemics of serotypes 1, 2, and 3 occurring at approximately the same time and an isolated epidemic of serotype 4 occurring in the intervening years. Phylogenetic analysis of virus s les collected over the same period shows that clade replacement events are linked to the epidemic cycle and indicates that there is an interserotypic immune reaction. Using an epidemic model with stochastic seasonal forcing showing 8- to 10-year epidemic oscillations, we demonstrate that moderate cross-protective immunity gives rise to persistent out-of-phase oscillations similar to those observed in the data, but that strong or weak cross-protection or cross-enhancement only produces in-phase patterns. This behavior suggests that the epidemic pattern observed in Bangkok is the result of cross-protective immunity and may be significantly altered by changes in the interserotypic immune reaction.
Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation
Publisher: Cold Spring Harbor Laboratory
Date: 27-06-2019
DOI: 10.1101/683516
Abstract: Influenza A viruses have regularly jumped to new hosts to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus, but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here we examine the processes of influenza A virus infection and evolution in mice by comparing deep sequence variation of a human H1N1 pandemic virus, a seasonal H3N2 virus, and a H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with that seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc. Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals, but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not effect influenza evolution in this model. Overall this shows that mice provide a useful animal model for influenza, but that host passage evolution will vary depending on the virus being tested.
Endogenous Hepadnaviruses in the Genome of the Budgerigar (Melopsittacus undulatus) and the Evolution of Avian Hepadnaviruses
Publisher: American Society for Microbiology
Date: 15-07-2012
DOI: 10.1128/JVI.00769-12
Abstract: Endogenous hepadnaviruses (hepatitis B viruses [HBVs]) were recently discovered in the genomes of passerine birds. We mined six additional avian genomes and discovered multiple copies of endogenous HBVs in the budgerigar (order Psittaciformes), designated eBHBV. A phylogenetic analysis reveals that the endogenous hepadnaviruses are more erse than their exogenous counterparts and that the endogenous and exogenous hepadnaviruses form distinct lineages even when s led from the same avian order, indicative of multiple genomic integration events.
Rapid turnover of intra-host genetic diversity in Zucchini yellow mosaic virus
Publisher: Elsevier BV
Date: 02-2011
Substantial viral and bacterial diversity at the bat–tick interface
Publisher: Microbiology Society
Date: 02-03-2023
Abstract: Ticks harbour a high ersity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle ( Pipistrellus pygmaeus , Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae , while other invertebrate-associated viruses included members of the Dicistroviridae , Iflaviridae, Nodaviridae , Partitiviridae , Permutotetraviridae , Polycipiviridae and Solemoviridae . Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable ersity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
Total infectomes of 162 SARS-CoV-2 cases using meta-transcriptomic sequencing
Publisher: Elsevier BV
Date: 2021
Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria
Publisher: Cold Spring Harbor Laboratory
Date: 05-2019
DOI: 10.1101/624403
Abstract: Parasites of the genus Plasmodium cause human malaria. Yet nothing is known about the viruses that infect these ergent eukaryotes. We investigated the Plasmodium virome by performing a meta-transcriptomic analysis of blood s les from malaria patients infected with P. vivax, P. falciparum or P. knowlesi . This revealed a novel bi-segmented narna-like RNA virus restricted to P. vivax and named Matryoshka RNA virus 1 (MaRNAV-1) to reflect its “Russian doll” nature: a virus, infecting a parasite, infecting an animal. MaRNAV-1 was abundant in geographically erse P. vivax from humans and mosquitoes. Notably, a related virus (MaRNAV-2) was identified in Australian birds infected with a Leucocytozoon - eukaryotic parasites that group with Plasmodium in the Apicomplexa subclass hematozoa. This is the first report of a Plasmodium virus. As well as broadening our understanding of the eukaryotic virosphere, the restriction to P. vivax may help understand P. vivax -specific biology in humans and mosquitoes.
Evolutionary genetics and emergence of RNA virus diseases
Publisher: Cambridge University Press
Date: 15-01-2004
Microevolution of Canine Influenza Virus in Shelters and Its Molecular Epidemiology in the United States
Publisher: American Society for Microbiology
Date: 15-12-2010
DOI: 10.1128/JVI.01350-10
Abstract: Canine influenza virus (CIV) emerged around 2000 when an equine influenza virus (EIV) was transmitted to dogs in Florida. After 2003, the canine virus was carried by infected greyhounds to various parts of the United States and then became established in several large animal shelters, where it has continued to circulate. To better understand the evolution of CIV since its emergence, and particularly its microevolution in spatially restricted populations, we examined multiple gene segments of CIV from dogs resident in two large animal shelters in New York City during the period 2006 to 2009. In particular, we focused on viruses circulating in the two shelters in 2008 and 2009, which we found shared a common ancestor. While viruses in each shelter were generally monophyletic, we observed some gene flow between them. These shelter sequences were compared to earlier CIV isolates. The shelter viruses differed in 1 to 6 amino acids in each gene segment compared to viruses isolated in Florida between 2003 and 2005 and in Colorado in 2006 and 2008. A comparison of the sequences of equine and canine viruses revealed amino acid replacements that distinguished the viruses from the two hosts, but no clear evidence of positive selection indicative of host adaptation was detected, suggesting that any host range adaptation in CIV occurred early in the emergence of this virus or even before it transferred to dogs.
Future issues in RNA virus evolution
Publisher: Future Medicine Ltd
Date: 03-2006
Abstract: The study of RNA virus evolution has developed rapidly during the past 30 years. This review outlines some important recent findings, as well as a number of the remaining major challenges, particularly those that might explain why RNA viruses are the most important class of emerging diseases, yet often have difficulties adapting to sustained transmission cycles in new hosts. The author emphasizes the relevance of research on the underlying dynamics of mutation, fitness landscapes and the constraints to viral adaptation, as well as the evolution of recombination and reassortment. It is also suggested that a combination of theoretical, experimental and comparative approaches is essential for future studies of viral evolution, coupled with new genome sequence data on intrahost genetic variation.
Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants
Publisher: Oxford University Press (OUP)
Date: 28-03-2023
DOI: 10.1093/GBE/EVAD052
Abstract: Developing a timely and effective response to emerging SARS-CoV-2 variants of concern (VOCs) is of paramount public health importance. Global health surveillance does not rely on genomic data alone to identify concerning variants when they emerge. Instead, methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages have the potential to serve as an early warning system. However, these methods assume that genomic data are uniformly reported across circulating lineages. In this study, we analyze differences in reporting delays among SARS-CoV-2 VOCs as a plausible explanation for the timing of the global response to the former VOC Mu. Mu likely emerged in South America in mid-2020, where its circulation was largely confined. In this study, we demonstrate that Mu was designated as a VOC ∼1 year after it emerged and find that the reporting of genomic data for Mu differed significantly than that of other VOCs within countries, states, and in idual laboratories. Our findings suggest that nonsystematic biases in the reporting of genomic data may have delayed the global response to Mu. Until they are resolved, the surveillance gaps that affected the global response to Mu could impede the rapid and accurate assessment of future emerging variants.
Genomic reassortment of influenza A virus in North American swine, 1998–2011
Publisher: Microbiology Society
Date: 12-2012
Abstract: Revealing the frequency and determinants of reassortment among RNA genome segments is fundamental to understanding basic aspects of the biology and evolution of the influenza virus. To estimate the extent of genomic reassortment in influenza viruses circulating in North American swine, we performed a phylogenetic analysis of 139 whole-genome viral sequences s led during 1998–2011 and representing seven antigenically distinct viral lineages. The highest amounts of reassortment were detected between the H3 and the internal gene segments (PB2, PB1, PA, NP, M and NS), while the lowest reassortment frequencies were observed among the H1γ, H1pdm and neuraminidase segments, particularly N1. Less reassortment was observed among specific haemagglutinin–neuraminidase combinations that were more prevalent in swine, suggesting that some genome constellations may be evolutionarily more stable.
Zoonotic risk assessment among farmed mammals
Publisher: Elsevier BV
Date: 04-2023
Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus
Publisher: Microbiology Society
Date: 08-2012
Abstract: The genetic ersity present in populations of RNA viruses is likely to be strongly modulated by aspects of their life history, including mode of transmission. However, how transmission mode shapes patterns of intra- and inter-host genetic ersity, particularly when acting in combination with de novo mutation, population bottlenecks and the selection of advantageous mutations, is poorly understood. To address these issues, this study performed ultradeep sequencing of zucchini yellow mosaic virus in a wild gourd, Cucurbita pepo ssp. texana , under two infection conditions: aphid vectored and mechanically inoculated, achieving a mean coverage of approximately 10 000×. It was shown that mutations persisted during inter-host transmission events in both the aphid vectored and mechanically inoculated populations, suggesting that the vector-imposed transmission bottleneck is not as extreme as previously supposed. Similarly, mutations were found to persist within in idual hosts, arguing against strong systemic bottlenecks. Strikingly, mutations were seen to go to fixation in the aphid-vectored plants, suggestive of a major fitness advantage, but remained at low frequency in the mechanically inoculated plants. Overall, this study highlights the utility of ultradeep sequencing in providing high-resolution data capable of revealing the nature of virus evolution, particularly as the full spectrum of genetic ersity within a population may not be uncovered without sequence coverage of at least 2500-fold.
Homologous Recombination in GB Virus C/Hepatitis G Virus
Publisher: Oxford University Press (OUP)
Date: 02-2001
DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A003799
Abstract: Analysis of 33 GB virus C/hepatitis G virus (GBV-C/HGV) full or nearly full genome sequences revealed several putative inter- and intrasubtype recombinants. The breakpoints of the recombinant regions were mapped using a maximum-likelihood method, and the statistical significance for each region was tested using Monte Carlo simulation. The results were highly significant and provided evidence for the existence of complex mosaic genomes showing as many as nine recombination events, with breakpoints in the 5' UTR and in all of the coding regions except the short NS4b gene. Recombination was confirmed by separate phylogenetic analysis of the various recombinant regions and by Sawyer's runs test. Taken together, these findings demonstrate for the first time that recombination is common in natural populations of GBV-C and that it takes place both within and between subtypes. The wide-ranging implications of such nonclonal history for reconstructing the spread and timescale of GBV-C evolution are discussed.
Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses
Publisher: Springer Science and Business Media LLC
Date: 22-03-2006
DOI: 10.1007/S00239-005-0221-1
Abstract: Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses.
Recombination Monophosphoryl Lipid A-Derived Vacosome for the Development of Preventive Cancer Vaccines
Publisher: American Chemical Society (ACS)
Date: 22-09-2020
Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line
Publisher: Microbiology Society
Date: 06-2018
DOI: 10.1099/JGV.0.001079
Abstract: A novel negative-sense RNA virus, Aedes aegypti anphevirus, was recently identified in wild Aedes aegypti mosquitoes. We show that this virus is also present in the Aag2 Aedes aegypti cell line and characterize its complete genome and evolutionary history. The Aedes aegypti anphevirus genome is estimated to be 12 916 nucleotides in length, contains four genes and has a genome structure similar to that of other anpheviruses. Phylogenetically, Aedes aegypti anphevirus falls within an unclassified group of insect-specific viruses in the order Mononegavirales that form a sister-group to the chuviruses. Notably, the Aag2 cell line used here was also experimentally infected with dengue virus and naturally contained a Phasi Charoen-like virus and cell-fusing agent virus. All four viruses were at relatively high abundance, with 0.5 % of sequence reads assigned to Aedes aegypti anphevirus. The Aag2 cell line is therefore permissive to efficient co-infection with dengue virus and multiple insect-specific viruses.
Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses
Publisher: Elsevier BV
Date: 03-2018
The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds
Publisher: Public Library of Science (PLoS)
Date: 30-05-2008
Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus
Publisher: Public Library of Science (PLoS)
Date: 28-10-2010
Outsiders in the Experts' World: A Grounded Theory Study of Consumers and the Social World of Health Care
Publisher: SAGE Publications
Date: 2020
Abstract: This article presents findings from a grounded theory study, which investigated interactions between health professionals and consumers. The authors used Corbin and Strauss’s evolved version of grounded theory, which is underpinned by symbolic interactionism. The study s le included 23 consumers and nine health professionals. Data collection methods included demographic questionnaires, interviews, consumer diaries, digital storytelling, observations, and field notes. Data analysis was conducted using essential grounded theory methods. The resultant grounded theory consists of five categories: (a) Unexpected entrance, (b) Learning a new role, (c) Establishing a presence, (d) Confronting the dichotomy of “us and them,” and (e) Tailored care. Findings suggest that despite consumers and health professionals’ roles, consumers are outsiders in the social world of health care. Progress toward empowered consumers who are in control of their health and health care is slow and care that is truly consumer-centered is still the exception not the rule.
Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas
Publisher: Public Library of Science (PLoS)
Date: 18-05-2007
Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
Publisher: Springer Science and Business Media LLC
Date: 23-03-2006
Abstract: Genetic ersity of the human immunodeficiency virus type 1 (HIV-1) population within an in idual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag ersity present in the donor is lost. This was consistent with the ersity present at seroconversion in nine other horizontally infected in iduals. Furthermore, we estimated viral ersity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic ersity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.
Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting
Publisher: Public Library of Science (PLoS)
Date: 08-04-2016
The Evolutionary Dynamics of Bluetongue Virus
Publisher: Springer Science and Business Media LLC
Date: 06-2010
DOI: 10.1007/S00239-010-9354-Y
Abstract: Bluetongue virus (BTV) is a midge-borne member of the genus Orbivirus that causes an eponymous debilitating livestock disease of great agricultural impact and which has expanded into Europe in recent decades. Reassortment among the ten segments comprising the double-stranded (ds) RNA genome of BTV has played an important role in generating the epidemic strains of this virus in Europe. In this study, we investigated the dynamics of BTV genome segment evolution utilizing time-structured data sets of complete sequences from four segments, totalling 290 sequences largely s led from ruminant hosts. Our analysis revealed that BTV genome segments generally evolve under strong purifying selection and at substitution rates that are generally lower (mean rates of approximately 0.5-7 x 10(-4) nucleotide substitutions per site, per year) than vector-borne positive-sense viruses with single-strand (ss) RNA genomes. These also represent the most robust estimates of the nucleotide substitution rate in a dsRNA virus generated to date. Additionally, we determined that patterns of geographic structure and times to most recent common ancestor differ substantially between each segment, including a relatively recent origin for the ersity of segment 10 within the past millennium. Together, these findings demonstrate the effect of reassortment to decouple the evolutionary dynamics of BTV genome segments.
Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits ( Oryctolagus cuniculus )
Publisher: Elsevier BV
Date: 09-2014
Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections
Publisher: Microbiology Society
Date: 06-2002
DOI: 10.1099/0022-1317-83-6-1419
Abstract: We compared the extent of positive selection acting on acute and persistent strains of measles virus (MV). Far stronger positive selection was found in the fusion (F) and haemagglutinin (H) genes from subacute sclerosing panencephalitis (SSPE) compared to acute MV cases. Most of the positively selected sites identified in these surface glycoprotein genes from SSPE cases correspond to structural, functional or antigenic areas, and could not be explained by the effects of cell passaging. The correlations between selected sites and functional studies of MV are discussed in detail with reference to the maintenance of persistent infection. No positive selection was found in the matrix (M) gene from acute cases of MV and the effects of including hypermutated SSPE M gene sequences in phylogenetic inference were also explored. Finally, using H gene data, we estimated the rate of molecular evolution for SSPE strains as 3·4×10 −4 substitutions/site/year, which is similar to previous estimates obtained for acute strains.
Endogenous RNA viruses of plants in insect genomes
Publisher: Elsevier BV
Date: 06-2012
Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales
Publisher: Springer Science and Business Media LLC
Date: 30-07-2014
Ledantevirus: A proposed new genus in the rhabdoviridae has a strong ecological association with bats
Publisher: American Society of Tropical Medicine and Hygiene
Date: 04-02-2015
Evolution of Genome Size and Complexity in the Rhabdoviridae
Publisher: Public Library of Science (PLoS)
Date: 13-02-2015
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds
Publisher: The Royal Society
Date: 18-01-2023
Abstract: Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum s les collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño–Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.
Characteristics of people with pressure ulcers using one year's routinely collected data in a defined diverse community
Publisher: Mark Allen Group
Date: 02-09-2019
DOI: 10.12968/JOWC.2019.28.9.576
Abstract: To determine if meaningful patient characteristics pertaining to pressure ulcers (PU) can be derived from routinely collected community health data. A retrospective cohort analysis of records was carried out. To provide a detailed dataset on PU for the community of interest, demographic, general medical and PU data were extracted from mandatory incident reports and audit of electronic and paper medical records. This study is reported in accordance with the RECORD Guidelines from the Equator Network. Adult patients were enrolled from a district nursing service in the target region (n=1085) during 2015. The target region was based on a geographical region bounded by a single postcode district (target region) consisting of 62,000 people of whom approximately 50,000 were adults, 3000 of whom were aged years. The total number of recorded PUs was n=137 in 103 in iduals. Data from mandatory incident reports was obtainable for nearly all variables. Electronic and paper medical records were less reliable due to missing data. Detailed characteristics of community-dwelling PU patients can be derived from routinely collected data, and provides various forms and levels of information which could feed into different projects. The use of mandatory reporting fields increases the level of reporting and reduces missing data. Data enriched with information from electronic and paper records could inform the addition of variables to mandatory forms to improve characterisation of community dwellers with PUs.
Differing Epidemiological Dynamics of Influenza B Virus Lineages in Guangzhou, Southern China, 2009-2010
Publisher: American Society for Microbiology
Date: 15-11-2013
DOI: 10.1128/JVI.01039-13
Abstract: The epidemiological and evolutionary dynamics of the two cocirculating lineages of influenza B virus, Victoria and Yamagata, are poorly understood, especially in tropical or subtropical areas of Southeast Asia. We performed a phylogenetic analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of influenza B viruses isolated in Guangzhou, a southern Chinese city, during 2009 to 2010 and compared the demographic and clinical features of infected patients. We identified multiple viral introductions of Victoria strains from both Chinese and international sources, which formed two phylogenetically and antigenically distinct clades (Victoria 1 and 2), some of which persisted between seasons. We identified one dominant Yamagata introduction from outside China during 2009. Our phylogenetic analysis reveals the occurrence of reassortment events among the Victoria and Yamagata lineages and also within the Victoria lineage. We found no significant difference in clinical severity by influenza B lineage, with the exceptions that (i) the Yamagata lineage infected older people than either Victoria lineage and (ii) fewer upper respiratory tract infections were caused by the Victoria 2 than the Victoria 1 clade. Overall, our study reveals the complex epidemiological dynamics of different influenza B lineages within a single geographic locality and has implications for vaccination policy in southern China.
Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom
Publisher: Cold Spring Harbor Laboratory
Date: 21-08-2020
DOI: 10.1101/2020.08.18.20174623
Abstract: In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on in iduals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected in idual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea – also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger s le of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.
The origin, emergence and evolutionary genetics of dengue virus
Publisher: Elsevier BV
Date: 05-2003
DOI: 10.1016/S1567-1348(03)00004-2
Abstract: Dengue is one of the most important emerging viruses, posing a threat to one-third of the global human population. Herein we show how the comparative analysis of gene sequence data has shed light on the origin and spread of dengue virus, as well as on the evolutionary processes that structure its genetic ersity. This reveals that dengue virus has a relatively recent evolutionary history, with the four serotypes originating approximately 1000 years ago and only establishing endemic transmission in humans in the last few hundred years. However, its place of origin remains uncertain as does the extent of genetic and phenotypic ersity present in the sylvatic (primate) transmission cycle. Although there is some evidence that viral strains differ in key phenotypic features such as virulence, and for positive selection at immunologically important sites, it seems likely that stochastic processes also play a major role in shaping viral genetic ersity, with lineage extinction a common occurrence. A more complete understanding of the evolution and epidemiology of dengue virus, particularly with respect to the aetiology of severe disease, will require large-scale prospective studies and the comparative analysis of complete genome sequences.
Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation
Publisher: American Society for Microbiology
Date: 12-2019
DOI: 10.1128/JVI.01039-19
Abstract: Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts, we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and that the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not affect influenza virus evolution in this model. Overall, our results show that while mice provide a useful animal model for influenza virus pathology, host passage evolution will vary depending on the specific virus tested.
Plague's progress
Publisher: Springer Science and Business Media LLC
Date: 10-2011
DOI: 10.1038/478465A
Bats are a major natural reservoir for hepaciviruses and pegiviruses
Publisher: Proceedings of the National Academy of Sciences
Date: 22-04-2013
Abstract: Although there are over 1,150 bat species worldwide, the ersity of viruses harbored by bats has only recently come into focus as a result of expanded wildlife surveillance. Such surveys are of importance in determining the potential for novel viruses to emerge in humans, and for optimal management of bats and their habitats. To enhance our knowledge of the viral ersity present in bats, we initially surveyed 415 sera from African and Central American bats. Unbiased high-throughput sequencing revealed the presence of a highly erse group of bat-derived viruses related to hepaciviruses and pegiviruses within the family Flaviridae . Subsequent PCR screening of 1,258 bat specimens collected worldwide indicated the presence of these viruses also in North America and Asia. A total of 83 bat-derived viruses were identified, representing an infection rate of nearly 5%. Evolutionary analyses revealed that all known hepaciviruses and pegiviruses, including those previously documented in humans and other primates, fall within the phylogenetic ersity of the bat-derived viruses described here. The prevalence, unprecedented viral bio ersity, phylogenetic ergence, and worldwide distribution of the bat-derived viruses suggest that bats are a major and ancient natural reservoir for both hepaciviruses and pegiviruses and provide insights into the evolutionary history of hepatitis C virus and the human GB viruses.
Contact Heterogeneity, Rather Than Transmission Efficiency, Limits the Emergence and Spread of Canine Influenza Virus
Publisher: Public Library of Science (PLoS)
Date: 23-10-2014
Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events
Publisher: Microbiology Society
Date: 06-2015
DOI: 10.1099/VIR.0.000070
Abstract: Rabbit hemorrhagic disease virus (RHDV), a Lagovirus of the family Caliciviridae, causes rabbit hemorrhagic disease (RHD) in the European rabbit (Oryctolagus cuniculus). The disease was first documented in 1984 in China and rapidly spread worldwide. In 2010, a new RHDV variant emerged, tentatively classified as 'RHDVb'. RHDVb is characterized by affecting vaccinated rabbits and those <2 months old, and is genetically distinct (~20 %) from older strains. To determine the evolution of RHDV, including the new variant, we generated 28 full-genome sequences from s les collected between 1994 and 2014. Phylogenetic analysis of the gene encoding the major capsid protein, VP60, indicated that all viruses s led from 2012 to 2014 were RHDVb. Multiple recombination events were detected in the more recent RHDVb genomes, with a single major breakpoint located in the 5' region of VP60. This breakpoint ides the genome into two regions: one that encodes the non-structural proteins and another that encodes the major and minor structural proteins, VP60 and VP10, respectively. Additional phylogenetic analysis of each region revealed two types of recombinants with distinct genomic backgrounds. Recombinants always include the structural proteins of RHDVb, with non-structural proteins from non-pathogenic lagoviruses or from pathogenic genogroup 1 strains. Our results show that in contrast to the evolutionary history of older RHDV strains, recombination plays an important role in generating ersity in the newly emerged RHDVb.
Sylvatic Dengue Viruses Share the Pathogenic Potential of Urban/Endemic Dengue Viruses
Publisher: American Society for Microbiology
Date: 04-2010
DOI: 10.1128/JVI.02640-09
Multiyear Persistence of 2 Pandemic A/H1N1 Influenza Virus Lineages in West Africa
Publisher: Oxford University Press (OUP)
Date: 19-01-2014
Host phylogeny shapes viral transmission networks in an island ecosystem
Publisher: Springer Science and Business Media LLC
Date: 07-09-2023
Phylogeography, Population Dynamics, and Molecular Evolution of European Bat Lyssaviruses
Publisher: American Society for Microbiology
Date: 15-08-2005
DOI: 10.1128/JVI.79.16.10487-10497.2005
Abstract: European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer the selection pressures, rates of nucleotide substitution, age of genetic ersity, geographical origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1—EBLV-1a and EBLV-1b—have both grown at a low exponential rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly in EBLV-1b. Our inferred rate of nucleotide substitution in EBLV-1, approximately 5 × 10 −5 substitutions per site per year, was also one of the lowest recorded for RNA viruses and implied that the current genetic ersity in the virus arose 500 to 750 years ago. We propose that the slow evolution of EBLVs reflects their distinctive epidemiology in bats, where they occupy a relatively stable fitness peak.
Investigating the processes used to develop and evaluate the effectiveness of health education resources for adult Indigenous people: A literature review
Publisher: Informa UK Limited
Date: 27-06-2019
Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia
Publisher: Springer Science and Business Media LLC
Date: 12-2016
Estimating evolutionary rates in giant viruses using ancient genomes
Publisher: Oxford University Press (OUP)
Date: 2018
DOI: 10.1093/VE/VEY006
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Publisher: Springer Science and Business Media LLC
Date: 15-07-2020
The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing
Publisher: Informa UK Limited
Date: 2020
Discovering the Phylodynamics of RNA Viruses
Publisher: Public Library of Science (PLoS)
Date: 26-10-2009
A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae
Publisher: Cold Spring Harbor Laboratory
Date: 08-02-2021
DOI: 10.1101/2021.02.08.430315
Abstract: Rubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Other matonaviruses, including two new rubella-like viruses, Rustrela virus and Ruhugu virus , have been identified in several mammalian species, along with more ergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses we mined published transcriptome data using genome sequences from Rubella, Rustrela , and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica (Pacific electric ray) that is more closely related to mammalian Rustrela virus than to the ergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the s le analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae , grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses still to be discovered.
The evolutionary dynamics of canid and mongoose rabies virus in southern Africa
Publisher: Springer Science and Business Media LLC
Date: 31-03-2007
DOI: 10.1007/S00705-007-0962-9
Abstract: Two variants of rabies virus (RABV) currently circulate in southern Africa: canid RABV, mainly associated with dogs, jackals, and bat-eared foxes, and mongoose RABV. To investigate the evolutionary dynamics of these variants, we performed coalescent-based analyses of the G-L inter-genic region, allowing for rate variation among viral lineages through the use of a relaxed molecular clock. This revealed that mongoose RABV is evolving more slowly than canid RABV, with mean evolutionary rates of 0.826 and 1.676 x 10(-3) nucleotide substitutions per site, per year, respectively. Additionally, mongoose RABV exhibits older genetic ersity than canid RABV, with common ancestors dating to 73 and 30 years, respectively, and while mongoose RABV has experienced exponential population growth over its evolutionary history in Africa, populations of canid RABV have maintained a constant size. Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology.
Multiple sources of genetic diversity of influenza A viruses during the Hajj
Publisher: American Society for Microbiology
Date: 06-2017
DOI: 10.1128/JVI.00096-17
Abstract: Outbreaks of respiratory virus infection at mass gatherings pose significant health risks to attendees, host communities, and ultimately the global population if they help facilitate viral emergence. However, little is known about the genetic ersity, evolution, and patterns of viral transmission during mass gatherings, particularly how much ersity is generated by in situ transmission compared to that imported from other locations. Here, we describe the genome-scale evolution of influenza A viruses s led from the Hajj pilgrimages at Makkah during 2013 to 2015. Phylogenetic analysis revealed that the ersity of influenza viruses at the Hajj pilgrimages was shaped by multiple introduction events, comprising multiple cocirculating lineages in each year, including those that have circulated in the Middle East and those whose origins likely lie on different continents. At the scale of in idual hosts, the majority of minor variants resulted from de novo mutation, with only limited evidence of minor variant transmission or minor variants circulating at subconsensus level despite the likely identification of multiple transmission clusters. Together, these data highlight the complexity of influenza virus infection at the Hajj pilgrimages, reflecting a mix of global genetic ersity drawn from multiple sources combined with local transmission, and reemphasize the need for vigilant surveillance at mass gatherings. IMPORTANCE Large population sizes and densities at mass gatherings such as the Hajj (Makkah, Saudi Arabia) can contribute to outbreaks of respiratory virus infection by providing local hot spots for transmission followed by spread to other localities. Using a genome-scale analysis, we show that the genetic ersity of influenza A viruses at the Hajj gatherings during 2013 to 2015 was largely shaped by the introduction of multiple viruses from erse geographic regions, including the Middle East, with only little evidence of interhost virus transmission at the Hajj and seemingly limited spread of subconsensus mutational variants. The ersity of viruses at the Hajj pilgrimages highlights the potential for lineage cocirculation during mass gatherings, in turn fuelling segment reassortment and the emergence of novel variants, such that the continued surveillance of respiratory pathogens at mass gatherings should be a public health priority.
Human-to-human transmission of Chlamydia psittaci in China, 2020: an epidemiological and aetiological investigation
Publisher: Elsevier BV
Date: 07-2022
Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes
Publisher: American Society for Microbiology
Date: 09-01-2020
DOI: 10.1128/MRA.01476-19
Abstract: Here, we report the detection of a novel alphavirus in Australian mosquitoes, provisionally named Yada Yada virus (YYV). Phylogenetic analysis indicated that YYV belongs to the mosquito-specific alphavirus complex. The assembled genome is 11,612 nucleotides in length and encodes two open reading frames.
Spatial but not temporal co-divergence of a virus and its mammalian host
Publisher: Wiley
Date: 31-08-2011
Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand
Publisher: Springer Science and Business Media LLC
Date: 12-10-2022
DOI: 10.1186/S42522-022-00072-Z
Abstract: Translocation is a common tool in wildlife management and its implementation has resulted in many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities (‘infectome’) and mitigate the long-term risks of reduced natural resistance. We used metatranscriptomic sequencing to characterise the cloacal infectome of 41 toutouwai (North Island robin, Petroica longipes ) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites. Although we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a ergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite. The presumably non-pathogenic viruses and microbial species identified here support the idea that most microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.
Further Characterization of 2 Types of Precore Variant Hepatitis B Virus Isolates from Hong Kong
Publisher: Oxford University Press (OUP)
Date: 06-1995
DOI: 10.1093/INFDIS/171.6.1461
Abstract: Two precore variants of hepatitis B virus occur in chronic carriers in the Chinese community in Hong Kong. One variant has a serine at amino acid (aa) 15, and the other has a stop codon at aa 28, which inhibits production of hepatitis B e (HBe) antigen (Ag). The serine 15 strain is shown here to produce antigenically normal amounts of HBeAg. These variants are mutually exclusive, probably due to sequence requirements for encapsidation, and are separate lineages. Sequential core sequences from patients with either variant revealed more aa substitutions in those who have the codon 28 change (P = .02), particularly T helper and B cell epitopes, implying different selection pressures. Most substitutions occurred around the time of selection of the stop codon, implying that complete loss of HBeAg, an immunomodulatory protein, is necessary for immune pressure on core epitopes. Serine 15 strains select small numbers of substitutions throughout the anti-HBe phase, probably because of persistent immunomodulation.
Novel hepatitis D-like agents in vertebrates and invertebrates
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2019
DOI: 10.1101/539924
Abstract: Hepatitis delta virus (HDV) is the smallest known RNA virus and encodes a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic s les from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly ergent HDV-like viruses are also present in fish, hibians and invertebrates. Notably, the novel viruses identified here share HDV-like genomic features such as a small genome size of ~1.7kb in length, circular genomes, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human HDAgs. Notably, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the ersity and host range of HDV in non-human species, but shed light on its origin and evolutionary history.
Populations and areas most at risk of methamphetamine-related harms: A commentary on Degenhardt et al.
Publisher: Wiley
Date: 23-03-2017
DOI: 10.1111/DAR.12533
Understanding the Impact of Resistance to Influenza Antivirals
Publisher: American Society for Microbiology
Date: 17-03-2022
DOI: 10.1128/CMR.00224-20
Abstract: Influenza poses a significant burden on society and health care systems. Although antivirals are an integral tool in effective influenza management, the potential for the emergence of antiviral-resistant viruses can lead to uncertainty and hesitation among front-line prescribers and policy makers.
Co-circulation and persistence of multiple A/H3N2 influenza variants in China
Publisher: Informa UK Limited
Date: 2019
Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 03-2021
Genome Scale Evolution of Myxoma Virus Reveals Host-Pathogen Adaptation and Rapid Geographic Spread
Publisher: American Society for Microbiology
Date: 12-2013
DOI: 10.1128/JVI.02060-13
Abstract: The evolutionary interplay between myxoma virus (MYXV) and the European rabbit ( Oryctolagus cuniculus ) following release of the virus in Australia in 1950 as a biological control is a classic ex le of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within in idual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.
Infectious disease phylodynamics with occurrence data
Publisher: Cold Spring Harbor Laboratory
Date: 08-04-2019
DOI: 10.1101/596700
Abstract: Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance of pathogens, especially amid the SARS-CoV-2 outbreak, new practical questions about their use are emerging. One such question focuses on the inclusion of un-sequenced case occurrence data alongside sequenced data to improve phylodynamic analyses. This approach can be particularly valuable if sequencing efforts vary over time. Using simulations, we demonstrate that birth-death phylodynamic models can employ occurrence data to eliminate bias in estimates of the basic reproductive number due to misspecification of the s ling process. In contrast, the coalescent exponential model is robust to such s ling biases, but in the absence of a s ling model it cannot exploit occurrence data. Subsequent analysis of the SARS-CoV-2 epidemic in the northwest USA supports these results. We conclude that occurrence data are a valuable source of information in combination with birth-death models. These data should be used to bolster phylodynamic analyses of infectious diseases and other rapidly spreading species in the future.
Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks
Publisher: MDPI AG
Date: 09-10-2021
DOI: 10.3390/V13102040
Abstract: Feline calicivirus (FCV) causes upper respiratory tract disease (URTD) and sporadic outbreaks of virulent systemic disease (FCV-VSD). The basis for the increased pathogenicity of FCV-VSD viruses is incompletely understood, and antivirals for FCV-VSD have yet to be developed. We investigated the clinicoepidemiology and viral features of three FCV-VSD outbreaks in Australia and evaluated the in vitro efficacy of nitazoxanide (NTZ), 2′-C-methylcytidine (2CMC) and NITD-008 against FCV-VSD viruses. Overall mortality among 23 cases of FCV-VSD was 39%. Metagenomic sequencing identified five genetically distinct FCV lineages within the three outbreaks, all seemingly evolving in situ in Australia. Notably, no mutations that clearly distinguished FCV-URTD from FCV-VSD phenotypes were identified. One FCV-URTD strain likely originated from a recombination event. Analysis of seven amino-acid residues from the hypervariable E region of the capsid in the cultured viruses did not support the contention that properties of these residues can reliably differentiate between the two pathotypes. On plaque reduction assays, dose–response inhibition of FCV-VSD was obtained with all antivirals at low micromolar concentrations NTZ EC50, 0.4–0.6 µM, TI = 21 2CMC EC50, 2.7–5.3 µM, TI 18 NITD-008, 0.5 to 0.9 µM, TI 111. Investigation of these antivirals for the treatment of FCV-VSD is warranted.
Genetic Constraints and the Adaptive Evolution of Rabies Virus in Nature
Publisher: Elsevier BV
Date: 2002
Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”
Publisher: Springer Science and Business Media LLC
Date: 12-2020
DOI: 10.1186/S13059-020-02203-Z
Abstract: We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.
Epidemiology and Diversity of Rickettsiales Bacteria in Humans and Animals in Jiangsu and Jiangxi provinces, China
Publisher: Springer Science and Business Media LLC
Date: 11-09-2019
DOI: 10.1038/S41598-019-49059-3
Abstract: Diseases caused by Rickettsiales bacteria are a global public health problem. To better understand the ersity and origins of Rickettsiales infection in humans and animals, we s led 134 febrile patients, 173 rodents and 43 shrews, as well as 358 ticks, from two cities in Jiangsu and Jiangxi provinces, China. Our data revealed a relatively high prevalence of scrub typhus cases in both localities. In addition, both serological tests and genetic analysis identified three patients infected with Anaplasma bovis , Rickettsia monacensis , and Orientia tsutsugamushi bacteria. Molecular epidemiological investigation revealed the co-circulation of multiple species of Rickettsiales bacteria in small mammals and ticks in both provinces, potentially including novel bacterial species. In sum, these data demonstrate the ongoing importance of Rickettsiales infection in China and highlight the need for the regular surveillance of local arthropods, mammals and humans.
Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.VIROL.2019.06.013
Abstract: Orthobunyaviruses of the Simbu serogroup are transmitted by insects (primarily biting midges) and infect mammals and/or birds. Many have been associated with disease in livestock or humans. The orthobunyavirus genome comprises three negative-sense RNA segments (L, M and S). We report the complete coding sequences of 57 isolates of Simbu serogroup viruses collected in Australia during 1968-1984. Phylogenetic analysis identified novel genogroups of Akabane virus (AKAV), Aino virus (AINOV) and Peaton virus, and provided evidence of constrained movement of AKAV between epidemiological systems in the northern and eastern regions of the continent. Differential clustering of AKAV isolates in trees inferred from L, M and S segments was indicative of intratypic segment reassortment. Similarly, intertypic segment reassortment was detected between AKAV and Tinaroo virus, and between AINOV and Douglas virus. L segments representing novel genogroups were detected in AINOV reassortants, suggesting the presence of unidentified Simbu group viruses in the episystem.
Genome-scale rates of evolutionary change in bacteria
Publisher: Cold Spring Harbor Laboratory
Date: 15-08-2016
DOI: 10.1101/069492
Abstract: Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are s led. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ ancient DNA ” data s led over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10 −6 to 10 −8 nucleotide substitutions site -1 year -1 . This variation was largely attributable to s ling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
Zoonotic disease and virome diversity in bats
Publisher: Elsevier BV
Date: 02-2022
Human tick-borne diseases in Australia
Publisher: Frontiers Media SA
Date: 28-01-2019
Seqotron: a user-friendly sequence editor for Mac OS X.
Publisher: Springer Science and Business Media LLC
Date: 17-02-2016
Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
Publisher: Proceedings of the National Academy of Sciences
Date: 02-01-2001
Abstract: The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical tests of congruence between gene trees to examine the extent and significance of recombination in six bacterial pathogens. For Neisseria meningitidis , Streptococcus pneumoniae , Streptococcus pyogenes, and Staphylococcus aureus , the congruence between the maximum likelihood trees reconstructed using seven house-keeping genes was in most cases no better than that between each tree and trees of random topology. The lack of congruence between gene trees in these four species, which include both naturally transformable and nontransformable species, is in three cases supported by high ratios of recombination to point mutation during clonal ersification (estimates of this parameter were not possible for Strep. pyogenes ). In contrast, gene trees constructed for Hemophilus influenzae and pathogenic isolates of Escherichia coli showed a higher degree of congruence, suggesting lower rates of recombination. The impact of recombination therefore varies between bacterial species but in many species is sufficient to obliterate the phylogenetic signal in gene trees.
Host Phylogeny Shapes Viral Transmission Networks in an Island Ecosystem
Publisher: Cold Spring Harbor Laboratory
Date: 05-10-2022
DOI: 10.1101/2022.10.04.510907
Abstract: Viral transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern cross-species virus transmission and zoonotic risk, although their relative impact is unknown. By characterising the virome of a relatively isolated island ecological community linked through a food web we show that phylogenetic barriers result in distantly related host species sharing fewer viruses. Host ecology had a much smaller influence on overall virome composition. Network analysis revealed that hosts with a high ersity of viruses were more likely to gain new viruses, and that generalist viruses were more likely to infect new hosts. Such a highly connected ecological community heightens the risk of disease emergence, particularly among closely related species. Sequencing of an entire island virome reveals that closely related hosts have highly connected virus communities, increasing emergence risk.
Within-Host Genetic Diversity of Endemic and Emerging Parvoviruses of Dogs and Cats
Publisher: American Society for Microbiology
Date: 15-11-2008
DOI: 10.1128/JVI.01003-08
Abstract: Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence ersity. To determine the extent and structure of intrahost genetic ersity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shortly after CPV emerged with more recent infections and examined the population structure of CPV after experimental cross-species transmission to cats. Infections with CPV and FPV showed limited genetic ersity regardless of the analyzed host tissue or year of isolation. Coinfections with genetically distinct viral strains were detected in some cases, and rearranged genomes were seen in both FPV and CPV. The sporadic presence of some sequences with multiple mutations suggested the occurrence of either particularly error-prone viral replication or coinfection by more distantly related strains. Finally, some potentially organ-specific host effects were seen during experimental cross-species transmission, with many of the mutations located in the nonstructural protein NS2. These included residues with evidence of positive selection at the population level, which is compatible with a role of this protein in host adaptation.
Puzzling Origins of the Ebola Outbreak in the Democratic Republic of the Congo, 2014
Publisher: American Society for Microbiology
Date: 10-2015
DOI: 10.1128/JVI.01226-15
Patterns of ‘at-home’ alcohol-related injury presentations to emergency departments
Publisher: Wiley
Date: 22-08-2016
DOI: 10.1111/JOCN.13472
Abstract: This study aimed to establish the scale of alcohol-related injuries originating in the home. Despite recent media and public attention on alcohol-related injuries occurring at licensed venues, many occur in other locations including the home. A retrospective observational study. Emergency department surveillance data sourced from the Queensland Injury Surveillance Unit were interrogated for alcohol-related emergency department presentations from 2003-2012 (n = 12,296). Descriptive analysis was undertaken to assess alcohol involvement in injury, and analysis of variance was used to determine the differences among group means and their associated presentations. The relationship between demographic variables and injury location was assessed using p value of <0·05 as statistically significant. Of all injuries that were positively identified as being alcohol related, 41·07% occurred at the 'other' location, 36·14% 'at home', 13·00% on the street and 9·78% at licensed premises. Of these, males (n = 2635 59%) represented a higher proportion than females (n = 1807 41%). Of injuries identified as domestic violence by spouse or partner (n = 510), 59·5% occurred 'at home'. This is the first study to investigate alcohol-related injuries occurring at home. The home accounts for a greater proportion of injuries than the frequently assessed licensed premises location. Further research is required to validate these findings in a wider setting. A public health c aign is required to minimise harm associated with alcohol-related injuries in the home, and nurses are positioned to inform health policy makers around this issue. Furthermore, emergency department nurses are in a unique position to provide brief interventions around safe alcohol consumption and injury prevention.
Fluid spatial dynamics of West Nile virus in the United States: Rapid spread in a permissive host environment
Publisher: American Society for Microbiology
Date: 15-01-2016
DOI: 10.1128/JVI.02305-15
Abstract: The introduction of West Nile virus (WNV) into North America in 1999 is a classic ex le of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates s led across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses s led from birds, and no strong phylogenetic association with well-s led avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and erse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers. IMPORTANCE How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic ex le of this process. Using approximately 300 new viral genomes s led from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
10 The Emergence of Dengue: Past Present and Future
Publisher: Elsevier
Date: 1998
Different rates of substitution may produce different phylogenies of the eutherian mammals
Publisher: Springer Science and Business Media LLC
Date: 09-1991
DOI: 10.1007/BF02100671
Abstract: Consensus development techniques were used in the late 1980s to create explicit criteria for the appropriateness of cholecystectomy. New diagnostic and treatment techniques have been developed in the last decade, so an updated appropriateness of indications tool was developed for cholecystectomy in patients with non-malignant diseases. The validity and reliability of panel results using this tool were tested. Criteria were developed using a modified Delphi panel judgement process. The level of agreement between the panelists (six gastroenterologists and six surgeons) was analysed and the ratings were compared with those of a second different panel using weighted kappa statistics. The results of the main panel were presented as a decision tree. Of the 210 scenarios evaluated by the main panel in the second round, 51% were found appropriate, 26% uncertain, and 23% inappropriate. Agreement was achieved in 54% of the scenarios and disagreement in 3%. Although the gastroenterologists tended to score fewer scenarios as appropriate, as a group they did not differ from the surgeons. Comparison of the ratings of the main panel with those of a second panel resulted in a weighted kappa statistic of 0.75. The parameters tested showed acceptable validity and reliability results for an evaluation tool. These results support the use of this algorithm as a screening tool for assessing the appropriateness of cholecystectomy.
Genome-scale rates of evolutionary change in bacteria
Publisher: Microbiology Society
Date: 30-11-2016
Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases
Publisher: American Society for Microbiology
Date: 09-2008
Abstract: Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as “spillover” infections into alternative hosts. Rarely, viruses gain the ability to spread efficiently within a new host that was not previously exposed or susceptible. These transfers involve either increased exposure or the acquisition of variations that allow them to overcome barriers to infection of the new hosts. In these cases, devastating outbreaks can result. Steps involved in transfers of viruses to new hosts include contact between the virus and the host, infection of an initial in idual leading to lification and an outbreak, and the generation within the original or new host of viral variants that have the ability to spread efficiently between in iduals in populations of the new host. Here we review what is known about host switching leading to viral emergence from known ex les, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population.
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
Publisher: Springer Science and Business Media LLC
Date: 09-07-2020
Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China
Publisher: Public Library of Science (PLoS)
Date: 17-02-2022
DOI: 10.1371/JOURNAL.PPAT.1010259
Abstract: At the end of 2019 Wuhan witnessed an outbreak of “atypical pneumonia” that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus denoted SARS-CoV-2. To provide a snapshot of the pathogens in pneumonia-associated respiratory s les from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid s les from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their “total infectome”, including viruses, bacteria and fungi. We identified 35 pathogen species, comprising 13 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (13.5%). SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen– Chlamydia psittaci . S les from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of in idual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more erse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016–2017.
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Publisher: Springer Science and Business Media LLC
Date: 09-06-2021
Share or perish: Social media and the International Journal of Mental Health Nursing
Publisher: Wiley
Date: 30-06-2019
DOI: 10.1111/INM.12600
Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia
Publisher: MDPI AG
Date: 06-09-2018
DOI: 10.3390/V10090476
Abstract: There is an ongoing global pandemic of human respiratory syncytial virus (RSV) infection that results in substantial annual morbidity and mortality. In Australia, RSV is a major cause of acute lower respiratory tract infections (ALRI). Nevertheless, little is known about the extent and origins of the genetic ersity of RSV in Australia, nor the factors that shape this ersity. We have conducted a genome-scale analysis of RSV infections in New South Wales (NSW). RSV genomes were successfully sequenced for 144 specimens collected between 2010–2016. Of these, 64 belonged to the RSVA and 80 to the RSVB subtype. Phylogenetic analysis revealed a wide ersity of RSV lineages within NSW and that both subtypes evolved rapidly in a strongly clock-like manner, with mean rates of approximately 6–8 × 10−4 nucleotide substitutions per site per year. There was only weak evidence for geographic clustering of sequences, indicative of fluid patterns of transmission within the infected population and no evidence of any clustering by patient age such that viruses in the same lineages circulate through the entire host population. Importantly, we show that both subtypes circulated concurrently in NSW with multiple introductions into the Australian population in each year and only limited evidence for multi-year persistence.
The impact of COVID-19 on Bangladeshi readymade garment (RMG) workers
Publisher: Oxford University Press (OUP)
Date: 31-07-2021
Abstract: This paper describes the potential impact of the coronavirus disease 2019 (COVID-19) pandemic on the readymade garment (RMG) workers of Bangladesh. It articulates the RMG workers’ existing vulnerability during the COVID-19 pandemic based on currently available evidence and personal conversations/communications with RMG workers. COVID-19 has already impacted RMG workers’ health (both physical and mental health status) and wellbeing, and resulted in loss of employment. We argue that the COVID-19 pandemic will have long-lasting effects on the garment workers, especially related to their health issues, financial hardship and inability to pay for essentials such as food, and future employment opportunities. The stakeholders (such as the international retailers/brands, Bangladesh Garment Manufacturers and Exporters Association, Government of Bangladesh) responsible for the global supply chain RMG factories should reconsider the health and overall wellbeing needs of the RMG workers during the ongoing COVID-19 pandemic.
The gorilla connection
Publisher: Springer Science and Business Media LLC
Date: 09-2010
DOI: 10.1038/467404A
Co-Circulation of Multiple Hemorrhagic Fever Diseases with Distinct Clinical Characteristics in Dandong, China
Publisher: Public Library of Science (PLoS)
Date: 27-02-2014
Co-Circulation and Persistence of Genetically Distinct Saffold Viruses, Denmark
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 03-2012
Abstract
Publisher: eLife Sciences Publications, Ltd
Date: 2016
Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures
Publisher: MDPI AG
Date: 19-10-2020
DOI: 10.3390/V12101180
Abstract: Our knowledge of the ersity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured s les from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to ergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
Invited Commentary: Evaluating Vaccination Programs Using Genetic Sequence Data
Publisher: Oxford University Press (OUP)
Date: 12-11-2009
DOI: 10.1093/AJE/KWP366
Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases
Publisher: Oxford University Press (OUP)
Date: 11-05-2019
DOI: 10.1093/BIOINFORMATICS/BTZ385
Abstract: Entrezpy is a Python library that automates the querying and downloading of data from the Entrez databases at National Center for Biotechnology Information by interacting with E-Utilities. Entrezpy implements complex queries by automatically creating E-Utility parameters from the results obtained that can then be used directly in subsequent queries. Entrezpy also allows the user to cache and retrieve results locally, implements interactions with all Entrez databases as part of an analysis pipeline and adjusts parameters within an ongoing query or using prior results. Entrezpy’s modular design enables it to easily extend and adjust existing E-Utility functions. Entrezpy is implemented in Python 3 (≥3.6) and depends only on the Python Standard Library. It is available via PyPi (roject/entrezpy/) and at cbipy/entrezpy.git. Entrezpy is licensed under the LGPLv3 and also at entrezpy.readthedocs.io/.
The evolutionary history of vertebrate RNA viruses (vol 556, pg 197, 2018)
Publisher: Springer Science and Business Media LLC
Date: 26-06-2018
DOI: 10.1038/S41586-018-0310-0
Abstract: Change history: In this Article, author Li Liu should be associated with affiliation number 5 (College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China), rather than affiliation number 4 (Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China). This has been corrected online.
No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine
Publisher: Elsevier BV
Date: 02-2012
Redefining the invertebrate RNA virosphere
Publisher: Springer Science and Business Media LLC
Date: 23-11-2016
DOI: 10.1038/NATURE20167
Abstract: Current knowledge of RNA virus bio ersity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species s led across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently ergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co- ergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically erse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma
Publisher: MDPI AG
Date: 30-08-2018
DOI: 10.3390/V10090464
Abstract: Lymphoma is one of the most common malignancies in domestic cats. The lymphomagenicpotential of Felis catus gammaherpesvirus 1 (FcaGHV1), a common infection in domestic cats,is unknown. In other species, including humans, cellular transformation by gammaherpesvirusesis typically mediated by viral genes expressed during latency. We analysed tumour RNA, fromdiffuse large B-cell lymphomas (DLBCL) appearing in cats coinfected with FcaGHV1 and felineimmunodeficiency virus (FIV) (n = 10). Analysis was done by high throughput transcriptomesequencing and reverse transcription PCR. A limited repertoire of FcaGHV transcripts was identifiedin five tumors, including homologs of oncogenic latency-associated transcripts, latency-associatednuclear antigen (LANA, ORF73) and vFLIP (F7), lytic genes (ORF50, ORF6, ORF59, F10), and an ORFunique to FcaGHV1, F20. In situ hybridization of FIV-associated DLBCLs (n = 9), post-transplantlymphomas (n = 6) and high-grade B and T-cell intestinal lymphomas (n = 8) identified a single casein which FcaGHV1 nucleic acid was detectable. These results demonstrate that FcaGHV1 transcriptscan be detected in some FIV-associated lymphomas, but with a low copy number, precludingassessment of a potential role for FcaGHV1 in lymphomagenesis. Future investigation of the FcaGHV1transcriptome in clinical s les might employ viral enrichment and greater sequencing depth toenhance the retrieval of viral reads. Our results suggest prioritization of a subset of intestinal T-celltumors and large granular lymphocyte lymphoma, for study.
Correction for Batovska et al., “Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes”
Publisher: American Society for Microbiology
Date: 05-03-2020
DOI: 10.1128/MRA.00103-20
Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 05-2021
The Evolutionary Genetics of Emerging Viruses
Publisher: Annual Reviews
Date: 12-2009
DOI: 10.1146/ANNUREV.ECOLSYS.110308.120248
Abstract: RNA viruses are the main agents of emerging disease. To understand how RNA viruses are able to jump species boundaries and spread in new hosts it is essential to determine the basic processes of evolutionary change in these infectious agents. RNA virus evolution is largely shaped by very high rates of mutation. This, coupled with potentially enormous intra- and interhost population sizes and continual replication, allows the rapid production of genetic ersity, including those mutations that facilitate host adaptation. However, high mutation rates also act to constrain aspects of RNA virus evolution, as the majority of mutations, including many at synonymous sites, are deleterious, which in turn places an upper limit on genome size. Ironically, although RNA viruses are characterized by their mutation rates, these rates may not be high enough to allow the onset of quasispecies dynamics, in which natural selection acts on the viral population as a whole.
Identification of diverse arthropod associated viruses in native Australian fleas
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.VIROL.2019.07.010
Abstract: Fleas are important vectors of zoonotic disease. However, little is known about the natural ersity and abundance of flea viruses, particularly in the absence of disease associations, nor the evolutionary relationships among those viruses found in different parasitic vector species. Herein, we present the first virome scale study of fleas, based on the meta-transcriptomic analysis of 52 fleas collected along the eastern coast of Australia. Our analysis revealed 18 novel RNA viruses belonging to nine viral families with erse genome organizations, although the majority (72%) possessed single-stranded positive-sense genomes. Notably, a number of the viruses identified belonged to the same phylogenetic groups as those observed in ticks s led at the same locations, although none were likely associated with mammalian infection. Overall, we identified high levels of genomic ersity and abundance of viruses in the flea species studied, and established that fleas harbor viruses similar to those seen to other vectors.
Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.
Publisher: eLife Sciences Publications, Ltd
Date: 21-01-2016
DOI: 10.7554/ELIFE.12994
Abstract: The 14th–18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague’s persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci s led to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
Rabbit Hemorrhagic Disease Virus 2 (RHDV2; GI.2) Is Replacing Endemic Strains of RHDV in the Australian Landscape within 18 Months of Its Arrival
Publisher: American Society for Microbiology
Date: 15-01-2018
DOI: 10.1128/JVI.01374-17
Abstract: Rabbit hemorrhagic disease virus 2 (RHDV2 Lagovirus GI.2) is a pathogenic calicivirus that affects European rabbits ( Oryctolagus cuniculus ) and various hare ( Lepus ) species. GI.2 was first detected in France in 2010 and subsequently caused epidemics in wild and domestic lagomorph populations throughout Europe. In May 2015, GI.2 was detected in Australia. Within 18 months of its initial detection, GI.2 had spread to all Australian states and territories and rapidly became the dominant circulating strain, replacing Rabbit hemorrhagic disease virus (RHDV/GI.1) in mainland Australia. Reconstruction of the evolutionary history of 127 Australian GI.2 isolates revealed that the virus arrived in Australia at least several months before its initial description and likely circulated unnoticed in wild rabbit populations in the east of the continent prior to its detection. GI.2 sequences isolated from five hares clustered with sequences from sympatric rabbit populations s led contemporaneously, indicating multiple spillover events into hares rather than an adaptation of the Australian GI.2 to a new host. Since the presence of GI.2 in Australia may have wide-ranging consequences for rabbit biocontrol, particularly with the release of the novel biocontrol agent GI.1a/RHDVa-K5 in March 2017, ongoing surveillance is critical to understanding the interactions of the various lagoviruses in Australia and their impact on host populations. IMPORTANCE This study describes the spread and distribution of Rabbit hemorrhagic disease virus 2 (GI.2) in Australia since its first detection in May 2015. Within the first 18 months following its detection, RHDV2 spread from east to west across the continent and became the dominant strain in all mainland states of Australia. This has important implications for pest animal management and for owners of pet and farmed rabbits, as there currently is no effective vaccine available in Australia for GI.2. The closely related RHDV (GI.1) is used to control overabundant wild rabbits, a serious environmental and agricultural pest in this country, and it is currently unclear how the widespread circulation of GI.2 will impact ongoing targeted wild rabbit management operations.
Does hepatitis C virus really form quasispecies?
Publisher: Elsevier BV
Date: 05-2010
Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity
Publisher: Microbiology Society
Date: 04-1993
DOI: 10.1099/0022-1317-74-4-661
Abstract: We have analysed the pattern of nucleotide sequence variability in the 5' non-coding region (5' NCR) of geographically dispersed variants of hepatitis C virus (HCV). Phylogenetic analysis of sequences in this region indicated the existence of a new virus type, provisionally termed type 4, the identity of which was confirmed by further analysis of the more variable part of the HCV core protein coding region. The geographical distribution of HCV type 4 was distinct from that of other HCV types, it being particularly widespread in Africa and absent or rare in Europe and the Far East. Much of the variability in the 5' NCR appears to be constrained by a requirement for specific secondary structures in the viral RNA. In one of the most variable regions of the 5' NCR (positions -169 to -114), most of the nucleotide changes that are characteristic of different HCV types were covariant, with complementary substitutions at other positions. According to the proposed secondary structure of the 5' NCR, such changes preserved base pairing within a stem-loop structure, whereas the nucleotide insertions found in a proportion of 5' NCR sequences, including those of type 4, localized exclusively to the non-base-paired terminal loop. The specific nucleotide substitutions in the 5' NCR that differentiate each of the four HCV types can be detected by restriction enzyme cleavage, providing a rapid and reliable method for virus typing.
Understanding the Divergent Evolution and Epidemiology of H3N8 Influenza Viruses in Dogs and Horses
Publisher: Cold Spring Harbor Laboratory
Date: 23-03-2023
DOI: 10.1101/2023.03.22.533763
Abstract: Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One ex le in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, Florida, USA, after emerging among horses in South America. In the early 21 st century the American lineage of EIV erged into two ‘Florida’ clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV. (242 words) The emergence of viruses in new hosts is a threat to human and animal health. The H3N8 equine influenza virus (EIV) emerged in 1963 by transfer of an avian influenza virus, and the H3N8 canine influenza virus (CIV) subsequently emerged in 1999 when EIV transferred to dogs. H3N8 CIV persistently circulated in only a few locations in the USA, and has not been detected since 2016. In the same period H3N8 EIV has circulated as two separate clades, one in North America and other regions of the world, while the other currently appears to be found only in Central Asia. By comparing the hosts, epidemiology, and evolution of these influenza viruses we explain how these lineages had different evolutionary fates, and show why elucidating these evolutionary processes is key to understanding zoonotic disease and viral emergence. (137 words)
1918 and All That
Publisher: American Association for the Advancement of Science (AAAS)
Date: 19-03-2004
Correction: Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
Publisher: Public Library of Science (PLoS)
Date: 15-12-2008
DOI: 10.1371/ANNOTATION/1391941E-93D3-48D3-8C9A-B7C6D98F9527
Genomic Epidemiology of a Dengue Virus Epidemic in Urban Singapore
Publisher: American Society for Microbiology
Date: 05-2009
DOI: 10.1128/JVI.02445-08
Abstract: Dengue is one of the most important emerging diseases of humans, with no preventative vaccines or antiviral cures available at present. Although one-third of the world's population live at risk of infection, little is known about the pattern and dynamics of dengue virus (DENV) within outbreak situations. By exploiting genomic data from an intensively studied major outbreak, we are able to describe the molecular epidemiology of DENV at a uniquely fine-scaled temporal and spatial resolution. Two DENV serotypes (DENV-1 and DENV-3), and multiple component genotypes, spread concurrently and with similar epidemiological and evolutionary profiles during the initial outbreak phase of a major dengue epidemic that took place in Singapore during 2005. Although DENV-1 and DENV-3 differed in viremia and clinical outcome, there was no evidence for adaptive evolution before, during, or after the outbreak, indicating that ecological or immunological rather than virological factors were the key determinants of epidemic dynamics.
Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021
Publisher: Cold Spring Harbor Laboratory
Date: 12-07-2022
DOI: 10.1101/2022.07.11.499512
Abstract: Severe acute diarrhea syndrome coronavirus (SADS-CoV) has had a major impact on the swine industry in China, but has not been detected since 2019. Using real-time qPCR and metagenomic surveillance we identified SADS-CoV in a pig farm experiencing diarrheal disease. Genomic analysis supported the undetected circulation of SADS-CoV since 2019.
Limited Cross-Species Virus Transmission in a Spatially Restricted Coral Reef Fish Community
Publisher: Cold Spring Harbor Laboratory
Date: 18-05-2022
DOI: 10.1101/2022.05.17.492384
Abstract: The Great Barrier Reef (GBR) – the largest coral reef ecosystem in the world – supports over 1200 fish species with some of the highest population densities and ersities seen in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community ersity on virus evolution and emergence. In recent decades the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. However, our understanding of virus ersity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of 61 reef fish species. This identified a total of 132 viruses, 38 of which were vertebrate-associated and therefore likely infecting the fish, including a novel isolate of Santee-cooper ranavirus ( Iridoviridae ). Notably, we found little evidence for virus transmission between fish species living within a very restricted geographical space – a 100 m 2 coral reef ecosystem – suggesting that there might be important host genetic barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition between reef fish families, such that cryptobenthic reef fishes – characterized by small body sizes and short life-spans – exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species transmission, and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.
Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants
Publisher: Microbiology Society
Date: 05-1992
DOI: 10.1099/0022-1317-73-5-1131
Abstract: Sequences obtained in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) were obtained from Scottish blood donors and compared with previously published HCV sequences. Phylogenetic analysis revealed the existence of three distinct groups of sequences two of these corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species. Nucleotide sequences of this latter group differed from all previously published 5'NCR sequence variants by at least 9%. This new virus type also differed considerably from previously published variants in other regions of the viral genome (core, NS-3 and NS-5), with corrected nucleotide distances of 15, 43 and 49% respectively from the prototype HCV-1 sequence. Formal phylogenetic analysis of each of the coding regions confirmed that HCV type 1 variants could be clearly differentiated into regional variants (Far East and U.S.A./European), in contrast to the clearly overlapping geographical distributions of the main HCV types in U.K. blood donors. We discuss the evidence for and against the hypothesis that the three main phylogenetic groups identified in this study represent separate species of HCV.
Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China
Publisher: American Society for Microbiology
Date: 15-06-2017
DOI: 10.1128/JVI.00143-17
Abstract: H5N6 avian influenza virus (AIV) has posed a potential threat to public health since its emergence in China in 2013. To understand the evolution and emergence of H5N6 AIV in the avian population, we performed molecular surveillance of live poultry markets (LPMs) in Wugang Prefecture, Hunan Province, in central China, during 2014 and 2015. Wugang Prefecture is located on the Eastern Asian-Australian migratory bird flyway, and a human death due to an H5N6 virus was reported in the prefecture on 21 November 2016. In total, we s led and sequenced the complete genomes of 175 H5N6 AIVs. Notably, our analysis revealed that H5N6 AIVs contain at least six genotypes arising from segment reassortment, including a rare variant that possesses an HA gene derived from H5N1 clade 2.3.2 and a novel NP gene that has its origins with H7N3 viruses. In addition, phylogenetic analysis revealed that genetically similar H5N6 AIVs tend to cluster according to their geographic regions of origin. These results help to reveal the evolutionary behavior of influenza viruses prior to their emergence in humans. IMPORTANCE The newly emerged H5N6 influenza A virus has caused more than 10 human deaths in China since 2013. In November 2016, a human death due to an H5N6 virus, in Wugang Prefecture, Hunan Province, was confirmed by the WHO. To better understand the evolution and emergence of H5N6 viruses, we surveyed live poultry markets (LPMs) in Wugang Prefecture before the reported human death, with a focus on revealing the ersity and genomic origins of H5N6 in birds during 2014 and 2015. In general, H5N6 viruses in this region were most closely related to H5N1 clade 2.3.4.4, with the exception of one virus with an HA gene derived from clade 2.3.2 such that it represents a novel reassortant. Clearly, the ongoing surveillance of LPMs is central to monitoring the emergence of pathogenic influenza viruses.
The rural mother's experience of caring for a child with a chronic health condition: An integrative review
Publisher: Wiley
Date: 06-2018
DOI: 10.1111/JOCN.14360
Abstract: To identify and review the literature on rural mothers' experiences in caring for a child with a chronic health condition. Families living with a child who has a chronic health condition experience many challenges these are often lified for families living in rural areas, where issues such as the distance from services add further challenges the family must manage. Like many children, rural children with chronic health conditions are primarily cared for by their mothers. The additional strain of geography creates its own unique experiences for mothers who need to access the high-quality care that their child requires. Integrative literature review using the Equator PRISMA guidelines. A search of databases Cochrane, CINAHL, Ovid, PubMed, ProQuest Health and Medicine, Informit and Scopus for studies published between 2005-2016 using an integrative review approach. A total of 1,484 studies were identified with an additional six studies found through snowballing. The search resulted in seven studies being meeting the inclusion criteria after using the Critical Appraisal Skills Programme. Data from the seven articles were analysed, and the mothers' experiences were synthesised into five themes: "struggling for resources," "barriers in accessing services," "strain of decision-making," "mother's physical and emotional breakdown" and "the daily management of family activities". These five themes formed the basis of this article. The findings indicate that mothers from rural areas face additional barriers related to their rurality, including transportation difficulties, socioeconomic status and social isolation, and are challenged by limited access to specialty medical services, educators and allied health professionals. The literature review outcome will assist in informing nursing practice through identifying and allocating resources to reduce these barriers rural mother experience will assist in enabling the child to reach their full developmental potential. There is a need for health professionals to understand the challenges and barriers rural mothers face in accessing services. Nurses can assist rural mothers to navigate and access the appropriate services in order to reduce health inequity, increase accessibility to services and reduce rural disadvantage for their child. Nurses and health professionals are in an ideal position to develop future models of care that optimise health outcomes and enable equity and access to services for rural children with chronic conditions similar to those experienced by their urban counterparts.
Depression and diabetes in the remote Torres Strait Islands
Publisher: Wiley
Date: 20-07-2017
DOI: 10.1071/HE15118
A phylogenetic survey of recombination frequency in plant RNA viruses
Publisher: Springer Science and Business Media LLC
Date: 15-11-2005
DOI: 10.1007/S00705-005-0675-X
Abstract: The severe economic consequences of emerging plant viruses highlights the importance of studies of plant virus evolution. One question of particular relevance is the extent to which the genomes of plant viruses are shaped by recombination. To this end we conducted a phylogenetic survey of recombination frequency in a wide range of positive-sense RNA plant viruses, utilizing 975 capsid gene sequences and 157 complete genome sequences. In total, 12 of the 36 RNA virus species analyzed showed evidence for recombination, comprising 17% of the capsid gene sequence alignments and 44% of the genome sequence alignments. Given the conservative nature of our analysis, we propose that recombination is a relatively common process in some plant RNA viruses, most notably the potyviruses.
Sequence data as evidence
Publisher: Springer Science and Business Media LLC
Date: 08-1993
DOI: 10.1038/364766B0
Abstract: To investigate effectiveness of anteromedial thigh perforator flap in repair of soft tissue defects of lower limbs. Between January 2015 and October 2018, 7 patients with soft tissue defects of the lower limbs were repaired with the anteromedial thigh perforator flaps. The patients were males, aged 8-30 years (median, 23 years). There were 5 cases of traffic accident injuries (the time from injury to admission was 1-4 hours, with an average of 1.5 hours), 1 case of scar formation after traffic accident, and 1 case of scar deformity after burn. The defect located in calf in 5 cases, foot in 1 case, and thigh in 1 case. The area of soft tissue defects ranged from 12 cm×4 cm to 21 cm×7 cm and the area of flaps ranged from 14 cm×5 cm to 24 cm×8 cm. The donor sites were sutured directly. The flaps survived completely after operation in 6 cases, and the wounds healed by the first intention the partial necrosis of flap occurred and healed after skin graft repair in 1 case. One incision partially ruptured in the donor site and healed after dressing change the other incisions healed by the first intetion. All patients were followed up 6 months to 2 years with an average of 9 months. Except 1 case complained of edema of the flap, the other patients had good shape, good color, and no swelling. For patients with soft tissue defects of lower limbs that cannot be repaired with anterolateral thigh perforator flap, the anteromedial thigh perforator flap can be used for good results.
Genome-Scale Evolution and Phylodynamics of Equine H3N8 Influenza A Virus
Publisher: American Society for Microbiology
Date: 06-2011
DOI: 10.1128/JVI.02619-10
Abstract: Equine influenza viruses (EIVs) of the H3N8 and H7N7 subtypes are the causative agents of an important disease of horses. While EIV H7N7 apparently is extinct, H3N8 viruses have circulated for more than 50 years. Like human influenza viruses, EIV H3N8 caused a transcontinental pandemic followed by further outbreaks and epidemics, even in populations with high vaccination coverage. Recently, EIV H3N8 jumped the species barrier to infect dogs. Despite its importance as an agent of infectious disease, the mechanisms that underpin the evolutionary and epidemiological dynamics of EIV are poorly understood, particularly at a genomic scale. To determine the evolutionary history and phylodynamics of EIV H3N8, we conducted an extensive analysis of 82 complete viral genomes s led during a 45-year span. We show that both intra- and intersubtype reassortment have played a major role in the evolution of EIV, and we suggest that intrasubtype reassortment resulted in enhanced virulence while heterosubtypic reassortment contributed to the extinction of EIV H7N7. We also show that EIV evolves at a slower rate than other influenza viruses, even though it seems to be subject to similar immune selection pressures. However, a relatively high rate of amino acid replacement is observed in the polymerase acidic (PA) segment, with some evidence for adaptive evolution. Most notably, an analysis of viral population dynamics provided evidence for a major population bottleneck of EIV H3N8 during the 1980s, which we suggest resulted from changes in herd immunity due to an increase in vaccination coverage.
The evolution of viral emergence
Publisher: Proceedings of the National Academy of Sciences
Date: 27-03-2006
Phylogeography of Influenza A(H3N2) Virus in Peru, 2010–2012
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 08-2015
The role of alternative genetic codes in viral evolution and emergence
Publisher: Elsevier BV
Date: 09-2008
DOI: 10.1016/J.JTBI.2008.05.024
Abstract: Although the 'universal' genetic code is widespread among life-forms, a number of erse lineages have evolved unique codon reassignments. The proteomes of these organisms and organelles must, by necessity, use the same codon assignments. Likewise, for an exogenous genetic element, such as an infecting viral genome, to be accurately and completely expressed with the host's translation system, it must employ the same genetic code. This raises a number of intriguing questions regarding the origin and evolution of viruses. In particular, it is extremely unlikely that viruses of hosts utilizing the universal genetic code would emerge, via cross-species transmission, in hosts utilizing alternative codes, and vice versa. Consequently, more parsimonious scenarios for the origins of such viruses include the prolonged co-evolution of viruses with cellular life, or the escape of genetic material from host genomes. Further, we raise the possibility that emerging viruses provide the selection pressure favoring the use of alternative codes in potential hosts, such that the evolution of a variant genetic code acts as a unique and powerful antiviral strategy. As such, in the face of new emerging viruses, hosts with codon reassignments would have a significant selective advantage compared to hosts utilizing the universal code.
Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins
Publisher: Public Library of Science (PLoS)
Date: 17-05-2023
DOI: 10.1371/JOURNAL.PPAT.1011384
Abstract: Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. However, little is known about its pathogenicity in pangolins. Using CT scans we show that SARSr-CoV-2 positive Malayan pangolins are characterized by bilateral ground-glass opacities in lungs in a similar manner to COVID-19 patients. Histological examination and blood gas tests are indicative of dyspnea. SARSr-CoV-2 infected multiple organs in pangolins, with the lungs the major target, and histological expression data revealed that ACE2 and TMPRSS2 were co-expressed with viral RNA. Transcriptome analysis indicated that virus-positive pangolins were likely to have inadequate interferon responses, with relative greater cytokine and chemokine activity in the lung and spleen. Notably, both viral RNA and viral proteins were detected in three pangolin fetuses, providing initial evidence for vertical virus transmission. In sum, our study outlines the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.
Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus
Publisher: Springer Science and Business Media LLC
Date: 14-09-2010
DOI: 10.1007/S00239-010-9385-4
Abstract: Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus-host co ergence over time-scales of many millions of years that is difficult to verify. An important ex le are viruses of the genus Tobamovirus, where the assumption of host-virus co ergence over 100 million years has led to rate estimates in the range of ~1 × 10(-8) nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-st ed sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10(-5) and 1.3 × 10(-3) substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the s led tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming co ergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect.
The Evolution of Viral Emergence
Publisher: Wiley
Date: 07-03-2008
Low frequency of paleoviral infiltration across the avian phylogeny
Publisher: Springer Science and Business Media LLC
Date: 12-2014
Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918
Publisher: Public Library of Science (PLoS)
Date: 29-02-2008
The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012
Publisher: Elsevier BV
Date: 02-2014
Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses
Publisher: Annual Reviews
Date: 31-08-2016
DOI: 10.1146/ANNUREV-GENOM-083115-022628
Abstract: The emergence and reemergence of rapidly evolving RNA viruses—particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses—pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic ersity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as s ling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
Low Intra-Host and Inter-Host Genetic Diversity of <em>Carnivore Protoparvovirus 1 </em>in Domestic Cats During A Feline Panleukopenia Outbreak
Publisher: MDPI AG
Date: 12-05-2022
DOI: 10.20944/PREPRINTS202205.0157.V1
Abstract: Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterized the ersity of these Carnivore protoparvovirus 1 variants in 18 faecal s les collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of & ,000 X coverage per site. All s les comprised FPV alone. Compared to the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were non-synonymous, including 9 in non-structural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit inter-host ersity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intra-host ersity at all polymorphic positions was low with sub-consensus variant frequencies (SVF) of & % except for two positions (2108 and 3208) in two s les with SVF of 1.1 & ndash 1.3%. Intra-host nucleotide ersity was measured across the whole genome (0.7 - 1.5%) and for each gene, and was highest in the NS2 gene of four s les (1.2 & ndash 1.9%). Overall, intra-host viral genetic ersity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.
Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses
Publisher: American Society for Microbiology
Date: 15-01-2017
DOI: 10.1128/JVI.01504-16
Abstract: Since the first description of adenoviruses in bats in 2006, a number of micro- and megabat species in Europe, Africa, and Asia have been shown to carry a wide ersity of adenoviruses. Here, we report on the evolutionary, biological, and structural characterization of a novel bat adenovirus (BtAdV) recovered from a Rafinesque's big-eared bat ( Corynorhinus rafinesquii ) in Kentucky, USA, which is the first adenovirus isolated from North American bats. This virus (BtAdV 250-A) exhibits a close phylogenetic relationship with Canine mastadenovirus A (CAdV A), as previously observed with other BtAdVs. To further investigate the relationships between BtAdVs and CAdVs, we conducted mass spectrometric analysis and single-particle cryo-electron microscopy reconstructions of the BtAdV 250-A capsid and also analyzed the in vitro host ranges of both viruses. Our results demonstrate that BtAdV 250-A represents a new mastadenovirus species that, in contrast to CAdV, has a unique capsid morphology that contains more prominent extensions of protein IX and can replicate efficiently in a phylogenetically erse range of species. These findings, in addition to the recognition that both the genetic ersity of BtAdVs and the number of different bat species from disparate geographic regions infected with BtAdVs appears to be extensive, tentatively suggest that bats may have served as a potential reservoir for the cross-species transfer of adenoviruses to other hosts, as theorized for CAdV. IMPORTANCE Although many adenoviruses are host specific and likely co erged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic ersity of adenoviruses in bats and their close phylogenetic relationship to Canine mastadenovirus A (CAdV A) has raised important questions about how CAdV A, and possibly other mammalian adenoviruses, may have emerged. Although most adenoviruses tend to cause limited disease in their natural hosts, CAdV A is unusual in that it may cause high morbidity and sometimes fatal infections in immunocompetent hosts and is thus an important pathogen of carnivores. Here, we performed a comparative evolutionary and structural study of representative bat and canine adenoviruses to better understand the relationship between these two viral groups.
RAPIDprep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples
Publisher: MDPI AG
Date: 19-04-2023
DOI: 10.3390/V15041006
Abstract: Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of s le collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and lification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory s les to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library lification across different s le types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
Selection-Driven Evolution of Emergent Dengue Virus
Publisher: Oxford University Press (OUP)
Date: 27-06-2003
Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV)
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.VIROL.2014.08.002
Abstract: European brown hare syndrome virus (EBHSV) is the aetiological agent of European brown hare syndrome (EBHS), a disease affecting Lepus europaeus and Lepus timidus first diagnosed in Sweden in 1980. To characterize EBHSV evolution we studied hare s les collected in Sweden between 1982 and 2008. Our molecular clock dating is compatible with EBHSV emergence in the 1970s. Phylogenetic analysis revealed two lineages: Group A persisted until 1989 when it apparently suffered extinction Group B emerged in the mid-1980s and contains the most recent strains. Antigenic differences exist between groups, with loss of reactivity of some MAbs over time, which are associated with amino acid substitutions in recognized epitopes. A role for immune selection is also supported by the presence of positively selected codons in exposed regions of the capsid. Hence, EBHSV evolution is characterized by replacement of Group A by Group B viruses, suggesting that the latter possess a selective advantage.
Unmapped RNA Virus Diversity in Termites and Their Symbionts
Publisher: MDPI AG
Date: 09-10-2020
DOI: 10.3390/V12101145
Abstract: Despite their ecological importance, nothing is known about the ersity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 erse species of termite that differ in both phylogenetic position and colony composition. From these s les, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and ergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic ersity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the s ling procedure had the strongest association with virome composition, with greater RNA virome ersity in libraries prepared from whole termite bodies than those that only s led heads.
Molecular Investigation of Human Immunodeficiency Virus (HIV) Infection in a Patient of an HIV-Infected Surgeon
Publisher: Oxford University Press (OUP)
Date: 06-1993
DOI: 10.1093/INFDIS/167.6.1411
Abstract: Recall of patients who had been treated by a human immunodeficiency virus (HIV)-infected surgeon uncovered 1 previously unknown HIV-seropositive person. Nucleotide sequencing of the gag gene and maximum likelihood phylogenetic analysis were used to investigate the relationships among sequences from the surgeon, the patient, and an anonymous blood donor from whom the patient had received blood products. The likelihoods of all possible pathways of transmission linking these persons were estimated. On these data, transmission from the surgeon to the patient was significantly less likely than from the blood donor to the patient. It is concluded that none of the recalled patients were infected by the surgeon.
RNA viromes from terrestrial sites across China expand environmental viral diversity
Publisher: Springer Science and Business Media LLC
Date: 28-07-2022
DOI: 10.1038/S41564-022-01180-2
Abstract: Environmental RNA viruses are ubiquitous and erse, and probably have important ecological and biogeochemical impacts. Understanding the global ersity of RNA viruses is limited by s ling biases, dependence on cell culture and PCR for virus discovery, and a focus on viruses pathogenic to humans or economically important animals and plants. To address this knowledge gap, we generated metatranscriptomic sequence data from 32 erse environments in 16 provinces and regions of China. We identified 6,624 putatively novel virus operational taxonomic units from soil, sediment and faecal s les, greatly expanding known ersity of the RNA virosphere. These newly identified viruses included positive-sense, negative-sense and double-strand RNA viruses from at least 62 families. Sediments and animal faeces were rich sources of viruses. Virome compositions were affected by local environmental factors, including organic content and eukaryote species abundance. Notably, environmental factors had a greater impact on the abundance and ersity of plant, fungal and bacterial viruses than of animal viromes. Our data confirm that RNA viruses are an integral part of both terrestrial and aquatic ecosystems.
Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility
Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2022
DOI: 10.1101/2022.06.02.494607
Abstract: To characterize the ongoing evolution of myxoma virus in Australian rabbits we used experimental infections of laboratory rabbits to determine the virulence and disease phenotypes of recent virus isolates. The viruses, collected between 2012-2015, fell into three lineages, one of which, lineage c, experienced a punctuated increase in evolutionary rate. All viruses were capable of causing acute death with aspects of neutropenic septicaemia, characterized by minimal signs of myxomatosis, the occurrence of pulmonary oedema and bacteria invasions throughout internal organs, but with no inflammatory response. For the viruses of highest virulence all rabbits usually died at this point. In more attenuated viruses some rabbits died acutely while others developed an amyxomatous phenotype. Rabbits that survived for longer periods developed greatly swollen cutaneous tissues with very high virus titres. This was particularly true of lineage c viruses. Unexpectedly, we identified a line of laboratory rabbits with some innate resistance to myxomatosis and used these in direct comparisons with the fully susceptible rabbit line. Importantly, the same disease phenotype occurred in both susceptible and resistant rabbits, although virulence was shifted towards more attenuated grades in resistant animals. We propose that selection against inflammation at cutaneous sites prolongs virus replication and enhances transmission, leading to the amyxomatous phenotype. In some virus backgrounds this creates an immunosuppressive state that predisposes to high virulence and acute death. The alterations in disease pathogenesis, particularly the overwhelming bacterial invasions that characterize the modern viruses, suggest that their virulence grades are not directly comparable with earlier studies. The evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook ex le of the co-evolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype. By conducting detailed experimental infections of recent isolates of MYXV in different lines of laboratory rabbits we examined the ongoing evolution of MYXV disease phenotypes. Our results reveal a wide range of phenotypes, including an amyxomatous type as well as the impact of invasive bacteria, that in part depended on the level of rabbit host resistance. These results provide a unique insight into the complex virus and host factors that combine to shape disease phenotype and viral evolution.
Spread of Canine Influenza A(H3N2) Virus, United States
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 12-2017
Endogenous Lentiviruses in the Ferret Genome
Publisher: American Society for Microbiology
Date: 15-03-2012
DOI: 10.1128/JVI.06652-11
Abstract: By screening 74 chordate genomes for endogenous lentiviruses using Pol sequences of exogenous lentiviruses as a reference, we identified a novel endogenous lentivirus in the genome of the ferret ( Mustela putorius furo ). Phylogenetic analysis suggested that the ferret endogenous lentivirus, denoted ELVmpf, erged early in the evolution of the mammalian lentiviruses, although with a lack of resolution at key nodes. These data support the notion that lentiviruses have evolved on timescales of millions of years.
Compassion fatigue in critical care nurses and its impact on nurse-sensitive indicators in Saudi Arabian hospitals
Publisher: Elsevier BV
Date: 11-2020
Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally
Publisher: MDPI AG
Date: 30-01-2019
DOI: 10.3390/V11020125
Abstract: The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) s led worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of rodent CoVs in more detail, particularly the relative frequencies of virus-host co- ergence and cross-species transmission, we recovered longer fragments of CoV genomes from previously discovered European rodent alpha-CoVs using a combination of PCR and high-throughput sequencing. Accordingly, the full genome sequence was retrieved from the UK rat coronavirus, along with partial genome sequences from the UK field vole and Poland-resident bank vole CoVs, and a short conserved ORF1b fragment from the French rabbit CoV. Genome and phylogenetic analysis showed that despite their erse geographic origins, all rodent alpha-CoVs formed a single monophyletic group and shared similar features, such as the same gene constellations, a recombinant beta-CoV spike gene, and similar core transcriptional regulatory sequences (TRS). These data suggest that all rodent alpha CoVs s led so far originate from a single common ancestor, and that there has likely been a long-term association between alpha CoVs and rodents. Despite this likely antiquity, the phylogenetic pattern of the alpha-CoVs was also suggestive of relatively frequent host-jumping among the different rodent species.
Francisella tularensis subsp holarctica in Ringtail Possums, Australia
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 07-2017
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
Publisher: Oxford University Press (OUP)
Date: 02-04-2010
Koolpinyah and Yata viruses: Two newly recognised ephemeroviruses from tropical regions of Australia and Africa
Publisher: Elsevier BV
Date: 12-2014
The phylogenomics of evolving virus virulence
Publisher: Springer Science and Business Media LLC
Date: 10-10-2018
Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): implications for the origin and emergence of Middle East respiratory syndrome coronavirus
Publisher: Springer Science and Business Media LLC
Date: 10-10-2013
Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia
Publisher: Public Library of Science (PLoS)
Date: 02-03-2017
Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2
Publisher: Oxford University Press (OUP)
Date: 13-07-2020
Abstract: Due to the scope and impact of the COVID-19 pandemic there exists a strong desire to understand where the SARS-CoV-2 virus came from and how it jumped species boundaries to humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness and ergence times of viruses and identifying past selective pressures. However, we must uphold rigorous standards of inference and interpretation on this topic because of the ramifications of being wrong. Here, we dispute the conclusions of Xia (2020. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense. Mol Biol Evol. doi:10.1093/molbev/masa095) that dogs are a likely intermediate host of a SARS-CoV-2 ancestor. We highlight major flaws in Xia’s inference process and his analysis of CpG deficiencies, and conclude that there is no direct evidence for the role of dogs as intermediate hosts. Bats and pangolins currently have the greatest support as ancestral hosts of SARS-CoV-2, with the strong caveat that s ling of wildlife species for coronaviruses has been limited.
The evolution of large DNA viruses: combining genomic information of viruses and their hosts
Publisher: Elsevier BV
Date: 10-2004
What is the time-scale of hantavirus evolution?
Publisher: Elsevier BV
Date: 07-2014
CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Publisher: Cold Spring Harbor Laboratory
Date: 17-05-2019
DOI: 10.1101/641332
Abstract: High-throughput sequencing of DNA and RNA from environmental and host-associated s les (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a s le. Taxonomic identification software usually align in idual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Using simulated fungal and bacterial metagenomes, we demonstrate that CCMetagen substantially outperforms other commonly used metagenome classifiers, attaining a 3 – 1580 fold increase in precision and a 2 – 922 fold increase in F1 scores for species-level classifications when compared to Kraken2, Centrifuge and KrakenUniq. CCMetagen is sufficiently fast and memory efficient to use the entire NCBI nucleotide collection (nt) as reference, enabling the assessment of species with incomplete genome sequence data from all biological kingdoms. Our pipeline efficiently produced a comprehensive overview of the microbiome of two biological data sets, including both eukaryotes and prokaryotes. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
Family level phylogenies reveal modes of macroevolution in RNA viruses
Publisher: Proceedings of the National Academy of Sciences
Date: 20-12-2010
Abstract: Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral ersification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different “species” are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage ersification in five representative families of RNA viruses. We ask whether the process of lineage ersification primarily occurs when viruses infect new host species, either through cross-species transmission or co ergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage ersification within in idual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral bio ersity, because we also find that better-s led human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage ersification within in idual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.
Frequent Cross-Species Transmission of Parvoviruses among Diverse Carnivore Hosts
Publisher: American Society for Microbiology
Date: 15-02-2013
DOI: 10.1128/JVI.02428-12
Abstract: Although parvoviruses are commonly described in domestic carnivores, little is known about their bio ersity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.
Evolutionary genetics and the emergence of SARS Coronavirus
Publisher: Oxford University Press
Date: 10-03-2005
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay
Publisher: Cold Spring Harbor Laboratory
Date: 17-04-2023
DOI: 10.1101/2023.04.16.23288635
Abstract: The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay
The Expanding Virosphere
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.CHOM.2016.08.007
Abstract: Multicomponent viruses are common in plants and fungi. In this issue of Cell Host & Microbe, Ladner et al. (2016) describe a multicomponent virus from animals. This supports an emerging view that invertebrates harbor a remarkable viral ersity and highlights how little of the virosphere has been explored.
The extent of codon usage bias in human RNA viruses and its evolutionary origin
Publisher: Elsevier BV
Date: 03-2003
DOI: 10.1016/S0168-1702(02)00309-X
Abstract: Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically erse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
Publisher: Springer Science and Business Media LLC
Date: 26-03-2020
Avian Influenza Virus Exhibits Rapid Evolutionary Dynamics
Publisher: Oxford University Press (OUP)
Date: 31-08-2006
Abstract: Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a erse array of avian influenza viruses (AIV) and allowing for rate variation among lineages. The rates observed were extremely high, at >10(-3) substitutions per site, per year, with little difference among wild and domestic host species or viral subtypes and were similar to those seen in mammalian influenza A viruses. Influenza A virus therefore exhibits rapid evolutionary dynamics across its host range, consistent with a high background mutation rate and rapid replication. Using the same approach, we also estimated that the common ancestors of the hemagglutinin and neuraminidase sequences of AIV arose within the last 3,000 years, with most intrasubtype ersity emerging within the last 100 years and suggestive of a continual selective turnover.
CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Publisher: Springer Science and Business Media LLC
Date: 28-04-2020
DOI: 10.1186/S13059-020-02014-2
Abstract: There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly, and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
Ancient lentiviruses leave their mark
Publisher: Proceedings of the National Academy of Sciences
Date: 10-04-2007
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
Publisher: Springer Science and Business Media LLC
Date: 11-12-2020
DOI: 10.1038/S41467-020-20235-8
Abstract: New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with s les collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic ersity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For ex le, the effective reproductive number, R e of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.
Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic
Publisher: American Society for Microbiology
Date: 06-2010
DOI: 10.1128/JVI.00018-10
Abstract: The initial wave of swine-origin influenza A virus (pandemic H1N1/09) in the United States during the spring and summer of 2009 also resulted in an increased vigilance and s ling of seasonal influenza viruses (H1N1 and H3N2), even though they are normally characterized by very low incidence outside of the winter months. To explore the nature of virus evolution during this influenza “off-season,” we conducted a phylogenetic analysis of H1N1 and H3N2 sequences s led during April to June 2009 in New York State. Our analysis revealed that multiple lineages of both viruses were introduced and cocirculated during this time, as is typical of influenza virus during the winter. Strikingly, however, we also found strong evidence for the presence of a large transmission chain of H3N2 viruses centered on the south-east of New York State and which continued until at least 1 June 2009. These results suggest that the unseasonal transmission of influenza A viruses may be more widespread than is usually supposed.
Evolutionary history and dynamics of dog rabies virus in western and central Africa
Publisher: Microbiology Society
Date: 04-2009
Abstract: The burden of rabies in Africa is estimated at 24 000 human deaths year −1 , almost all of which result from infection with dog rabies viruses (RABV). To investigate the evolutionary dynamics of RABV in western and central Africa, 92 isolates s led from 27 African countries over 29 years were collected and sequenced. This revealed that RABV currently circulating in dogs in this region fell into a single lineage designated ‘Africa 2’. A detailed analysis of the phylogeographical structure of this Africa 2 lineage revealed strong population sub ision at the country level, with only limited movement of virus among localities, including a possible east-to-west spread across Africa. In addition, Bayesian coalescent analysis suggested that the Africa 2 lineage was introduced into this region of Africa only recently (probably years ago), in accordance with the timescale of expanding European colonial influence and urbanization, and then spread relatively slowly, perhaps occupying the entire region in a 100 year period.
Health vulnerabilities of readymade garment (RMG) workers: a systematic review
Publisher: Springer Science and Business Media LLC
Date: 15-01-2019
Geographic and species association of hepatitis B virus genotypes in non-human primates
Publisher: Elsevier BV
Date: 09-2003
DOI: 10.1016/S0042-6822(03)00430-6
Abstract: Infection with hepatitis B virus (HBV) has been detected in human populations throughout the world, as well as in a number of ape species (Pan troglodytes, Gorilla gorilla, gibbons [Nomascus and Hylobates species] and Pongo pygmaeus). To investigate the distribution of naturally occurring HBV infection in these species and other African Old World monkey species (Cercopithecidae), we screened 137 plasma s les from mainly wild caught animals by polymerase chain reaction (PCR) using several of highly conserved primers from the HB surface (HBs) gene, and for HBs antigen (HBsAg) by ELISA. None of the 93 Cercopithecidae screened (6 species) showed PCR or serology evidence for HBV infection in contrast 2 from 8 chimpanzees and 5 from 22 gibbons were PCR-positive with each set of primers. Complete genome sequences from each of the positive apes were obtained and compared with all previously published complete and surface gene sequences. This extended phylogenetic analysis indicated that HBV variants from orangutans were interspersed by with HBV variants from southerly distributed gibbon species (H. agilis and H. moloch) occupying overlapping or adjacent habitat ranges with orangutans in contrast, HBV variants from gibbon species in mainland Asia were phylogenetically distinct. A geographical rather than (sub)species association of HBV would account for the distribution of HBV variants in different subspecies of chimpanzees in Africa, and explain the inlier position of the previously described lowland gorilla sequence in the chimpanzee clade. These new findings have a number of implication for understanding the origins and epidemiology of HBV infection in non-human primates.
An Allometric Relationship between the Genome Length and Virion Volume of Viruses
Publisher: American Society for Microbiology
Date: 06-2014
DOI: 10.1128/JVI.00362-14
Abstract: Virions vary in size by at least 4 orders of magnitude, yet the evolutionary forces responsible for this enormous ersity are unknown. We document a significant allometric relationship, with an exponent of approximately 1.5, between the genome length and virion volume of viruses and find that this relationship is not due to geometric constraints. Notably, this allometric relationship holds regardless of genomic nucleic acid, genome structure, or type of virion architecture and therefore represents a powerful scaling law. In contrast, no such relationship is observed at the scale of in idual genes. Similarly, after adjusting for genome length, no association is observed between virion volume and the number of proteins, ruling out protein number as the explanation for the relationship between genome and virion sizes. Such a fundamental allometric relationship not only sheds light on the constraints to virus evolution, in that increases in virion size but not necessarily structure are associated with concomitant increases in genome size, but also implies that virion sizes in nature can be broadly predicted from genome sequence data alone. IMPORTANCE Viruses vary dramatically in both genome and virion sizes, but the factors responsible for this ersity are uncertain. Through a comparative and quantitative investigation of these two fundamental biological parameters across erse viral taxa, we show that genome length and virion volume conform to a simple allometric scaling law. Notably, this allometric relationship holds regardless of the type of virus, including those with both RNA and DNA genomes, and encompasses viruses that exhibit more than 3 logs of genome size variation. Accordingly, this study helps to reveal the basic rules of virus design.
Expanding the RNA Virosphere by Unbiased Metagenomics
Publisher: Annual Reviews
Date: 29-09-2019
DOI: 10.1146/ANNUREV-VIROLOGY-092818-015851
Abstract: Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus ersity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable ersity of viruses s led from erse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of ersity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.
Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites
Publisher: American Society for Microbiology
Date: 18-05-2020
DOI: 10.1128/JVI.02119-19
Abstract: Ectoparasites play an important role in the transmission of many vertebrate-infecting viruses, including Zika and dengue viruses. Although it is becoming increasingly clear that invertebrate species harbor substantial virus ersity, it is unclear how many of the viruses carried by invertebrates have the potential to infect vertebrate species. We used the European rabbit ( Oryctolagus cuniculus ) as a model species to compare virome compositions in a vertebrate host and known associated ectoparasite mechanical vectors, in this case, fleas and blowflies. In particular, we aimed to infer the extent of viral transfer between these distinct types of host. Our analysis revealed that despite extensive viral ersity in both rabbits and associated ectoparasites, and the close interaction of these vertebrate and invertebrate species, biological viral transmission from ectoparasites to vertebrate species is rare. We did, however, find evidence to support the idea of a role of blowflies in transmitting viruses without active replication in the insect.
Zucchini yellow mosaic virus (ZYMV, Potyvirus): Vertical transmission, seed infection and cryptic infections
Publisher: Elsevier BV
Date: 09-2013
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021
Publisher: MDPI AG
Date: 10-11-2022
DOI: 10.20944/PREPRINTS202211.0195.V1
Abstract: Epizootic haemorrhagic disease (EHD) is a Culicoides-borne viral disease caused by epizootic haemorrhagic disease virus (EHDV) and associated with clinical manifestations in cervids and bovids. In late September 2021, EHDV was reported in cattle farms in central/western Tunisia. It rapidly spread throughout the country with more than 200 confirmed outbreaks. A combination of classical and molecular techniques was applied to characterize the causative virus as a member of EHDV-8 serotype. This is the first evidence of EHDV- 8 circulation since 1982 when the prototype EHDV-8 strain was isolated in Australia. This work highlights the urgent need for vaccines for a range of EHDV serotypes.
Cross-species transmission of honey bee viruses in associated arthropods
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.VIRUSRES.2013.06.013
Abstract: There are a number of RNA virus pathogens that represent a serious threat to the health of managed honey bees (Apis mellifera). That some of these viruses are also found in the broader pollinator community suggests the wider environmental spread of these viruses, with the potential for a broader impact on ecosystems. Studies on the ecology and evolution of these viruses in the arthropod community as a whole may therefore provide important insights into these potential impacts. We examined managed A. mellifera colonies, nearby non-Apis hymenopteran pollinators, and other associated arthropods for the presence of five commonly occurring picorna-like RNA viruses of honey bees - black queen cell virus, deformed wing virus, Israeli acute paralysis virus, Kashmir bee virus and sacbrood virus. Notably, we observed their presence in several arthropod species. Additionally, detection of negative-strand RNA using strand-specific RT-PCR assays for deformed wing virus and Israeli acute paralysis virus suggests active replication of deformed wing virus in at least six non-Apis species and active replication of Israeli acute paralysis virus in one non-Apis species. Phylogenetic analysis of deformed wing virus also revealed that this virus is freely disseminating across the species s led in this study. In sum, our study indicates that these viruses are not specific to the pollinator community and that other arthropod species have the potential to be involved in disease transmission in pollinator populations.
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Publisher: Springer Science and Business Media LLC
Date: 24-05-2017
DOI: 10.1038/NATURE22401
The evolutionary history of vertebrate RNA viruses
Publisher: Springer Science and Business Media LLC
Date: 04-04-2018
DOI: 10.1038/S41586-018-0012-7
Abstract: Our understanding of the ersity and evolution of vertebrate RNA viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, hibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA viruses. In summary, this study reveals erse virus-host associations across the entire evolutionary history of the vertebrates.
The diversity, evolution and origins of vertebrate RNA viruses
Publisher: Elsevier BV
Date: 08-2018
Phylodynamics of H5N1 avian influenza virus in Indonesia
Publisher: Wiley
Date: 11-05-2012
The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain
Publisher: Microbiology Society
Date: 04-2012
Abstract: GII.4 noroviruses are a major cause of acute gastroenteritis in humans. A new variant of GII.4, the 2008 variant, has recently increased its prevalence on a global scale. A previous study of this variant in Japan suggested that it might be of recombinant origin, with a breakpoint at the ORF1–ORF2 junction. Here, examination of the evolutionary origin of the 2008 variant based on a larger s le of worldwide GII.4 norovirus sequences revealed a more complex pattern of recombination between the 2006a- and 2006b-like variants of genotype GII.4, involving the P2 antigenic domain. Double (termed ‘2008i’) and triple (termed ‘2008ii’) recombinant forms of 2008 variants were identified. This study highlights the possible importance of intra-genotypic recombination over antigenic regions in driving norovirus evolution, and is suggestive of a process analogous to the antigenic shift of influenza A virus by reassortment.
Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion
Publisher: MDPI AG
Date: 04-08-2019
DOI: 10.3390/V11080713
Abstract: Papillomaviruses (PVs) have been identified in a wide range of animal species and are associated with a variety of disease syndromes including classical papillomatosis, aural plaques, and genital papillomas. In horses, 13 PVs have been described to date, falling into six genera. Using total RNA sequencing (meta-transcriptomics) we identified a novel equine papillomavirus in semen taken from a thoroughbred stallion suffering a genital lesion, which was confirmed by nested RT-PCR. We designate this novel virus Equus caballus papillomavirus 9 (EcPV9). The complete 7656 bp genome of EcPV9 exhibited similar characteristics to those of other horse papillomaviruses. Phylogenetic analysis based on concatenated E1-E2-L2-L1 amino acid sequences revealed that EcPV9 clustered with EcPV2, EcPV4, and EcPV5, although was distinct enough to represent a new viral species within the genus Dyoiotapapillomavirus (69.35%, 59.25%, and 58.00% nucleotide similarity to EcPV2, EcPV4, and EcPV5, respectively). In sum, we demonstrate the presence of a novel equine papillomavirus for which more detailed studies of disease association are merited.
Global patient experience of paramedic practice
Publisher: Mark Allen Group
Date: 02-03-2019
Abstract: Paramedics occupy an ever-increasing role within healthcare and the development of this role should be informed by the voice of patients. This systematic literature review seeks to explore patient experience during a paramedic intervention. Using a ‘state of the art’ review style, a systematic search was conducted of the literature published between 2006 and 2018. Following PRISMA guidelines, a total of seven articles meeting the inclusion criteria were identified. A definition of experience which incorporates several dimensions was used to frame the search. Three themes were identified, with the available literature focusing mainly on satisfaction. Satisfaction is improved through certainty and clarity of the progression through treatment and is high among patients of paramedics. Our understanding of patient experience in paramedic interventions is largely limited to an understanding of satisfaction. While this may provide some useful insights, other facets such as the lived experience and physiologic aspects are underrepresented in the current evidence base.
A novel gyrovirus associated with a fatal respiratory disease in yellow-eyed penguin (Megadyptes antipodes) chicks
Publisher: Cold Spring Harbor Laboratory
Date: 16-09-2022
DOI: 10.1101/2022.09.15.508173
Abstract: Yellow-eyed penguins ( Megadyptes antipodes ), or hoiho in te reo Māori, are predicted to become extinct on mainland Aotearoa New Zealand in the next few decades, with infectious disease a significant contributor to their decline. A recent disease phenomenon termed respiratory distress syndrome (RDS) causing lung pathology has been identified in very young chicks. To date, no causative pathogens for RDS have been identified. In 2020 and 2021, the number of chick deaths from suspected RDS increased four- and five-fold, respectively, with a mortality rate of %. Here, we aimed to identify possible pathogens responsible for RDS disease impacting yelloweyed penguins. Total RNA was extracted from tissue s les collected during post-mortem of 43 chicks and subject to metatranscriptomic sequencing. From these data we identified a novel and highly abundant gyrovirus in 80% of tissue s les. This virus exhibited only 41% amino acid identity within VP1 to its closest relative, Gyrovirus 8 , discovered in a diseased seabird. No other exogenous viral transcripts, nor pathogenic bacterial, protozoal and fungal organisms, were identified in these tissues. Due to the high relative abundance of viral reads, it is likely that this novel gyrovirus is associated with RDS in yellow-eyed penguin chicks. New Zealand’s population of yellow-eyed penguins, also called hoiho , are predicted to become extinct in the next 20-30 years, with disease a major factor contributing to their decline. A new disease, causing fluid and bleeding into the lungs, was initially identified in 2019 in very young chicks. It was characterised as causing respiratory distress with a mortality of % usually within the first week of life. To date, no causative pathogens of the disease have been identified. We aimed to identify possible pathogens responsible for respiratory disease in these penguin chicks. A metatranscriptomic survey of dead chicks identified a novel and highly abundant gyrovirus present in diseased tissue, with closely related viruses causing disease in other avian hosts. It is, therefore, highly likely that this novel gyrovirus is associated with respiratory disease in these chicks. This finding offers the potential to increase the success of disease management in the critically endangered yellow-eyed penguin and possibly other at-risk penguin species. The potential to lessen mortality and slow the decline of the species is essential in protecting the bio ersity of New Zealand’s fauna and flora.
Molecular epidemiology of dengue virus type 3 in Venezuela
Publisher: Microbiology Society
Date: 06-2003
Abstract: During the past 40 years, dengue haemorrhagic fever and dengue shock syndrome (DHF/DSS) have emerged in humans, with approximately 3 million cases reported and over 58 000 deaths. Dengue virus serotypes 1, 2 and 4 (DENV-1, -2 and -4) have been co-circulating in Venezuela for at least the past 10 years, causing minor or major outbreaks of dengue fever (DF) and DHF/DSS. The first recorded outbreak due to DENV-3 in Venezuela dates to 1964 and the virus then seems to have disappeared. However, DENV-3 re-appeared recently (in July, 2000) in Venezuela after 32 years of absence and produced a prolonged major outbreak, which, by the end of 2001, involved 83 180 cases of dengue, mostly DF (92 %). Previous phylogenetic studies revealed that the DENV-3 circulating during the 1960s Latin American outbreak was a genotype V virus. To gain a better understanding of the nature of the current epidemic, the complete sequence was determined of the envelope (E) gene of 15 Venezuelan DENV-3 viruses isolated during 2000 and 2001 from patients presenting with different disease severity. Sequence data were used in phylogenetic comparisons with global s les of DENV-3. Analysis revealed that the strain circulating in Venezuela is closely related to isolates that were previously present in Panama and Nicaragua in 1994 and since then have spread through Central American countries and Mexico. This study also confirms previous reports showing that the DENV-3 strain currently circulating in the Americas is related to the strain that caused DHF epidemics in Sri Lanka and India in 1989-1991 (genotype III). Finally, no evidence of the re-emergence of the strain that circulated in Venezuela in the late 1960s and 1970s (genotype V) was found.
Extending our understanding of mentoring: The potential of peer mentoring for, and by, at-risk young people
Publisher: Wiley
Date: 14-03-2017
DOI: 10.1111/INM.12326
Emergence of a New Lineage of Dengue Virus Type 2 Identified in Travelers Entering Western Australia from Indonesia, 2010-2012
Publisher: Public Library of Science (PLoS)
Date: 30-01-2015
A Revised Evolutionary History of Hepatitis B Virus (HBV)
Publisher: Springer Science and Business Media LLC
Date: 06-2002
DOI: 10.1007/S00239-001-0084-Z
Abstract: Previous studies of the evolutionary history of hepatitis B virus (HBV) have been compromised by intergenotype recombination and complex patterns of nucleotide substitution, perhaps caused by differential selection pressures. We examined the phylogenetic distribution of recombination events among human HBV genotypes and found that genotypes A plus D, and genotypes B plus C, had distinct patterns of recombination suggesting differing epidemiological relationships among them. By analyzing the nonoverlapping regions of the viral genome we found strong bootstrap support for some intergenotypic groupings, with evidence of a ision between human genotypes A-E from the viruses s led from apes and human genotype F. However, the earliest events in the ergence of HBV remain uncertain. These uncertainties could not be explained by differential selection pressures, as the ratio of nonsynonymous-to-synonymous substitutions ( d(N)/ d(S)) did not vary extensively among lineages and there is no strong evidence for positive selection across the whole tree. Finally, we provide a new estimate of the mean substitution rate in HBV, 4.2 x 10(-5), which suggests that ergence of HBV in humans and apes has occurred only in the last 6000 years.
Gene Duplication Is Infrequent in the Recent Evolutionary History of RNA Viruses
Publisher: Oxford University Press (OUP)
Date: 13-03-2013
Abstract: Gene duplication generates genetic novelty and redundancy and is a major mechanism of evolutionary change in bacteria and eukaryotes. To date, however, gene duplication has been reported only rarely in RNA viruses. Using a conservative BLAST approach we systematically screened for the presence of duplicated (i.e., paralogous) proteins in all RNA viruses for which full genome sequences are publicly available. Strikingly, we found only nine significantly supported cases of gene duplication, two of which are newly described here--in the 25 and 26 kDa proteins of Beet necrotic yellow vein virus (genus Benyvirus) and in the U1 and U2 proteins of Wongabel virus (family Rhabdoviridae). Hence, gene duplication has occurred at a far lower frequency in the recent evolutionary history of RNA viruses than in other organisms. Although the rapidity of RNA virus evolution means that older gene duplication events will be difficult to detect through sequence-based analyses alone, it is likely that specific features of RNA virus biology, and particularly intrinsic constraints on genome size, reduce the likelihood of the fixation and maintenance of duplicated genes.
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes
Publisher: Springer Science and Business Media LLC
Date: 08-04-2019
Intra-host growth kinetics of dengue virus in the mosquito Aedes aegypti
Publisher: Public Library of Science (PLoS)
Date: 02-12-2019
Origins, evolution, and vector⧸host coadaptations within the Genus Flavivirus
Publisher: Elsevier
Date: 2003
DOI: 10.1016/S0065-3527(03)59008-X
Abstract: Although viruses in the genus Flavivirus share complex antigenic interrelationships, they can be ided into four phylogenetic/ecological groups: two mosquito-borne groups, a tick-borne group, and nonvectored viruses. These isions largely reflect the selective constraints imposed on the viruses by the vertebrate hosts, the invertebrate vectors, and the associated ecologies. Phylogenetic trees based on the flavivirus genetic sequence show characteristic branching patterns that reflect these groupings. This review describes the evolution and possible origins of in idual flaviviruses, correlating ecological and epidemiological characteristics with their phylogenies and geographic dispersal. It will also become apparent that many of the phylogenetic lineages that define species erged relatively recently, and the subsequent dispersal and epidemiology of these viruses have therefore been significantly influenced by increasing human population densities and activities such as recreation, urbanization, land reclamation, transportation, and deforestation. This review also considers some of the likely implications of persistent/chronic infections in relation to virus dispersal and recombination between related flaviviruses on phylogenetic analysis and vaccine development strategies.
Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease
Publisher: Public Library of Science (PLoS)
Date: 30-12-2019
Primer Master: a new program for the design and analysis of PCR primers
Publisher: Oxford University Press (OUP)
Date: 1996
Assessing the epidemiological effect of wolbachia for dengue control
Publisher: Elsevier BV
Date: 07-2015
Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.TTBDIS.2017.03.006
Abstract: Rickettsiales bacteria are important agents of (re)emerging infectious diseases, with ticks playing a key role in their evolution and transmission. We collected 1079 hard ticks belonging to five species (Ixodes sinensis, Rhipicephalus microplus, Haemaphysalis flava, Haemaphysalis hystricis and Haemaphysalis longicornis) from cattle and goats in Wuhan city, Hubei province, China. The dominant tick species was H. longicornis (578, 53.57%), followed by R. microplus (354, 32.81%), H. hystricis (62, 5.75%), H. flava (57, 5.28%), and I. sinensis (28, 2.59%). Rickettsiales bacteria were identified in these ticks by lifying the Rickettsiales 16S rRNA (rrs), citrate synthase (gltA), and heat shock protein (groEL) genes. The rrs gene of Rickettsiales was positive in 32 (2.97%) ticks, including 2 cases of co-infection, with 4 (0.69%) in H. longicornis, 15 (4.24%) in R. microplus, 7 (12.28%) in H. flava, 1 (1.61%) in H. hystricis, and 5 (17.86%) in I. sinensis ticks. Phylogenetic analysis revealed the presence of six recognized and seven Candidatus species of Rickettsiaceae, Anaplasmataceae and Candidatus Midichloriaceae. Notably, one lineage within both Ehrlichia and Candidatus Midichloriaceae was distinct from any known Rickettsiales, suggesting the presence of potentially novel species of Rickettsiales bacteria. In sum, these data reveal an extensive ersity of Rickettsiales in ticks from Wuhan, highlighting the need to understand Rickettsiales infection in local animals and humans.
Dengue Virus in Sub-tropical Northern and Central Viet Nam: Population Immunity and Climate Shape Patterns of Viral Invasion and Maintenance
Publisher: Public Library of Science (PLoS)
Date: 05-12-2013
Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity
Publisher: Microbiology Society
Date: 12-1996
DOI: 10.1099/0022-1317-77-12-3013
Abstract: Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity values or evolutionary distances corresponding to isions of HCV into types, subtypes and isolates. Using these criteria, novel variants of HCV from Vietnam, Thailand and Indonesia have been classified as types 7, 8, 9, 10 and 11, many of which can be further sub ided into between two to four subtypes. In this study, this distance-based method of virus classification was compared with phylogenetic analysis and statistical measures to establish the confidence of the groupings. Using bootstrap res ling of phylogenetic trees in several subgenomic regions (core, E1, NS5) and with complete genomic sequences, we found that one set of novel HCV variants ('types 7, 8, 9 and 11') consistently grouped together into a single clade that also contained type 6a, while 'type 10a' grouped with type 3. In contrast, no robust higher-order groupings were observed between any of the other five previously described HCV genotypes (types 1-5). In each subgenomic region, the distribution of pairwise distances between members of the type 6 clade were consistently bi-modal and therefore provided no justification for classification of these variants into the three proposed categories (type, subtype, isolate). Based on these results, we propose that a more useful classification would regard all these variants as subtypes of type 6 or type 3, even though the level of sequence ersity within the clade was greater than observed for other genotypes. Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus.
Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
Publisher: Public Library of Science (PLoS)
Date: 26-07-2005
Evolution of Novel Reassortant A/H3N2 Influenza Viruses in North American Swine and Humans, 2009–2011
Publisher: American Society for Microbiology
Date: 15-08-2012
DOI: 10.1128/JVI.00259-12
Abstract: Novel H3N2 influenza viruses (H3N2v) containing seven genome segments from swine lineage triple-reassortant H3N2 viruses and a 2009 pandemic H1N1 (H1N1pdm09) matrix protein segment (pM) were isolated from 12 humans in the United States between August and December 2011. To understand the evolution of these novel H3N2 viruses in swine and humans, we undertook a phylogenetic analysis of 674 M sequences and 388 HA and NA sequences from influenza viruses isolated from North American swine during 2009–2011, as well as HA, NA, and M sequences from eight H3N2v viruses isolated from humans. We identified 34 swine influenza viruses (termed rH3N2p) with the same combination of H3, N2, and pM segments as the H3N2v viruses isolated from humans. Notably, these rH3N2p viruses were generated in swine via reassortment events between H3N2 viruses and the pM segment approximately 4 to 10 times since 2009. The pM segment has also reassorted with multiple distinct lineages of H1 virus, especially H1δ viruses. Importantly, the N2 segment of all H3N2v viruses isolated from humans is derived from a genetically distinct N2 lineage that has circulated in swine since being acquired by reassortment with seasonal human H3N2 viruses in 2001–2002, rather than from the N2 that is associated with the 1998 H3N2 swine lineage. The identification of this N2 variant may have implications for influenza vaccine design and the potential pandemic threat of H3N2v to human age groups with differing levels of prior exposure and immunity.
Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy
Publisher: Elsevier BV
Date: 08-2004
Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses
Publisher: Cold Spring Harbor Laboratory
Date: 06-07-2022
DOI: 10.1101/2022.07.06.498921
Abstract: Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae , with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting ( Coronaviridae, Caliciviridae, Retroviridae ) and one possible mammalian-infecting ( Birnaviridae ) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus ) and a novel bat sapovirus ( Caliciviridae ), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two s ling locations 1,375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal s les for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.
Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru
Publisher: Microbiology Society
Date: 04-2014
Abstract: Arboretum virus (ABTV) and Puerto Almendras virus (PTAMV) are two mosquito-associated rhabdoviruses isolated from pools of Psorophora albigenu and Ochlerotattus fulvus mosquitoes, respectively, collected in the Department of Loreto, Peru, in 2009. Initial tests suggested that both viruses were novel rhabdoviruses and this was confirmed by complete genome sequencing. Analysis of their 11 482 nt (ABTV) and 11 876 (PTAMV) genomes indicates that they encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with an additional gene (U1) encoding a small hydrophobic protein. Evolutionary analysis of the L protein indicates that ABTV and PTAMV are novel and phylogenetically distinct rhabdoviruses that cannot be classified as members of any of the eight currently recognized genera within the family Rhabdoviridae , highlighting the vast ersity of this virus family.
Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis
Publisher: Research Square Platform LLC
Date: 07-12-2021
DOI: 10.21203/RS.3.RS-1146895/V1
Abstract: Plague has an enigmatic history as a zoonotic pathogen. This potentially devastating infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences s led globally. We perform a detailed Bayesian evaluation of temporal signal in subsets of these data and demonstrate that a Y. pestis-wide molecular clock model is unstable. To resolve this, we devised a new approach in which each Y. pestis population was assessed independently. This enabled us to recover significant temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this, we only obtain robust ergence dates from populations s led over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics. Finally, we identify key historical data sets that can be used in future research, which will complement the strengths and mitigate the weaknesses of genomic data.
Cloacal virome of an ancient host lineage – the tuatara (Sphenodon punctatus) – reveals abundant and diverse diet-related viruses
Publisher: Cold Spring Harbor Laboratory
Date: 15-06-2022
DOI: 10.1101/2022.06.14.496210
Abstract: 1. Tuatara ( Sphenodon punctatus ) are one of the most phylogenetically isolated species and provide a unique host system to study virus evolution. While the tuatara genome, sequenced in 2020, revealed many endogenous viral elements, we know little of the exogenous viruses that infect tuatara. We performed a metatranscriptomics study of tuatara cloaca s les from a wild population on Takapourewa (Stephens Island), Aotearoa New Zealand. From these data we identified 49 potentially novel viral species that spanned 20 RNA viral families and/or orders, the vast majority (48) of which were likely dietary related. Notably, using a protein structure homology search, we identified a highly ergent novel virus within the Picornaviridae which may directly infect tuatara. Additionally, two endogenous tuatara adintoviruses were characterised that exhibited long-term viral-host co- ergence. Overall, our results indicate that the tuatara cloacal virome is highly erse likely due a large number of dietary related viruses.
On the origin and evolution of the human immunodeficiency virus (HIV)
Publisher: Wiley
Date: 05-2001
DOI: 10.1017/S1464793101005668
Abstract: The human AIDS viruses--HIV-1 and HIV-2--impose major burdens on the health and economic status of many developing countries. Surveys of other animal species have revealed that related viruses--the SIVs are widespread in a large number of African simian primates where they do not appear to cause disease. Phylogenetic analyses indicate that these SIVs are the reservoirs for the human viruses, with SIVsm from the sooty mangabey monkey the most likely source of HIV-2, and SIVcpz from the common chimpanzee the progenitor population for HIV-1. Although it is clear that AIDS has a zoonotic origin, it is less certain when HIV-1 and HIV-2 first entered human populations and whether cross-species viral transmission is common among primates. Within infected in iduals the process of HIV evolution takes the form of an arms race, with the virus continually fixing mutations by natural selection which allow it to escape from host immune responses. The arms race is less intense in SIV-infected monkeys, where a weaker immune response generates less selective pressure on the virus. Such a difference in virus-host interaction, along with a broadening of co-receptor usage such that HIV strains are able to infect cells with both CCR5 and CXCR4 chemokine receptors, may explain the increased virulence of HIV in humans compared to SIV in other primates.
Helping the Resistance
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-06-2010
Abstract: Phylogenetic analysis reveals mutations that led to the rise of drug resistance in seasonal H1N1 influenza.
Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors
Publisher: Wiley
Date: 27-06-2021
DOI: 10.1111/JEB.13890
Abstract: Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3‐ or α2,6‐linkage) and form ( N ‐glycolylneuraminic acid [Neu5Gc] or N ‐acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host‐specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3‐linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6‐linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK‐Type I or MDCK‐Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus‐level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor‐binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor‐binding site when passaged in cells displaying Neu5Gc or α2,6‐linkages. Viruses replicated to low titres in MDCK‐Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
Off-season RSV epidemics in Australia after easing of COVID-19 restrictions
Publisher: Springer Science and Business Media LLC
Date: 24-05-2022
DOI: 10.1038/S41467-022-30485-3
Abstract: Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection with the most severe disease in the young and elderly. Non-pharmaceutical interventions and travel restrictions for controlling COVID-19 have impacted the circulation of most respiratory viruses including RSV globally, particularly in Australia, where during 2020 the normal winter epidemics were notably absent. However, in late 2020, unprecedented widespread RSV outbreaks occurred, beginning in spring, and extending into summer across two widely separated regions of the Australian continent, New South Wales (NSW) and Australian Capital Territory (ACT) in the east, and Western Australia. Through genomic sequencing we reveal a major reduction in RSV genetic ersity following COVID-19 emergence with two genetically distinct RSV-A clades circulating cryptically, likely localised for several months prior to an epidemic surge in cases upon relaxation of COVID-19 control measures. The NSW/ACT clade subsequently spread to the neighbouring state of Victoria and to cause extensive outbreaks and hospitalisations in early 2021. These findings highlight the need for continued surveillance and sequencing of RSV and other respiratory viruses during and after the COVID-19 pandemic, as mitigation measures may disrupt seasonal patterns, causing larger or more severe outbreaks.
The evolutionary history and dynamics of bat rabies virus
Publisher: Elsevier BV
Date: 11-2006
DOI: 10.1016/J.MEEGID.2006.02.007
Abstract: Rabies virus (RABV) is endemic in terrestrial mammals throughout the world and in bats on the American continent. We performed the most extensive phylogenetic analyses of bat RABV sequences undertaken to date using a variety of genes. Our study supported previous suggestions that viral sequences are grouped according to the behaviour of the host species. However, there was more genetic and geographical ersity within each phylogenetic group than previously recognised, including evidence for new groups. Furthermore, three clades of Latin American bat RABV that were distinct from the previously identified "group IV" bat RABV clade and more closely related to North American bat RABV clades, were identified. Strikingly, phylogenetic trees for the G (glycoprotein) gene had a significantly different evolutionary history to those inferred for the N (nucleoprotein) and P (phosphoprotein) genes, and an analysis of these competing topologies revealed that it is not possible on current data to resolve whether bat RABV arose from terrestrial mammal RABV, or vice-versa. Finally, using coalescent approaches, we estimated that RABV had similar rates of population growth and nucleotide substitution (approximately 2.5-4x10(-4) substitutions per site, per year) in both bats and terrestrial mammals, despite underlying differences in epidemiology.
Copy Number Aberration Analysis to Predict Response to Neoadjuvant Anti-HER2 Therapy: Results from the NeoALTTO Phase III Clinical Trial
Publisher: American Association for Cancer Research (AACR)
Date: 28-07-2021
DOI: 10.1158/1078-0432.CCR-21-1317
Abstract: The heterogeneity of response to anti-HER2 agents represents a major challenge in patients with HER2-positive breast cancer. To better understand the sensitivity and resistance to trastuzumab and lapatinib, we investigated the role of copy number aberrations (CNA) in predicting pathologic complete response (pCR) and survival outcomes in the NeoALTTO trial. The neoadjuvant phase III NeoALTTO trial enrolled 455 patients with HER2-positive early-stage breast cancer. DNA s les from 269 patients were assessed for genome-wide copy number profiling. Recurrent CNAs were found with GISTIC2.0. CNA estimates were obtained for 184 patients included in NeoALTTO. Among those, matched transcriptome and whole-exome data were available for 154 and 181 patients, respectively. A significant association between gene copy number and pCR was demonstrated for ERBB2 lification. Nevertheless, ERBB2 lification ceased to be predictive once ERBB2 expression level was considered. GISTIC2.0 analysis revealed 159 recurrent CNA regions. Lower copy number levels of the 6q23-24 locus predicted absence of pCR in the whole cohort and in the estrogen receptor–positive subgroup. 6q23-24 deletion was significantly more frequent in TP53 wild-type (WT) compared with TP53-mutated, resulting in copy number levels significantly associated with lack of pCR only in the TP53 WT subgroup. Interestingly, a gene-ontology analysis highlighted several immune processes correlated to 6q23-24 copy number. Our analysis identified ERBB2 copy number as well as 6q23-24 CNAs as predictors of response to anti–HER2-based treatment. ERBB2 expression outperformed ERBB2 lification. The complexity of the 6q23-24 region warrants further investigation.
An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
Publisher: Oxford University Press (OUP)
Date: 2020
DOI: 10.1093/VE/VEAA027
Abstract: The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral ersity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.
Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza A (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance
Publisher: Oxford University Press (OUP)
Date: 15-01-2011
AT LEAST FOUR MHC CLASS I GENES ARE TRANSCRIBED IN THE HORSE: PHYLOGENETIC ANALYSIS SUGGESTS AN UNUSUAL EVOLUTIONARY HISTORY FOR THE MHC IN THIS SPECIES
Publisher: Wiley
Date: 06-1995
DOI: 10.1111/J.1744-313X.1995.TB00239.X
Abstract: Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are predicted to code for surface expressed, functional molecules. The number of different sequences identified demonstrate that at least four genes are transcribed, although variations in transmembrane length (which is generally conserved in class I loci) suggest that five genes could be represented. Evolutionary analysis of these sequences (and two additional sequences known to represent different horse class I loci) reveals no firm relationships, such that the ision between the different loci cannot be discerned. These results suggest an unusual evolutionary history for the horse MHC, the precise nature of which may be revealed only following further cross-species comparisons.
Participants' voices from within a healthy lifestyle group
Publisher: Informa UK Limited
Date: 08-12-2017
DOI: 10.1080/01612840.2016.1248255
Abstract: Weight gain is a serious health concern. People with mental illnesses are at increased risk of weight gain. The primary treatment is lifestyle changes such as increasing physical activity and dietary changes. This qualitative study explored the experience of people with schizophrenia who participated in a healthy lifestyle program. Four themes were identified. The findings indicate that benefits of the program were more than physical health improvements and included regular access to a health professional, gaining social relationships, and a sense of belonging. Future recommendations include retaining a group structure in lifestyle interventions to facilitate these additional benefits.
Newly identified viral genomes in pangolins with fatal disease
Publisher: Oxford University Press (OUP)
Date: 2020
DOI: 10.1093/VE/VEAA020
Abstract: Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence ergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the s ling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks s led close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens.
Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses
Publisher: Oxford University Press (OUP)
Date: 16-07-2020
Abstract: Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high ersity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review, we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major s ling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird – poultry interface as well as from birds to mammals. Clarifying the ecology and ersity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.
Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States
Publisher: American Society for Microbiology
Date: 15-02-2016
DOI: 10.1128/JVI.02418-15
Abstract: In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory s les with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic ersity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or in idual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies. IMPORTANCE Until recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.
A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility
Publisher: American Society for Microbiology
Date: 05-2018
DOI: 10.1128/JB.00050-18
Abstract: Yersinia pestis , the causative agent of plague, evolved from the closely related pathogen Yersinia pseudotuberculosis . During its emergence, Y. pestis is believed to have acquired its unique pathogenic characteristics through numerous gene gains/losses, genomic rearrangements, and single nucleotide polymorphism (SNP) changes. One such SNP creates a single amino acid variation in the DNA binding domain of PhoP, the response regulator in the PhoP/PhoQ two-component system. Y. pseudotuberculosis and the basal human-avirulent strains of Y. pestis harbor glycines at position 215 of PhoP, whereas the modern human-virulent strains (e.g., KIM and CO92) harbor serines at this residue. Since PhoP plays multiple roles in the adaptation of Y. pestis to stressful host conditions, we tested whether this amino acid substitution affects PhoP activity or the ability of Y. pestis to survive in host environments. Compared to the parental KIM6+ strain carrying the modern allele of phoP ( phoP-S215 ), a derivative carrying the basal allele ( phoP-G215 ) exhibited slightly defective growth under a low-Mg 2+ condition and decreased transcription of a PhoP target gene, ugd , as well as an ∼8-fold increase in the susceptibility to the antimicrobial peptide polymyxin B. The phoP-G215 strain showed no apparent defect in flea colonization, although a phoP -null mutant showed decreased flea infectivity in competition experiments. Our results suggest that the amino acid variation at position 215 of PhoP causes subtle changes in the PhoP activity and raise the possibility that the change in this residue have contributed to the evolution of increased virulence in Y. pestis . IMPORTANCE Y. pestis acquired a single nucleotide polymorphism (SNP) in phoP when the highly human-virulent strains erged from less virulent basal strains, resulting in an amino acid substitution in the DNA binding domain of the PhoP response regulator. We show that Y. pestis carrying the modern phoP allele has an increased ability to induce the PhoP-regulated ugd gene and resist antimicrobial peptides compared to an isogenic strain carrying the basal allele. Given the important roles PhoP plays in host adaptation, the results raise an intriguing possibility that this amino acid substitution contributed to the evolution of increased virulence in Y. pestis . Additionally, we present the first evidence that phoP confers a survival fitness advantage to Y. pestis inside the flea midgut.
Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia
Publisher: MDPI AG
Date: 27-05-2019
DOI: 10.3390/V11050482
Abstract: Australia’s response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world’s lowest HIV incidence rates—0.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE s led in NSW, were combined with those s led globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences however, five large clades comprising ≥10 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016/2017. Seven such clades each comprised ≥10 sequences, and are representative of in idual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, in idual sub-epidemics are present and should be closely monitored.
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2021
DOI: 10.1101/2021.02.17.431744
Abstract: The ersity of lagoviruses ( Caliciviridae ) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
Publisher: American Association for the Advancement of Science (AAAS)
Date: 16-01-2004
Abstract: A key priority for infectious disease research is to clarify how pathogen genetic variation, modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the wide variety of pathogen phylogenies observed at scales that range from in idual host to population. We call the melding of immunodynamics, epidemiology, and evolutionary biology required to achieve this synthesis pathogen “phylodynamics.” We introduce a phylodynamic framework for the dissection of dynamic forces that determine the ersity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates. A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission.
Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy
Publisher: Frontiers Media SA
Date: 23-08-2016
A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae
Publisher: MDPI AG
Date: 31-03-2021
DOI: 10.3390/V13040585
Abstract: Rubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Recently, two new rubella-like matonaviruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more ergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses, we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica—order Torpediniformes (Pacific electric ray)—that is more closely related to mammalian Rustrela virus than to the ergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the s le analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses that remain undiscovered.
Host Species Barriers to Influenza Virus Infections
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-04-2006
Abstract: Most emerging infectious diseases in humans originate from animal reservoirs to contain and eradicate these diseases we need to understand how and why some pathogens become capable of crossing host species barriers. Influenza virus illustrates the interaction of factors that limit the transmission and subsequent establishment of an infection in a novel host species. Influenza species barriers can be categorized into virus-host interactions occurring within in iduals and host-host interactions, either within or between species, that affect transmission between in iduals. Viral evolution can help surmount species barriers, principally by affecting virus-host interactions however, evolving the capability for sustained transmission in a new host species represents a major adaptive challenge because the number of mutations required is often large.
The Molecular Epidemiology Of Human Immunodeficiency Virus Type 1 In Edinburgh
Publisher: Oxford University Press (OUP)
Date: 1995
Abstract: Human immunodeficiency virus (HIV) type 1 sequences obtained from HIV-infected persons in different risk groups in Edinburgh were studied to determine the number and origin of virus variants and patterns of virus transmission. Phylogenetic analysis revealed that 12 of 14 hemophiliac patients who had been exposed to a single common batch of factor VIII had closely related gag gene sequences. Sequences from intravenous drug users and patients infected through heterosexual contact formed another distinct group, and 2 other hemophiliacs formed a third group. However, epidemiologic relationships inferred from analysis of the V3 region of the env gene were less conclusive, especially when the V3 loop was taken in isolation. This appears to be due to the length of time since infection and the action of selection, which has favored the independent appearance of similar V3 loop variants.
Freezing viruses in time
Publisher: Proceedings of the National Academy of Sciences
Date: 17-11-2014
Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities
Publisher: Cold Spring Harbor Laboratory
Date: 21-03-2019
DOI: 10.1101/584649
Abstract: High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using licon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based licon sequencing: it is less susceptible to lification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a defined mock community comprised of 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species-level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were erse but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study therefore establishes a base-line for the application of metatranscriptomics in clinical mycology and ecological studies.
Transcriptome Mining Reveals a Spectrum of RNA Viruses in Primitive Plants
Publisher: Cold Spring Harbor Laboratory
Date: 23-02-2022
DOI: 10.1101/2022.02.07.479358
Abstract: Current knowledge of plant viruses stems largely from those affecting economically important plants. Yet, plant species in cultivation represent a small and bias subset of the plant kingdom. Here, we describe virus ersity and abundance from a survey of 1079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analysing open-source data from the One Thousand Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% comprised single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales , Tymovirales , Cryppavirales , Martellivirales and Picornavirales . One-third of the newly described viruses comprised double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales . The remaining were negative-sense RNA viruses from the Rhabdoviridae , Aspiviridae, Yueviridae, Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae ) and four virus families to include algae hosts (e.g., Tymoviridae and Chrysoviridae) . The discovery of the first 30 kDa movement protein in a non-vascular plant, suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. More broadly, however, a co-phylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the scarcity of RNA viruses found in lower plants to date likely reflects a lack of investigation rather than their absence. Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting primitive plant lineages such as the ferns, lycophytes, bryophytes and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We find that primitive plants harbour a wide ersity of RNA viruses including some that are sufficiently ergent to comprise a new virus family. The primitive plant virome we reveal offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasises that the scarcity of viruses found in these species to date likely reflects the absence of research in this area.
Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts
Publisher: Public Library of Science (PLoS)
Date: 15-12-2016
Sexual transmission of HIV in Africa
Publisher: Springer Science and Business Media LLC
Date: 04-2003
DOI: 10.1038/422679A
Comparative analysis reveals no consistent association between the secondary structure of the 3′-untranslated region of dengue viruses and disease syndrome
Publisher: Microbiology Society
Date: 09-2006
Abstract: A comparative analysis was performed of the 3′-untranslated region (UTR) of Dengue virus (DENV) s led from Bangkok, Thailand, over a 30 year period and representing all four serotypes. Considerable genetic variation was observed both within and among serotypes. Notably, a full-length version of the critical 3′-long stable hairpin structure was absent from some isolates, suggesting the occurrence of complex structural interactions within the 3′-UTR, including the influence of upstream mutations. The Thai sequences were then combined with 61 globally s led isolates of DENV taken from patients with either dengue fever or severe dengue disease. No consistent association was found between 3′-UTR secondary structure and the clinical outcome of DENV infection, although some evidence for a trend in this direction was observed in DENV-2. It was concluded that the 3′-UTR is not the sole determinant of DENV virulence in nature, although variation in secondary structure may greatly influence viral fitness.
Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom
Publisher: American Society for Microbiology
Date: 21-12-2022
DOI: 10.1128/JVI.00260-22
Abstract: Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus ersity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the
Metagenomic identification of diverse animal hepaciviruses and pegiviruses
Publisher: Cold Spring Harbor Laboratory
Date: 17-05-2020
DOI: 10.1101/2020.05.16.100149
Abstract: The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently ided into four genera - Hepacivirus , Pegivirus , Pestivirus and Flavivirus – each of which have a erse host range. Members of the genus Hepacivirus are associated with a erse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the ersity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko ( Gehyra lauta ). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots ( Perameles nasuta ). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae , comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co- ergence over evolutionary time-scales.
Genomic Diversity and Evolution of the Lyssaviruses
Publisher: Public Library of Science (PLoS)
Date: 30-04-2008
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
Publisher: Springer Science and Business Media LLC
Date: 16-04-2021
DOI: 10.1038/S41467-021-22607-0
Abstract: Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015–2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.
Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread
Publisher: American Society for Microbiology
Date: 12-12-2019
DOI: 10.1128/JVI.01162-19
Abstract: Rapid mutation rates and correspondingly high levels of intra- and interhost ersity are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little known about evolutionary processes in viruses with single-stranded DNA (ssDNA) genomes. Here, we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intrahost evolutionary processes of an ssDNA virus that emerged to cause a pandemic in a new host animal. Our analysis reveals that successful host jumping and sustained transmission does not necessarily depend on a high level of intrahost ersity nor result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of the biology and ecology of a virus are relevant when considering their adaptability.
Positively Charged Amino Acid Substitutions in the E2 Envelope Glycoprotein Are Associated with the Emergence of Venezuelan Equine Encephalitis Virus
Publisher: American Society for Microbiology
Date: 15-02-2002
DOI: 10.1128/JVI.76.4.1718-1730.2002
Abstract: Epidemic-epizootic Venezuelan equine encephalitis (VEE) viruses (VEEV) have emerged repeatedly via convergent evolution from enzootic predecessors. However, previous sequence analyses have failed to identify common sets of nucleotide or amino acid substitutions associated with all emaergence events. During 1993 and 1996, VEEV subtype IE epizootics occurred on the Pacific Coast of the states of Chiapas and Oaxaca in southern Mexico. Like other epizootic VEEV strains, when inoculated into guinea pigs and mice, the Mexican isolates were no more virulent than closely related enzootic strains, complicating genetic studies of VEE emergence. Complete genomic sequences of 4 of the Mexican strains were determined and compared to those of closely related enzootic subtype IE isolates from Guatemala. The epizootic viruses were less than 2% different at the nucleotide sequence level, and phylogenetic relationships confirmed that the equine-virulent Mexican strains probably evolved from enzootic progenitors on the Pacific Coast of Mexico or Guatemala. Of 35 amino acids that varied among the Guatemalan and Mexican isolates, only 8 were predicted phylogenetically to have accompanied the phenotypic change. One mutation at position 117 of the E2 envelope glycoprotein, involving replacement of Glu by Lys, resulted in a small-plaque phenotype characteristic of epizootic VEEV strains. Analysis of additional E2 sequences from representative enzootic and epizootic VEEV isolates implicated similar surface charge changes in the emergence of previous South American epizootic phenotypes, indicating that E2 mutations are probably important determinants of the equine-virulent phenotype and of VEE emergence. Maximum-likelihood analysis indicated that one change at E2 position 213 has been influenced by positive selection and convergent evolution of the epizootic phenotype.
Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses
Publisher: Elsevier BV
Date: 2014
Introductions and Evolution of Human-Origin Seasonal Influenza A Viruses in Multinational Swine Populations
Publisher: American Society for Microbiology
Date: 09-2014
DOI: 10.1128/JVI.01080-14
Abstract: The capacity of influenza A viruses to cross species barriers presents a continual threat to human and animal health. Knowledge of the human-swine interface is particularly important for understanding how viruses with pandemic potential evolve in swine hosts. We sequenced the genomes of 141 influenza viruses collected from North American swine during 2002 to 2011 and identified a swine virus that possessed all eight genome segments of human seasonal A/H3N2 virus origin. A molecular clock analysis indicates that this virus—A/sw/Saskatchewan/02903/2009(H3N2)—has likely circulated undetected in swine for at least 7 years. For historical context, we performed a comprehensive phylogenetic analysis of an additional 1,404 whole-genome sequences from swine influenza A viruses collected globally during 1931 to 2013. Human-to-swine transmission occurred frequently over this time period, with 20 discrete introductions of human seasonal influenza A viruses showing sustained onward transmission in swine for at least 1 year since 1965. Notably, human-origin hemagglutinin (H1 and H3) and neuraminidase (particularly N2) segments were detected in swine at a much higher rate than the six internal gene segments, suggesting an association between the acquisition of swine-origin internal genes via reassortment and the adaptation of human influenza viruses to new swine hosts. Further understanding of the fitness constraints on the adaptation of human viruses to swine, and vice versa, at a genomic level is central to understanding the complex multihost ecology of influenza and the disease threats that swine and humans pose to each other. IMPORTANCE The swine origin of the 2009 A/H1N1 pandemic virus underscored the importance of understanding how influenza A virus evolves in these animals hosts. While the importance of reassortment in generating genetically erse influenza viruses in swine is well documented, the role of human-to-swine transmission has not been as intensively studied. Through a large-scale sequencing effort, we identified a novel influenza virus of wholly human origin that has been circulating undetected in swine for at least 7 years. In addition, we demonstrate that human-to-swine transmission has occurred frequently on a global scale over the past decades but that there is little persistence of human virus internal gene segments in swine.
Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia
Publisher: American Society for Microbiology
Date: 12-2015
DOI: 10.1128/JVI.01937-15
Abstract: To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.
Ngoye virus: a novel evolutionary lineage within the genus Flavivirus
Publisher: Microbiology Society
Date: 11-2006
Abstract: By using degenerate primers deduced from conserved patterns in the flavivirus polymerase gene, a novel RNA virus was discovered in Rhipicephalus ticks s led from members of the family Bovidae in Senegal. It was named Ngoye virus (NGOV) after the location from which it was isolated. Viral particles could be observed by electron microscopy, but isolation in vertebrate or invertebrate cell lines or by intracerebral infection of newborn mice remained unsuccessful. This is atypical of recognized arboviruses. The characterization of 4176 nt of the non-structural genes revealed that NGOV is a novel flavivirus species. It forms a distinct phylogenetic lineage related distantly to previously identified members of the genus Flavivirus . Analysis of genetic data suggested that the processing of the NGOV polyprotein and the organization of its replication complex are similar to those of flaviviruses. Together with other recent data, these findings suggest that a large number of viruses related distantly to ‘classical’ arthropod-borne flaviviruses remain to be discovered.
Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala
Publisher: MDPI AG
Date: 02-03-2019
DOI: 10.3390/V11030211
Abstract: Koalas (Phascolarctos cinereus) are native Australian marsupials whose populations are in decline from a range of threats. Infectious diseases caused by the bacterium Chlamydia pecorum and other pathogens are of particular concern. We analysed 26 poly-A selected RNA-sequencing libraries from a data set designed to study the immune response of koalas to ocular chlamydial infection. Using virus discovery techniques, we identified the coding-complete genome sequence of a novel picorna-like virus, denoted Burpengary virus, that was most common in south-east Queensland. Notably, abundance measurements of the virus across all 26 libraries revealed an inverse relationship between abundance and ocular disease in koalas, suggesting that the co-infection of Burpengary virus and Chlamydia pecorum is inhibited.
The Effect of Gene Overlapping on the Rate of RNA Virus Evolution
Publisher: Oxford University Press (OUP)
Date: 17-05-2013
Mixed Infection and the Genesis of Influenza Virus Diversity
Publisher: American Society for Microbiology
Date: 09-1970
DOI: 10.1128/JVI.00773-09
Abstract: The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic ersity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences s led from in idual influenza patients we reveal a high level of mixed infection, including erse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that in iduals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.
Global migration of influenza A viruses in swine
Publisher: Springer Science and Business Media LLC
Date: 27-03-2015
DOI: 10.1038/NCOMMS7696
Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor
Publisher: American Society for Microbiology
Date: 15-01-2018
DOI: 10.1128/JVI.00921-17
Abstract: Since its emergence in 2013, the H7N9 low-pathogenic avian influenza virus (LPAIV) has been circulating in domestic poultry in China, causing five waves of human infections. A novel H7N9 highly pathogenic avian influenza virus (HPAIV) variant possessing multiple basic amino acids at the cleavage site of the hemagglutinin (HA) protein was first reported in two cases of human infection in January 2017. More seriously, those novel H7N9 HPAIV variants have been transmitted and caused outbreaks on poultry farms in eight provinces in China. Herein, we demonstrate the presence of three different amino acid motifs at the cleavage sites of these HPAIV variants which were isolated from chickens and humans and likely evolved from the preexisting LPAIVs. Animal experiments showed that these novel H7N9 HPAIV variants are both highly pathogenic in chickens and lethal to mice. Notably, human-origin viruses were more pathogenic in mice than avian viruses, and the mutations in the PB2 gene associated with adaptation to mammals (E627K, A588V, and D701N) were identified by next-generation sequencing (NGS) and Sanger sequencing of the isolates from infected mice. No polymorphisms in the key amino acid substitutions of PB2 and HA in isolates from infected chicken lungs were detected by NGS. In sum, these results highlight the high degree of pathogenicity and the valid transmissibility of this new H7N9 variant in chickens and the quick adaptation of this new H7N9 variant to mammals, so the risk should be evaluated and more attention should be paid to this variant. IMPORTANCE Due to the recent increased numbers of zoonotic infections in poultry and persistent human infections in China, influenza A(H7N9) virus has remained a public health threat. Most of the influenza A(H7N9) viruses reported previously have been of low pathogenicity. Now, these novel H7N9 HPAIV variants have caused human infections in three provinces and outbreaks on poultry farms in eight provinces in China. We analyzed the molecular features and compared the relative characteristics of one H7N9 LPAIV and two H7N9 HPAIVs isolated from chickens and two human-origin H7N9 HPAIVs in chicken and mouse models. We found that all HPAIVs both are highly pathogenic and have valid transmissibility in chickens. Strikingly, the human-origin viruses were more highly pathogenic than the avian-origin viruses in mice, and dynamic mutations were confirmed by NGS and Sanger sequencing. Our findings offer important insight into the origin, adaptation, pathogenicity, and transmissibility of these viruses to both poultry and mammals.
Detection of Hepatitis B Virus Infection in Wild-Born Chimpanzees ( Pan troglodytes verus ): Phylogenetic Relationships with Human and Other Primate Genotypes
Publisher: American Society for Microbiology
Date: 05-2000
DOI: 10.1128/JVI.74.9.4253-4257.2000
Abstract: Infection with hepatitis B virus (HBV) was detected by serological testing for HBV surface antigen and by PCR assay for HBV DNA in serum s les from two common chimpanzees ( Pan troglodytes subsp. verus ) born in West Africa. The complete genome sequences obtained by nucleotide sequencing of overlapping DNA fragments lified by PCR were compared with HBV variants recovered from other primates and with human genotypes A to F. Both chimpanzee sequences were 3,182 nucleotides in length, and the surface gene sequence predicted the existence of a , d , and w serological determinants. Neither sequence contained stop codons in the precore region. On phylogenetic analysis, the HBV variants infecting the chimpanzees clustered together with a third chimpanzee HBV isolate independently obtained from an infected captive animal (A. J. Zuckerman, A. Thornton, C. R. Howard, K. N. Tsiquaye, D. M. Jones, and M. R. Brambell, Lancet ii:652–654, 1978), with an overall sequence similarity of %. This provides strong evidence for a chimpanzee-specific genotype of HBV which circulates in nature. These findings add to the recent evidence for infection in the wild of other Old and New World primates (gibbon, orangutan, and woolly monkey) with species-specific variants of HBV. There is no evidence for close phylogenetic clustering of variants found so far in primates with any of the established HBV genotypes from humans. With the new evidence for the widespread distribution of HBV in primates, hypotheses for the origins of human infection are reviewed.
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae
Publisher: Cold Spring Harbor Laboratory
Date: 22-03-2019
DOI: 10.1101/2021.03.22.436364
Abstract: The Nidovirales comprise a genetically erse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae , in a range of aquatic hosts including fish, hibians and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data, and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of ergent viruses that fell within the Letovirinae subfamily of the Coronaviridae , including those in a jawless fish – the pouched l rey. By mining fish transcriptome data we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae , but formed a distinct and erse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationships of viruses within the Letovirinae does not mirror that of their hosts. For ex le, the coronavirus found in the pouched l rey fell within the phylogenetic ersity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection
Publisher: Springer Science and Business Media LLC
Date: 24-01-2001
Abstract: Cattle in Africa are a genetically erse population that has resulted from successive introduction of Asian Bos indicus and European B. taurus cattle. However, analysis of mitochondrial genetic ersity in African cattle identified three lineages, one associated with Asian B. indicus, one with European B. taurus, and a third ascribed to an indigenous African sub-species of cattle. Due to their extended coevolution, indigenous African herbivores are generally tolerant to endemic African pathogens. We are interested in identifying alleles derived from the indigenous African cattle that may be associated with tolerance to African pathogens. An analysis of the locus which encodes the abundant plasma membrane-associated tyrosine phosphatase, CD45, identified three highly ergent allelic families in Kenya Boran cattle. Analysis of allelic distribution in a erse range of cattle populations suggests a European B. taurus, an Asian B. indicus, and an African origin. This demonstrates not only significant allelic polymorphism at the CD45 locus in cattle but also convincing autosomal evidence for a distinct African sub-species of cattle. Furthermore, maximum-likelihood analysis of selection pressures revealed that the CD45 locus is subject to exceptionally strong natural selection which we suggest may be pathogen driven.
The extent of homologous recombination in members of the genus Flavivirus
Publisher: Microbiology Society
Date: 2003
Abstract: The family Flaviviridae includes important human pathogens, such as dengue (DEN) virus, yellow fever (YF) virus and hepatitis C virus, many of which have emerged or re-emerged in recent years. Until recently, flavivirus evolution was thought to proceed in a clonal manner, with ersity generated mainly through the accumulation of mutational changes. However, this assumption has now been shown to be invalid, with homologous recombination demonstrated in all three genera of the FLAVIVIRIDAE: Since recombination has important implications for the study of virus evolution, a survey of recombination in the viruses of the genus Flavivirus was carried out. Using envelope gene sequence data and a combination of graphical and phylogenetic analyses, hitherto unreported recombination in Japanese encephalitis virus and St Louis encephalitis virus was detected, as well as further recombinants in DEN virus. However, no evidence for recombination was found in West Nile or YF viruses, or in the tick-borne flavivirus group. It is proposed that the difference between the mosquito- and tick-borne viruses can be accounted for by their differing modes of transmission, whilst the variation among the mosquito-borne flaviviruses reflects both the ecology of the particular host and vector species and also bias in the s ling process.
Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission
Publisher: The Royal Society
Date: 19-03-2013
Abstract: In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic ersity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of s ling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.
Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing
Publisher: Microbiology Society
Date: 29-04-2022
DOI: 10.1099/JGV.0.001736
Abstract: Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical s les from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. S les were subjected to total RNA sequencing (‘metatranscriptomics’) to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system s ling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.
Evolutionary dynamics of human and avian metapneumoviruses
Publisher: Microbiology Society
Date: 12-2008
DOI: 10.1099/VIR.0.2008/006957-0
Abstract: Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic ersity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The s led genetic ersity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic ersity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.
Evolutionary History and Attenuation of Myxoma Virus on Two Continents
Publisher: Public Library of Science (PLoS)
Date: 04-10-2012
Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus
Publisher: Cold Spring Harbor Laboratory
Date: 19-01-2023
DOI: 10.1101/2023.01.18.524668
Abstract: Canine parvovirus (CPV) is a small non-enveloped single-stranded DNA virus that causes serious diseases in dogs worldwide. The original strain of the virus (CPV-2) emerged in dogs during the late-1970s due to a host range switch of a virus similar to the feline panleukopenia virus (FPV) that infected another host. The virus that emerged in dogs had altered capsid receptor- and antibody-binding sites, with some changes affecting both functions. Further receptor and antibody binding changes arose when the virus became better adapted to dogs or to other hosts. Here, we use in vitro selection and deep sequencing to reveal how two antibodies with known interactions select for escape mutations in CPV. The antibodies bind two distinct epitopes, and one largely overlaps the host receptor binding site. We also engineered antibody variants with altered binding structures. Viruses were passaged with the wild type or mutated antibodies, and their genomes deep sequenced during the selective process. A small number of mutations were detected only within the capsid protein gene during the first few passages of selection, and most sites remained polymorphic or were slow to go to fixation. Mutations arose both within and outside the antibody binding footprints on the capsids, and all avoided the TfR-binding footprint. Many selected mutations matched those that have arisen in the natural evolution of the virus. The patterns observed reveal the mechanisms by which these variants have been selected in nature and provide a better understanding of the interactions between antibody and receptor selections. Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system. Here, we use an in vitro model system and deep genome sequencing to reveal the mutations that arise in the virus genome during selection by each of two monoclonal antibodies or their engineered variants. High-resolution structures of each of the Fab: capsid complexes revealed their binding interactions. The engineered forms of the wild-type antibodies or mutant forms allowed us to examine how changes in antibody structure influence the mutational selection patterns seen in the virus. The results shed light on the processes of antibody binding, neutralization escape, and receptor binding, and likely have parallels for many other viruses.
Quantifying influenza virus diversity and transmission in humans
Publisher: Springer Science and Business Media LLC
Date: 04-01-2016
DOI: 10.1038/NG.3479
The population genetics and evolutionary epidemiology of RNA viruses
Publisher: Springer Science and Business Media LLC
Date: 04-2004
DOI: 10.1038/NRMICRO863
Diversity and circulation of Jingmen tick virus in ticks and mammals
Publisher: Oxford University Press (OUP)
Date: 07-2020
DOI: 10.1093/VE/VEAA051
Abstract: Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents, and primates. To better understand the ersity, evolution, and transmission of JMTV, we s led 215 ticks, 104 cattle bloods, 216 bats, and 119 rodents in Wenzhou city, Zhejiang Province, China as well as 240 bats from Guizhou and Henan Provinces. JMTV was identified in 107 ticks (from two species), 54 bats (eleven species), 8 rodents (three species), and 10 cattle, with prevalence levels of 49.8, 11.8, 6.7, and 9.6 per cent, respectively, suggesting that bats may be a natural reservoir of JMTV. Phylogenetic analyses revealed that all the newly identified JMTVs were closely related to each other and to previously described viruses. Additionally, all tick and mammalian JMTV s led in Wenzhou shared a consistent genomic structure, suggesting that the virus can cocirculate between ticks and mammals without observable variation in genome organization. All JMTVs s led globally could be ided into two phylogenetic groups, Mantel tests suggested that geographic isolation, rather than host species, may be the main driver of JMTV ersity. However, the exact geographical origin of JMTV was difficult to determine, suggesting that this virus has a complex evolutionary history.
Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and in vitro Efficacy of Novel Antivirals in Australian Outbreaks
Publisher: MDPI AG
Date: 16-08-2021
DOI: 10.20944/PREPRINTS202108.0341.V1
Abstract: Feline calicivirus (FCV) causes upper respiratory tract disease (URTD) and sporadic outbreaks of virulent systemic disease (FCV-VSD). The basis for the increased pathogenicity of FCV-VSD viruses is incompletely understood, and antivirals for FCV have yet to be developed. We investigated the clinicoepidemiology and viral features of three FCV-VSD outbreaks in Australia and evaluated the in vitro efficacy of nitazoxanide (NTZ), 2& rsquo -C-methylcytidine (2CMC) and NITD-008 against FCV-VSD viruses. Overall mortality among 23 cases of FCV-VSD was 39%. Metagenomic sequencing identified five genetically distinct FCV lineages within the three outbreaks, all seemingly evolving in situ in Australia. Notably, no mutations that clearly distinguished FCV-URTD from FCV-VSD phenotypes were identified. One FCV-URTD strain likely originated from a recombination event. Analysis of seven amino acid residues from the hypervariable E region of the capsid in the cultured viruses provided no support for the contention that properties of these residues can reliably differentiate between the two pathotypes. On plaque reduction assays, dose-response inhibition of FCV-VSD was obtained with all antivirals at low micromolar concentrations NTZ EC50, 0.4-0.6 & micro M, TI 21 2CMC EC50, 2.7-5.3 & micro M, TI & NITD-008, 0.5 to 0.9 & micro M, TI & . Investigation of these antivirals for treatment of FCV-VSD is warranted.
Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits
Publisher: MDPI AG
Date: 31-12-2019
DOI: 10.3390/V12010047
Abstract: The advent of unbiased metagenomic virus discovery has revolutionized studies of virus bio ersity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a narmovirus (paramyxovirus). In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often ergent from those previously described. The novel astrovirus was most closely related to a virus s led from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel narmovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent narmoviruses s led globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly ergent picorna-like virus found in the gut of the French rabbit virus was only ~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.
Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling
Publisher: Cold Spring Harbor Laboratory
Date: 22-04-2020
DOI: 10.1101/2020.04.19.048751
Abstract: Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.
Global Rinderpest Eradication: Lessons Learned and Why Humans Should Celebrate Too
Publisher: Oxford University Press (OUP)
Date: 15-08-2011
Reduced Positive Selection in Vector-Borne RNA Viruses
Publisher: Oxford University Press (OUP)
Date: 12-2002
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/VE/VEAC006
Abstract: Although metagenomic sequencing has revealed high numbers of viruses in mosquitoes s led globally, our understanding of how their ersity and abundance varies in time and space as well as by host species and gender remains unclear. To address this, we collected 23,109 mosquitoes over the course of 12 months from a bat-dwelling cave and a nearby village in Yunnan province, China. These s les were organized by mosquito species, mosquito gender, and s ling time for meta-transcriptomic sequencing. A total of 162 eukaryotic virus species were identified, of which 101 were novel, including representatives of seventeen RNA virus multi-family supergroups and four species of DNA virus from the families Parvoviridae, Circoviridae, and Nu iridae. In addition, two known vector-borne viruses—Japanese encephalitis virus and Banna virus—were found. Analyses of the entire virome revealed strikingly different viral compositions and abundance levels in warmer compared to colder months, a strong host structure at the level of mosquito species, and no substantial differences between those viruses harbored by male and female mosquitoes. At the scale of in idual viruses, some were found to be ubiquitous throughout the year and across four mosquito species, while most of the other viruses were season and/or host specific. Collectively, this study reveals the ersity, dynamics, and evolution of the mosquito virome at a single location and sheds new lights on the ecology of these important vector animals.
Distinct Lineages of Feline Parvovirus Associated with Epizootic Outbreaks in Australia, New Zealand and the United Arab Emirates
Publisher: MDPI AG
Date: 13-12-2019
DOI: 10.3390/V11121155
Abstract: Feline panleukopenia (FPL), a frequently fatal disease of cats, is caused by feline parvovirus (FPV) or canine parvovirus (CPV). We investigated simultaneous outbreaks of FPL between 2014 and 2018 in Australia, New Zealand and the United Arab Emirates (UAE) where FPL outbreaks had not been reported for several decades. Case data from 989 cats and clinical s les from additional 113 cats were obtained to determine the cause of the outbreaks and epidemiological factors involved. Most cats with FPL were shelter-housed, 9 to 10 weeks old at diagnosis, unvaccinated, had not completed a primary vaccination series or had received vaccinations noncompliant with current guidelines. Analysis of parvoviral VP2 sequence data confirmed that all FPL cases were caused by FPV and not CPV. Phylogenetic analysis revealed that each of these outbreaks was caused by a distinct FPV, with two virus lineages present in eastern Australia and virus movement between different geographical locations. Viruses from the UAE outbreak formed a lineage of unknown origin. FPV vaccine virus was detected in the New Zealand cases, highlighting the difficulty of distinguishing the co-incidental shedding of vaccine virus in vaccinated cats. Inadequate vaccination coverage in shelter-housed cats was a common factor in all outbreaks, likely precipitating the multiple re-emergence of infection events.
Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?
Publisher: American Society for Microbiology
Date: 30-04-2019
Avian oncogenesis induced by lymphoproliferative disease virus: A neglected or emerging retroviral pathogen?
Publisher: Elsevier BV
Date: 02-2014
Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions
Publisher: Elsevier BV
Date: 09-2023
Disaster Preparedness in Hospitals in the Middle East: An Integrative Literature Review
Publisher: Cambridge University Press (CUP)
Date: 11-02-2019
DOI: 10.1017/DMP.2018.138
Abstract: Disasters occur rarely but have significant adverse consequences when they do. Recent statistics suggest that millions of lives and billions of US dollars have been lost in the last decade due to disaster events globally. It is crucial that hospitals are well prepared for disasters to minimize their effects. This integrative review study evaluates the preparedness level of hospitals in the Middle East for disasters using the Preferred Reporting Items for Systematic and Meta-Analyses (PRISMA) guidelines. The key terms include disaster preparedness OR disaster management OR emergency response AND Middle East AND hospitals . The study reviews articles published between January 2005 and December 2015, which focused on the hospitals’ preparedness for disasters in the Middle East nations. Based on their meeting 5 eligibility criteria, 19 articles were included in the review. Twelve of the articles focused on both natural and man-made disasters, whereas 6 of them were based on mass casualty events and 1 on earthquake. Thirteen of the reviewed articles ranked the level of preparedness of hospitals for disasters to be generally “very poor,” “poor,” or “moderate,” whereas 6 reported that hospitals were “well” or “very well prepared” for disasters. Factors affecting preparedness level were identified as a lack of contingency plans and insufficient availability of resources, among others. ( Disaster Med Public Health Preparedness . 2019 :806–816).
MicrobiologyThe Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution. By EdwardC.Holmes. Oxford and New York: Oxford University Press. $130.00 (hardcover); $60.
Publisher: University of Chicago Press
Date: 09-2010
DOI: 10.1086/655075
Sun protective behaviours during maximum exposure to ultraviolet radiation when undertaking outdoor activities: an integrated literature review
Publisher: Springer Science and Business Media LLC
Date: 19-06-2018
Red fox viromes in urban and rural landscapes
Publisher: Oxford University Press (OUP)
Date: 07-2020
DOI: 10.1093/VE/VEAA065
Abstract: The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human–wildlife interface.
Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates.
Publisher: Oxford University Press (OUP)
Date: 07-2020
DOI: 10.1093/VE/VEAA064
Abstract: The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently ided into four genera—Hepacivirus, Pegivirus, Pestivirus, and Flavivirus—each with a erse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co- ergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the ersity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species
Publisher: Public Library of Science (PLoS)
Date: 06-11-2014
Comment on Large-Scale Sequence Analysis of Avian Influenza Isolates
Publisher: American Association for the Advancement of Science (AAAS)
Date: 15-09-2006
Abstract: Obenauer et al . (Research Articles, 17 March 2006, p. 1576) reported that the influenza A virus PB1-F2 gene is evolving under strong positive selection, as documented by an extremely high ratio of the number of nonsynonymous nucleotide substitutions to the number of synonymous substitutions (dN/dS). However, we show that this observation is likely to be an artifact related to the location of PB1-F2 in the +1 reading frame of the PB1 gene.
Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy
Publisher: Microbiology Society
Date: 16-09-2009
Abstract: Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic ersity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic ersity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.
Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many
Publisher: Wiley
Date: 09-12-2014
DOI: 10.1111/MEC.12596
Bayesian Estimates of the Evolutionary Rate and Age of Hepatitis B Virus
Publisher: Springer Science and Business Media LLC
Date: 08-2007
DOI: 10.1007/S00239-007-0054-1
Abstract: Accurately estimating the evolutionary rate and age of hepatitis B virus (HBV) has proven to be one of the most difficult problems in studies of viral evolution. To help resolve these issues we employed a recently developed Bayesian coalescent approach to globally s led human and avian hepadnavirus genome sequences, accounting for lineage-specific rate variation, the presence of overlapping reading frames, and the potential impact of recombination. Our analysis revealed an unexpectedly high rate of evolutionary change--up to 10(-4) nucleotide substitutions (subs) per site per year and always more than approximately 10(-6) subs/site/year. These rates suggested a time to the most recent common ancestor (tMRCA) of the s led isolates of consistently less than approximately 1500 years ago for human HBV and less than 6000 years ago for the avian hepadnaviruses. Notably, the evolutionary rate of nonoverlapping regions of the viral genome was approximately 2-fold greater than that of overlapping genome regions, reflecting the complex patterns of selective constraint inherent in the former. We also reveal that most recombination events in both human and avian HBV tend to fall in a specific region of the viral genome, which contains all four viral open reading frames and which may therefore represent a "hot spot" for recombination. However, while recombination affects estimates of both evolutionary rate and tMRCA, in no case was this sufficient to challenge the hypothesis that the dominant mode of HBV evolution is by recent cross-species transmission. We conclude that HBV exhibits rapid evolutionary dynamics, typical of other viruses dependent on reverse transcriptase-mediated replication.
Evolution of Equine Influenza Virus in Vaccinated Horses
Publisher: American Society for Microbiology
Date: 15-04-2013
DOI: 10.1128/JVI.03379-12
Abstract: Influenza A viruses are characterized by their ability to evade host immunity, even in vaccinated in iduals. To determine how prior immunity shapes viral ersity in vivo , we studied the intra- and interhost evolution of equine influenza virus in vaccinated horses. Although the level and structure of genetic ersity were similar to those in naïve horses, intrahost bottlenecks may be more stringent in vaccinated animals, and mutations shared among horses often fall close to putative antigenic sites.
Australian perioperative nurses’ attitudes, levels of knowledge, education and support needs related to organ donation and procurement surgery: A national survey
Publisher: Australian College of Perioperative Nurses
Date: 06-2019
Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation
Publisher: The Royal Society
Date: 07-01-2013
Abstract: Influenza A viruses (IAVs) cause acute, highly transmissible infections in a wide range of animal species. Understanding how these viruses are transmitted within and between susceptible host populations is critical to the development of effective control strategies. While viral gene sequences have been used to make inferences about IAV transmission dynamics at the epidemiological scale, their utility in accurately determining patterns of inter-host transmission in the short-term—i.e. who infected whom—has not been strongly established. Herein, we use intra-host sequence data from the viral HA1 (hemagglutinin) gene domain from two transmission studies employing different IAV subtypes in their natural hosts—H3N8 in horses and H1N1 in pigs—to determine how well these data recapitulate the known pattern of inter-host transmission. Although no mutations were fixed over the course of either experimental transmission chain, we show that some minor, transient alleles can provide evidence of host-to-host transmission and, importantly, can be distinguished from those that cannot.
Diversity and evolution of the animal virome
Publisher: Springer Science and Business Media LLC
Date: 04-01-2022
DOI: 10.1038/S41579-021-00665-X
Abstract: The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their ersity than that of any other biological entity. Most documented animal viruses have been s led from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the ersity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic ersity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the ersity and evolution of the viruses they carry.
Critical review on biofilm methods
Publisher: Informa UK Limited
Date: 21-11-2016
Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates
Publisher: American Society for Microbiology
Date: 06-2011
DOI: 10.1128/JVI.00628-11
Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/VE/VEAC055
Abstract: The RNA virus phylum Lenarviricota is composed of the fungi-associated families Narnaviridae and Mitoviridae, the RNA bacteriophage Leviviridae, and the plant and fungi-associated Botourmiaviridae. Members of the Lenarviricota are abundant in most environments and boast remarkable phylogenetic and genomic ersity. As this phylum includes both RNA bacteriophage and fungi- and plant-associated species, the Lenarviricota likely mark a major evolutionary transition between those RNA viruses associated with prokaryotes and eukaryotes. Despite the remarkable expansion of this phylum following metagenomic studies, the phylogenetic relationships among the families within the Lenarviricota remain uncertain. Utilising a large data set of relevant viral sequences, we performed phylogenetic and genomic analyses to resolve the complex evolutionary history within this phylum and identify patterns in the evolution of virus genome organisation. Despite limitations reflecting very high levels of sequence ersity, our phylogenetic analyses suggest that the Leviviridae comprise the basal lineage within the Lenarviricota. Our phylogenetic results also support the construction of a new virus family—the Narliviridae—comprising a set of erse and phylogenetically distinct species, including a number of uniquely encapsidated viruses. We propose a taxonomic restructuring within the Lenarviricota to better reflect the phylogenetic relationships documented here, with the Botourmiaviridae and Narliviridae combined into the order Ourlivirales, the Narnaviridae remaining in the order Wolframvirales, and these orders combined into the single class, the Amabiliviricetes. In sum, this study provides insights into the complex evolutionary relationships among the erse families that make up the Lenarviricota.
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
Publisher: Springer Science and Business Media LLC
Date: 05-08-2012
DOI: 10.1038/NG.2369
Strong phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2022
DOI: 10.1101/2022.02.14.480463
Abstract: Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, age or season. While key features have been revealed for avian influenza A virus (AIV) in waterfowl of the Northern Hemisphere, the role of host phylogeny has received limited attention. Herein, we analysed 12339 oropharyngeal and cloacal swabs and 10826 serum s les collected over 11 years from wild birds in Australia. As well as describing species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in susceptibility. We confirm the role of age in AIV seroprevalence and viral prevalence. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño– Southern Oscillation. Taken together, our study provides new insights into evolutionary ecology of AIV in its avian hosts, defining distinctive processes on the continent of Australia and expanding our understanding of AIV globally.
Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae
Publisher: Cold Spring Harbor Laboratory
Date: 08-06-2020
DOI: 10.1101/2020.06.08.141184
Abstract: Our knowledge of the ersity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae in few RNA viruses have been documented to date. By combining meta-transcriptomic approaches with sequence and structural-based homology detection, followed by PCR confirmation, we identified 18 novel RNA viruses in two major groups of microbial algae – the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to those from the families Tombusviridae and Amalgaviridae that have previously been associated with plants, suggesting that these viruses have an evolutionary history that extends to when their host groups shared a common ancestor. In contrast, seven ulvophyte associated viruses exhibited clear similarity with the mitoviruses that are most commonly found in fungi. This is compatible with horizontal virus transfer between algae and fungi, although mitoviruses have recently been documented in plants. We also document, for the first time, RNA viruses in the chlorarachniophytes, including the first observation of a negative-sense (bunya-like) RNA virus in microalgae. The other virus-like sequence detected in chlorarachniophytes is distantly related to those from the plant virus family Virgaviridae , suggesting that they may have been inherited from the secondary chloroplast endosymbiosis event that marked the origin of the chlorarachniophytes. More broadly, this work suggests that the scarcity of RNA viruses in algae most likely results from limited investigation rather than their absence. Greater effort is needed to characterize the RNA viromes of unicellular eukaryotes, including through structure-based methods that are able to detect distant homologies, and with the inclusion of a wider range of eukaryotic microorganisms. RNA viruses are expected to infect all living organisms on Earth. Despite recent developments in and the deployment of large-scale sequencing technologies, our understanding of the RNA virosphere remains anthropocentric and largely restricted to human, livestock, cultivated plants and vectors for viral disease. However, a broader investigation of the ersity of RNA viruses, especially in protists, is expected to answer fundamental questions about their origin and long-term evolution. This study first investigates the RNA virus ersity in unicellular algae taxa from the phylogenetically distinct ulvophytes and chlorarachniophytes taxa. Despite very high levels of sequence ergence, we were able to identify 18 new RNA viruses, largely related to plant and fungi viruses, and likely illustrating a past history of horizontal transfer events that have occurred during RNA virus evolution. We also hypothesise that the sequence similarity between a chlorarachniophyte-associated virga-like virus and members of Virgaviridae associated with plants may represent inheritance from a secondary endosymbiosis event. A promising approach to detect the signals of distant virus homologies through the analysis of protein structures was also utilised, enabling us to identify potential highly ergent algal RNA viruses.
Reemergence and Autochthonous Transmission of Dengue Virus, Eastern China, 2014
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 09-2015
Level of Gene Expression Is a Major Determinant of Protein Evolution in the Viral Order Mononegavirales
Publisher: American Society for Microbiology
Date: 05-2012
DOI: 10.1128/JVI.06050-11
Abstract: Although the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a erse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3′-5′ stepwise attenuation of transcription in the Mononegavirales , a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13 Mononegavirales species. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions in Mononegavirales genomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.
Identifying the Risk of SARS-CoV-2 Infection and Environmental Monitoring in Airborne Infectious Isolation Rooms (AIIRs)
Publisher: Elsevier BV
Date: 28-09-2020
Extensive Diversity of RNA Viruses in Australian Ticks
Publisher: Cold Spring Harbor Laboratory
Date: 07-08-2018
DOI: 10.1101/386573
Abstract: Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi senso lato, are present in Australia. The ersity of bacteria infecting Australian ticks has been the subject of a number of studies using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including those that may have the potential to infect mammalian species. We used a meta-transcriptomics approach to reveal the viral ersity within Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel species of RNA virus belonging to 10 families, as well as one previously described RNA virus. The majority of these viruses clustered phylogenetically with arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian associated Hepacivirus and Pestivirus genera ( Flaviviridae ). Notably, another bandicoot tick yielded a novel Coltivirus ( Reoviridae ) – a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l.. in any tick s le, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a erse virome, including some viruses that merit additional screening in the context of emerging infectious disease. Each year a growing number of in iduals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi seno lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a erse set of families. Notably, three of these viruses were related to known mammalian viruses, including one that fell within the genus Coltivirus and related to the human pathogen, Colorado tick fever virus.
Novel Viral and Microbial Species in a Translocated Toutouwai (Petroica longipes) Population from Aotearoa/New Zealand
Publisher: Cold Spring Harbor Laboratory
Date: 13-07-2022
DOI: 10.1101/2022.07.13.499983
Abstract: Translocation is a common tool in wildlife management and been responsible for many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities (‘infectome’) and mitigate the long-term risks of reduced natural resistance. We used metatranscriptomic sequencing to characterise the infectome of 41 toutouwai (North Island robin, Petroica longipes ) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites. Although we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a ergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite. The presumably non-pathogenic viruses and microbial species identified here support the idea that the majority of microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.
Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses
Publisher: Elsevier BV
Date: 11-2022
DOI: 10.1016/J.VIROL.2022.09.002
Abstract: Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two s ling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal s les for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.
Viral Capsid, Antibody, and Receptor Interactions: Experimental Analysis of the Antibody Escape Evolution of Canine Parvovirus
Publisher: American Society for Microbiology
Date: 29-06-2023
DOI: 10.1128/JVI.00090-23
Abstract: Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system.
Evolutionary Processes among Sylvatic Dengue Type 2 Viruses
Publisher: American Society for Microbiology
Date: 09-2007
DOI: 10.1128/JVI.02776-06
Abstract: Sylvatic dengue viruses (DENV) are transmitted in an enzootic cycle between nonhuman primates and arboreal Aedes mosquitoes in Southeast Asia and West Africa. Although previous analyses have revealed the evolutionary processes among endemic (human) DENV, little is known about viral evolution in the sylvatic cycle. Through an analysis of 14 complete coding regions of sylvatic Dengue type 2 virus s led over a 33-year period, we show that both the rate of evolutionary change and the pattern of natural selection are similar among endemic and sylvatic DENV, although the latter have a uniquely high frequency of positive selection in the NS4B protein gene. Our findings support a recent cross-species transmission event and suggest the possibility of future DENV reemergence from the sylvatic cycle.
Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species
Publisher: American Society for Microbiology
Date: 15-04-2017
DOI: 10.1128/JVI.02381-16
Abstract: Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses s led in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within in idual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone. IMPORTANCE Determining the processes that shape virus genomes is central to understanding virus evolution and emergence. One question of particular importance is why nucleotide and dinucleotide frequencies differ so markedly between viruses. In particular, it is currently unclear whether host species or virus family has the biggest impact on dinucleotide frequencies and whether dinucleotide composition can be used to accurately predict host species. Using a comparative analysis, we show that dinucleotide composition has a strong phylogenetic association across different RNA virus families, such that dinucleotide composition can predict the family from which a virus sequence has been isolated. Conversely, dinucleotide composition has a poorer predictive power for the different host species within a virus family and across different virus families, indicating that the host has a relatively small impact on the dinucleotide composition of a virus genome.
Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia
Publisher: American Society for Microbiology
Date: 15-04-2019
DOI: 10.1128/JVI.01994-18
Abstract: The coevolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia, we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a breakdown in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple nonsynonymous and indel mutations. We suggest that this punctuated evolutionary event may reflect a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
Vaccine nationalism and the dynamics and control of SARS-CoV-2
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-09-2021
Abstract: A triumph that has emerged from the catastrophe of the severe acute respiratory syndrome coronavirus 2 pandemic has been the rapid development of several potent vaccines. However, 18 months into the pandemic and more than 6 months after vaccine approval, wealthy countries remain the major beneficiaries. Wagner et al . model the consequences of vaccine stockpiling in affluent countries on disease rates in lower- and middle-income countries and the consequences for the eruption of new variants that could jeopardize the early success of vaccines. For countries that can readily access vaccines, it would be better to share vaccines equitably to lower disease burdens in countries with less access, reduce the cost of having to be constantly vigilant for case imports, and minimize virus evolution. —CA
The causes and consequences of genetic variation in dengue virus
Publisher: Elsevier BV
Date: 02-2000
DOI: 10.1016/S0966-842X(99)01669-8
Abstract: Despite the fact that dengue is one of the most prevalent viral infections of humans, the mechanisms responsible for its pathogenesis remain uncertain. Evolutionary studies of dengue virus have revealed that its genetic ersity is increasing. This, coupled with evidence that viral strains could naturally differ in virulence, suggests that in the future we might be exposed to viruses with an expanded range of pathogenic properties.
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus
Publisher: Springer Science and Business Media LLC
Date: 26-10-2006
Abstract: The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance. We performed phylogenetic analyses of the recently obtained large and relatively unbiased s les of the HA sequences from 1995–2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements – the same amino acid substitution occurring independently in different lineages – were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals. We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains. Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Lee
Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine
Publisher: Public Library of Science (PLoS)
Date: 09-06-2011
The proximal origin of SARS-CoV-2
Publisher: Springer Science and Business Media LLC
Date: 17-03-2020
Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts
Publisher: Elsevier BV
Date: 08-2009
Intrapatient Escape in the A*0201-Restricted Epitope SLYNTVATL Drives Evolution of Human Immunodeficiency Virus Type 1 at the Population Level
Publisher: American Society for Microbiology
Date: 07-2005
DOI: 10.1128/JVI.79.14.9363-9366.2005
Abstract: The hypothesis that the intrapatient emergence of cytotoxic T-lymphocyte escape variants contributes to the evolution of human immunodeficiency virus type 1 at the population (interpatient) level was tested using the HLA-A*0201-restricted gag p17 epitope SLYNTVATL. Using a simple experimental design, we investigated the evolutionary processes operating within this epitope among patients while compensating for the confounding influence of intrapatient natural selection. Using this approach, we revealed a pattern of A*0201-driven escape within patients, followed by the sustained transmission of these escape variants among patients irrespective of their HLA type.
Causes of HIV diversity
Publisher: Springer Science and Business Media LLC
Date: 07-1995
DOI: 10.1038/376125A0
Abstract: Whether changes in vascular endothelial growth factor (VEGF) and annexin IV during implantation are regulated through the LH/hCG-R needs further research. To investigate the mechanism of hCG on the expression of annexin IV and VEGF in human endometrial cells. Endometrial cells were isolated and identified from human specimens. The proportion of glandular and epithelial cells was analyzed. Annexin IV and VEGF were analyzed by qRT-PCR (mRNA), western blot (proteins), and immunohistochemistry (proteins). Protein location was identified by immunohistochemistry. The cells were cultured with hCG, hCG/PD98059 (a MAPK inhibitor), or no treatment (control). The proportions between the glandular epithelial cells and stromal cells at inoculation and when adding hCG were 25.8 ± 0.2% and 27.8 ± 0.04%, respectively ( hCG could upregulate the mRNA and protein expression of annexin IV and VEGF. The upregulation of annexin IV by hCG could not be inhibited by PD98059, but the upregulation of VEGF by hCG could.
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Publisher: Springer Science and Business Media LLC
Date: 29-01-2021
Unbiased whole genome deep sequencing of Rotavirus Group A positive samples from rural Kenya, 2012-14 reveals high frequency of coinfection and genetic reassortment
Publisher: Elsevier BV
Date: 08-2018
Human land use impacts viral diversity and abundance in a New Zealand river
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/VE/VEAC032
Abstract: Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral ersity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the ersity and abundance of viruses at s ling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly ergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates—most likely fish and water birds—from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher ersity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river s ling sites in farming and urban areas that were not present at the native forest sites. Although based on a small s le size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.
Transcriptome mining extends the host range of theFlaviviridaeto non-bilaterians
Publisher: Cold Spring Harbor Laboratory
Date: 24-11-2022
DOI: 10.1101/2022.11.24.517790
Abstract: The Flaviviridae are a family of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the time-scale of flaviviral evolution is uncertain. An ancient origin, spanning time-scales of millions of years, is supported by their presence in both vertebrates and invertebrates and the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome ( Craspedacusta Sowerby , phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirus sequences have been identified in these hosts. To help resolve the antiquity of the Flavivirdae we mined publicly available transcriptome data across the Metazoa. From this, we expanded the ersity within the family through the identification of 32 novel viral sequences, and extended the host range of the pestiviruses to include hibians, reptiles, and ray-finned fish. Through cophylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flaviviral genera (median, 68%), including a cross-species transmission event between bats and rodents, although long-term virus-host co- ergence was still a regular occurrence (median, 23%). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group that include a variety of invertebrate and vertebrate viruses. Combined, these data attest an ancient origin of the flaviviruses, close to the emergence of the metazoans 750–800 million years ago.
Ancient invasion of an extinct gammaretrovirus in cetaceans
Publisher: Elsevier BV
Date: 06-2013
DOI: 10.1016/J.VIROL.2013.03.006
Abstract: Endogenous gammaretroviruses (EGVs) have been widely studied in terrestrial mammals but seldom so in marine species. A genomic mining of the bottlenose dolphin (Tursiops truncatus) genome revealed a new EGV, termed Tursiops truncatus endogenous retrovirus (TTEV), which is ergent from extant mammalian EGVs. Molecular clock dating estimated the invasion time of TTEV into the host genome to be approximately 10-19 million years ago (MYA), while a previously identified killer whale endogenous gammaretrovirus (KWERV) was estimated to have invaded the host genome approximately 3-5 MYA. Using a PCR-based technique, we then verified that similar endogenous viruses exist in nine cetacean genomes. Phylogenetic analysis revealed that these cetacean EGVs are highly ergent from their counterparts in other mammals, including KWERV from the killer whale. In sum, we conclude that there have been at least two invasion episodes of EGVs into cetaceans during their evolutionary history.
Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats
Publisher: MDPI AG
Date: 12-11-2020
DOI: 10.3390/V12111301
Abstract: Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal s les, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.
Evolution and Phylogeography of the Nonpathogenic Calicivirus RCV-A1 in Wild Rabbits in Australia
Publisher: American Society for Microbiology
Date: 12-2010
DOI: 10.1128/JVI.00777-10
Abstract: Despite its potential importance for the biological control of European rabbits, relatively little is known about the evolution and molecular epidemiology of rabbit calicivirus Australia 1 (RCV-A1). To address this issue we undertook an extensive evolutionary analysis of 36 RCV-A1 s les collected from wild rabbit populations in southeast Australia between 2007 and 2009. Based on phylogenetic analysis of the entire capsid sequence, six clades of RCV-A1 were defined, each exhibiting strong population sub ision. Strikingly, our estimates of the time to the most recent common ancestor of RCV-A1 coincide with the introduction of rabbits to Australia in the mid-19th century. Subsequent ergence events visible in the RCV-A1 phylogenies likely reflect key moments in the history of the European rabbit in Australia, most notably the bottlenecks in rabbit populations induced by the two viral biocontrol agents used on the Australian continent, myxoma virus and rabbit hemorrhagic disease virus (RHDV). RCV-A1 strains therefore exhibit strong phylogeographic separation and may constitute a useful tool to study recent host population dynamics and migration patterns, which in turn could be used to monitor rabbit control in Australia.
Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission
Publisher: Public Library of Science (PLoS)
Date: 02-06-2011
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis
Publisher: Springer Science and Business Media LLC
Date: 02-2002
DOI: 10.1007/S00239-001-0064-3
Abstract: The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic ergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic ergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed.
Virological factors that increase the transmissibility of emerging human viruses
Publisher: Proceedings of the National Academy of Sciences
Date: 21-03-2016
Abstract: With changes in land use and increased urbanization, the frequency with which pathogens jump species barriers to emerge in new hosts is expected to rise. Knowing which viruses may be more likely to become transmissible among humans, as opposed to only generating dead-end spillover infections, would be of considerable benefit to pandemic planning. Using multivariate modeling and multimodel inference, we sought to both identify and quantify those biological features of viruses that best determine interhuman transmissibility. This analysis revealed that chronic, nonsegmented, non–vector-borne, nonenveloped viruses with low host mortality had the highest likelihood of being transmissible among humans whereas genomic features had little predictive power. Our analysis therefore reveals that multiple virological features determine the likelihood of successful emergence.
The Epidemic Behavior of the Hepatitis C Virus
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-06-2001
Abstract: Hepatitis C virus (HCV) is a leading worldwide cause of liver disease. Here, we use a new model of HCV spread to investigate the epidemic behavior of the virus and to estimate its basic reproductive number from gene sequence data. We find significant differences in epidemic behavior among HCV subtypes and suggest that these differences are largely the result of subtype-specific transmission patterns. Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease.
Complete sequence of two tick-borne flaviviruses isolated from Siberia and the UK: analysis and significance of the 5′ and 3′-UTRs
Publisher: Elsevier BV
Date: 05-1997
DOI: 10.1016/S0168-1702(97)01451-2
Abstract: The complete nucleotide sequence of two tick-transmitted flaviviruses, Vasilchenko (Vs) from Siberia and louping ill (LI) from the UK, have been determined. The genomes were respectively, 10928 and 10871 nucleotides (nt) in length. The coding strategy and functional protein sequence motifs of tick-borne flaviviruses are presented in both Vs and LI viruses. The phylogenies based on maximum likelihood, maximum parsimony and distance analysis of the polyproteins, identified Vs virus as a member of the tick-borne encephalitis virus subgroup within the tick-borne serocomplex, genus Flavivirus, family Flaviviridae. Comparative alignment of the 3'-untranslated regions revealed deletions of different lengths essentially at the same position downstream of the stop codon for all tick-borne viruses. Two direct 27 nucleotide repeats at the 3'-end were found only for Vs and LI virus. Immediately following the deletions a region of 332-334 nt with relatively conserved primary structure (67-94% identity) was observed at the 3'-non-coding end of the virus genome. Pairwise comparisons of the nucleotide sequence data revealed similar levels of variation between the coding region, and the 5' and 3'-termini of the genome, implying an equivalent strong selective control for translated and untranslated regions. Indeed the predicted folding of the 5' and 3'-untranslated regions revealed patterns of stem and loop structures conserved for all tick-borne flaviviruses suggesting a purifying selection for preservation of essential RNA secondary structures which could be involved in translational control and replication. The possible implications of these findings are discussed.
The performance of the date-randomization test in phylogenetic analyses of time-structured virus data
Publisher: Oxford University Press (OUP)
Date: 13-03-2015
Abstract: Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the s ling times of the viral sequences. However, the spread of these s ling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the s ling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct s ling times should not overlap with those obtained with randomized s ling times. We also investigated the behavior of the test when the s ling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.
Extensive Diversity of RNA Viruses in Australian Ticks
Publisher: American Society for Microbiology
Date: 02-2019
DOI: 10.1128/JVI.01358-18
Abstract: Each year a growing number of in iduals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia b urgdorferi sensu lato , in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a erse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.
Phylogenetic Evidence for Deleterious Mutation Load in RNA Viruses and Its Contribution to Viral Evolution
Publisher: Oxford University Press (OUP)
Date: 11-01-2007
Abstract: Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our understanding of viral emergence, immune evasion, and drug resistance. Here we develop a phylogenetic method, based on the distribution of nonsynonymous and synonymous changes, to assess the relative fitness of polymorphisms in the structural genes of 143 RNA viruses. This reveals that a substantial proportion of the amino acid variation observed in natural populations of RNA viruses comprises transient deleterious mutations that are later purged by purifying selection, potentially limiting virus adaptability. We also demonstrate, for the first time, the existence of a relationship between amino acid variability and the phylogenetic distribution of polymorphisms. From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses.
Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods
Publisher: Oxford University Press (OUP)
Date: 13-07-2016
DOI: 10.1093/BIOINFORMATICS/BTW421
Abstract: Motivation: In rapidly evolving pathogens, including viruses and some bacteria, genetic change can accumulate over short time-frames. Accordingly, their s ling times can be used to calibrate molecular clocks, allowing estimation of evolutionary rates. Methods for estimating rates from time-structured data vary in how they treat phylogenetic uncertainty and rate variation among lineages. We compiled 81 virus data sets and estimated nucleotide substitution rates using root-to-tip regression, least-squares dating and Bayesian inference. Results: Although estimates from these three methods were often congruent, this largely relied on the choice of clock model. In particular, relaxed-clock models tended to produce higher rate estimates than methods that assume constant rates. Discrepancies in rate estimates were also associated with high among-lineage rate variation, and phylogenetic and temporal clustering. These results provide insights into the factors that affect the reliability of rate estimates from time-structured sequence data, emphasizing the importance of clock-model testing. Contact: sduchene@unimelb.edu.au or garzonsebastian@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents
Publisher: Public Library of Science (PLoS)
Date: 07-02-2013
Sequence Analysis of In Vivo Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus
Publisher: American Society for Microbiology
Date: 15-07-2013
DOI: 10.1128/JVI.00240-13
Abstract: Influenza virus defective interfering (DI) particles are naturally occurring noninfectious virions typically generated during in vitro serial passages in cell culture of the virus at a high multiplicity of infection. DI particles are recognized for the role they play in inhibiting viral replication and for the impact they have on the production of infectious virions. To date, influenza virus DI particles have been reported primarily as a phenomenon of cell culture and in experimentally infected embryonated chicken eggs. They have also been isolated from a respiratory infection of chickens. Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. The distribution of these in vivo -derived DI-like RNAs was similar to that of in vitro DIs, with the majority of the defective RNAs generated from the PB2 (segment 1) of the polymerase complex, followed by PB1 and PA. The lengths of the in vivo -derived DI-like segments also are similar to those of known in vitro DIs, and the in vivo -derived DI-like segments share internal deletions of the same segments. The presence of identical DI-like RNAs in patients linked by direct contact is compatible with transmission between them. The functional role of DI-like RNAs in natural infections remains to be established.
A Genomic Perspective on the Origin and Emergence of SARS-CoV-2
Publisher: Elsevier BV
Date: 04-2020
Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association
Publisher: MDPI AG
Date: 18-09-2020
DOI: 10.3390/V12091042
Abstract: Influenza viruses (family Orthomyxoviridae) infect a variety of vertebrates, including birds, humans, and other mammals. Recent metatranscriptomic studies have uncovered ergent influenza viruses in hibians, fish and jawless vertebrates, suggesting that these viruses may be widely distributed. We sought to identify additional vertebrate influenza-like viruses through the analysis of publicly available RNA sequencing data. Accordingly, by data mining, we identified the complete coding segments of five ergent vertebrate influenza-like viruses. Three fell as sister lineages to influenza B virus: salamander influenza-like virus in Mexican walking fish (Ambystoma mexicanum) and plateau tiger salamander (Ambystoma velasci), Siamese algae-eater influenza-like virus in Siamese algae-eater fish (Gyrinocheilus aymonieri) and chum salmon influenza-like virus in chum salmon (Oncorhynchus keta). Similarly, we identified two influenza-like viruses of hibians that fell as sister lineages to influenza D virus: cane toad influenza-like virus and the ornate chorus frog influenza-like virus, in the cane toad (Rhinella marina) and ornate chorus frog (Microhyla fissipes), respectively. Despite their ergent phylogenetic positions, these viruses retained segment conservation and splicing consistent with transcriptional regulation in influenza B and influenza D viruses, and were detected in respiratory tissues. These data suggest that influenza viruses have been associated with vertebrates for their entire evolutionary history.
Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States
Publisher: American Society for Microbiology
Date: 15-08-2018
DOI: 10.1128/JVI.00323-18
Abstract: The relatively recent appearance of influenza A virus (IAV) epidemics in dogs expands our understanding of IAV host range and ecology, providing useful and relevant models for understanding critical factors involved in viral emergence. Here we integrate viral whole-genome sequence analysis and comprehensive surveillance data to examine the evolution of the emerging avian-origin H3N2 canine influenza virus (CIV), particularly the factors driving ongoing circulation and recent increases in incidence of the virus within the United States. Our results provide a detailed understanding of how H3N2 CIV achieves sustained circulation within the United States despite widespread host contact heterogeneity and recurrent epidemic fade-out. Moreover, our findings suggest that the types and intensities of selection pressures an emerging virus experiences are highly dependent on host population structure and ecology and may inhibit an emerging virus from acquiring sustained epidemic or pandemic circulation.
A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners
Publisher: Informa UK Limited
Date: 2021
Evolutionary Virology at 40
Publisher: Oxford University Press (OUP)
Date: 12-2018
DOI: 10.1534/GENETICS.118.301556
Abstract: Geoghegan and Holmes describe the history of evolutionary ideas in the study of viruses, showing that two different approaches to studying virus evolution—the comparative and the experimental—were both established in seminal papers published in the late... RNA viruses are erse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus–host transmission, but is orced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
We shouldn’t worry when a virus mutates during disease outbreaks
Publisher: Springer Science and Business Media LLC
Date: 18-02-2020
Diversity and Origin of Dengue Virus Serotypes 1, 2, and 3, Bhutan
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 10-2009
Adaptation and Immunity
Publisher: Public Library of Science (PLoS)
Date: 14-09-2004
Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom
Publisher: Microbiology Society
Date: 06-2021
DOI: 10.1099/JGV.0.001595
Abstract: In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on in iduals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected in idual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV-2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea – also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger s le of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.
Safety, risk, and aggression: Health professionals’ experiences of caring for people affected by methamphetamine when presenting for emergency care
Publisher: Wiley
Date: 27-09-2017
DOI: 10.1111/INM.12345
Abstract: The crystalline form of meth hetamine, commonly known as crystal meth (crystal meth hetamine) or ICE, is a highly-addictive and powerful stimulant. Users of crystal meth often require emergency care, and are associated with a substantial burden of care by emergency care providers. The aim of the present qualitative study was to explore health professionals' experiences of providing care for patients affected by ICE who presented to the emergency department (ED). Nine semistructured interviews were conducted. The major theme, 'staying safe', was revealed, in which participants described their experiences of being exposed to potentially unsafe situations, and their responses to challenging behaviours, including aggression. The findings highlight the need for ED staff to understand the nature of ICE use and its adverse impact on the mental and physical health of users. Furthermore, it is clear that establishing and maintaining safety in the emergency care setting is of utmost importance, and should be a priority for health-care managers.
Different Evolutionary Trajectories of European Avian-Like and Classical Swine H1N1 Influenza A Viruses
Publisher: American Society for Microbiology
Date: 06-2009
DOI: 10.1128/JVI.02565-08
Abstract: In 1979, a lineage of avian-like H1N1 influenza A viruses emerged in European swine populations independently from the classical swine H1N1 virus lineage that had circulated in pigs since the Spanish influenza pandemic of 1918. To determine whether these two distinct lineages of swine-adapted A/H1N1 viruses evolved from avian-like A/H1N1 ancestors in similar ways, as might be expected given their common host species and origin, we compared patterns of nucleotide and amino acid change in whole genome sequences of both groups. An analysis of nucleotide compositional bias across all eight genomic segments for the two swine lineages showed a clear lineage-specific bias, although a segment-specific effect was also apparent. As such, there appears to be only a relatively weak host-specific selection pressure. Strikingly, despite each lineage evolving in the same species of host for decades, amino acid analysis revealed little evidence of either parallel or convergent changes. These findings suggest that although adaptation due to evolutionary lineages can be distinguished, there are functional and structural constraints on all gene segments and that the evolutionary trajectory of each lineage of swine A/H1N1 virus has a strong historical contingency. Thus, in the context of emergence of an influenza A virus strain via a host switch event, it is difficult to predict what specific polygenic changes are needed for mammalian adaptation.
Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus
Publisher: American Society for Microbiology
Date: 15-01-2008
DOI: 10.1128/JVI.01929-07
Abstract: Geminiviruses are devastating viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiviruses. We report here the evolutionary rate of the tomato yellow leaf curl disease-causing viruses, an intensively studied group of monopartite begomoviruses. Sequences from GenBank, isolated from diseased plants between 1988 and 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 × 10 −4 nucleotide substitutions per site per year (subs/site/year), although this rate could be confounded by frequent recombination within Tomato yellow leaf curl virus genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 × 10 −4 subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of ∼1.56 × 10 −3 subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA viruses and RNA viruses. Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
On being the right size
Publisher: Springer Science and Business Media LLC
Date: 09-2005
DOI: 10.1038/NG0905-923
Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metagenomic next-generation sequencing
Publisher: Cold Spring Harbor Laboratory
Date: 10-05-2021
DOI: 10.1101/2021.05.10.443367
Abstract: Encephalitis is most often caused by a variety of infectious agents, the identity of which is commonly determined through diagnostic tests utilising cerebrospinal fluid (CSF). Immune-mediated disorders are also a differential in encephalitis cases. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic next-generation sequencing of residual clinical s les of multiple tissue types and independent clinical review. A total of 43 specimens, from both sterile and non-sterile sites, were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. S les were subjected to total RNA sequencing to determine the presence and abundance of potential pathogens, to reveal mixed infections, pathogen genotypes, and epidemiological origins, and to describe the possible aetiologies of unexplained encephalitis. From this, we identified five RNA and two DNA viruses associated with human infection from both non-sterile (nasopharyngeal aspirates, nose/throat swabs, urine, stool rectal swab) and sterile (cerebrospinal fluid, blood) sites. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. With the exception of picobirnavirus all have been previously associated with respiratory disease. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases reported here. Immune-mediated encephalitis was considered clinically likely in six cases and RNA sequencing did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasises the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that the routine inclusion of non-CNS s ling in encephalitis clinical guidelines rotocols could improve the diagnostic yield. Encephalitis is caused by both infectious agents and auto-immune disorders. However, the aetiological agents, including viruses, remain unknown in around half the cases of encephalitis in many cohorts. Importantly, diagnostic tests are usually based on the analysis of cerebrospinal fluid which may limit their utility. We used a combination of meta-transcriptomic sequencing and independent clinical review to identify the potential causative pathogens in cases of unexplained childhood encephalitis. Accordingly, we identified seven viruses associated with both sterile and non-sterile s ling sites. Human rhinovirus and seasonal coronaviruses were considered as most likely responsible for five of the 18 encephalitis cases studied, while immune-mediated encephalitis was considered the cause in six cases, and we were unable to determine the aetiology in nine cases. Overall, we demonstrate the role of respiratory viruses as a cause of unexplained encephalitis and that s ling sites other than cerebrospinal fluid is of diagnostic value.
Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
Publisher: Microbiology Society
Date: 10-2003
Abstract: Recombination is increasingly seen as an important means of shaping genetic ersity in RNA viruses. However, observed recombination frequencies vary widely among those viruses studied to date, with only sporadic occurrences reported in RNA viruses with negative-sense genomes. To determine the extent of homologous recombination in negative-sense RNA viruses, phylogenetic analyses of 79 gene sequence alignments from 35 negative-sense RNA viruses (a total of 2154 sequences) were carried out. Powerful evidence was found for recombination, in the form of incongruent phylogenetic trees between different gene regions, in only five sequences from Hantaan virus , Mumps virus and Newcastle disease virus . This is the first report of recombination in these viruses. More tentative evidence for recombination, where conflicting phylogenetic trees were observed (but were without strong bootstrap support) and/or where putative recombinant regions were very short, was found in three alignments from La Crosse virus and Puumala virus . Finally, patterns of sequence variation compatible with the action of recombination, but not definitive evidence for this process, were observed in a further ten viruses: Canine distemper virus , Crimean-Congo haemorrhagic fever virus , Influenza A virus , Influenza B virus , Influenza C virus , Lassa virus , Pirital virus , Rabies virus , Rift Valley Fever virus and Vesicular stomatitis virus . The possibility of recombination in these viruses should be investigated further. Overall, this study reveals that rates of homologous recombination in negative-sense RNA viruses are very much lower than those of mutation, with many viruses seemingly clonal on current data. Consequently, recombination rate is unlikely to be a trait that is set by natural selection to create advantageous or purge deleterious mutations.
Long-Term Transmission of Defective RNA Viruses in Humans and Aedes Mosquitoes
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-01-2006
Abstract: In 2001, dengue virus type 1 (DENV-1) populations in humans and mosquitoes from Myanmar acquired a stop-codon mutation in the surface envelope (E) protein gene. Within a year, this stop-codon strain had spread to all in iduals s led. The presence of truncated E protein species within in idual viral populations, along with a general relaxation in selective constraint, indicated that the stop-codon strain represents a defective lineage of DENV-1. We propose that such long-term transmission of defective RNA viruses in nature was achieved through complementation by coinfection of host cells with functional viruses.
Emergence of the Asian 1 Genotype of Dengue Virus Serotype 2 in Viet Nam: In Vivo Fitness Advantage and Lineage Replacement in South-East Asia
Publisher: Public Library of Science (PLoS)
Date: 20-07-2010
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
Publisher: Public Library of Science (PLoS)
Date: 08-02-2017
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis
Publisher: Springer Science and Business Media LLC
Date: 19-01-2023
DOI: 10.1038/S42003-022-04394-6
Abstract: Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis , regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences s led globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis -wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust ergence dates from populations s led over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.
Dengue viruses cluster antigenically but not as discrete serotypes
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-09-2015
Abstract: Along with their mosquito vectors, dengue viruses are spreading worldwide to infect millions of people. For a few, subsequent infection results in lethal hemorrhagic disease. Katzelnick et al. used antibody-binding data to map structural ergence and antigenic variation among dengue viruses. Comparing results in monkeys and humans, the viruses approximately clustered into the four known groups. However, the four virus groups showed as much antigenic distance within a group as between groups. This finding helps explain why immune responses to dengue are highly variable, and it has complex implications for epidemiology, disease, and vaccine deployment. Science , this issue p. 1338
Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells
Publisher: Public Library of Science (PLoS)
Date: 21-02-2013
Current challenges to virus discovery by metatranscriptomics
Publisher: Elsevier BV
Date: 12-2021
DOI: 10.1016/J.COVIRO.2021.09.007
Abstract: Meta-transcriptomic next-generation sequencing has transformed virus discovery, dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of meta-transcriptomics for virus discovery faces important challenges. As this technology becomes more widely adopted, the proportion of viral sequences in public databases with incorrect (e.g. mis-assignment of host) or limited information (e.g. lacking taxonomic classification) is likely to grow, limiting their utility in bioinformatic pipelines for virus discovery. In addition, we currently lack the bioinformatic tools that can accurately identify viruses showing little or no sequence similarity to database viruses or those that represent likely reagent contaminants. Herein, we outline some of the challenges to effective meta-transcriptomic virus discovery as well as their potential solutions.
Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy
Publisher: MDPI AG
Date: 29-04-2021
DOI: 10.3390/V13050794
Abstract: Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences s led in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.
A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences
Publisher: Oxford University Press (OUP)
Date: 07-08-2018
Rewriting stories of trauma through peer‐to‐peer mentoring for and by at‐risk young people
Publisher: Wiley
Date: 02-2019
DOI: 10.1111/INM.12579
Abstract: Adverse childhood experiences are strongly associated with the development of mental health disorders during the life span. When mental health issues are not effectively dealt with during the adolescent period, young people can become long-term consumers in the mental health system. A widely accepted method of intervention is the provision of mentoring. More recently, young people have been fulfilling the role of mentor to their peers and mentoring has played a large role in supporting young people who are considered at-risk of not achieving the expected psychosocial, educational, and/or developmental goals. What is not known is why young people, previously identified as being at-risk, are motivated to mentor their at-risk peers. The study aim was to examine what motivates previously recognized at-risk young people to provide mentoring to their at-risk peers. Participants were twelve previously recognized at-risk young people recruited through a formal peer-to-peer mentoring programme. Semi-structured interviews were conducted, and the data analysed through narrative inquiry and reported in accordance with the consolidated criteria for reporting qualitative research guidelines (COREQ). Results indicate that young people are motivated by their own lived experiences of trauma(s) to provide at-risk peer mentoring. The experience of mentoring afforded opportunities to rewrite in idual personal journeys of trauma through mentoring their at-risk peers, thus constructing a more positive self-identity. Outcomes of developing positive peer relationships and prosocial behaviours could significantly assist mental health clinicians in providing more acceptable care to clients in an age group known to be reluctant to accept traditional mental health intervention.
Identification of bovine coronavirus in a Daurian ground squirrel expands the host range of Betacoronavirus 1
Publisher: Elsevier BV
Date: 04-2023
Sustained RNA virome diversity in Antarctic penguins and their ticks
Publisher: Springer Science and Business Media LLC
Date: 14-04-2020
DOI: 10.1038/S41396-020-0643-1
Abstract: Despite its isolation and extreme climate, Antarctica is home to erse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome ersity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial ersity we determined the RNA viromes of three species of penguins and their ticks s led on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses ( n = 13), penguin diet and microbiome associated viruses ( n = 82), and tick viruses ( n = 8), two of which may have the potential to infect penguins. Notably, the level of virome ersity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.
The limits of molecular phylogeny: the case of the genus Flavivirus and the family Flaviviridae
Publisher: Sociedade Brasileira de Virologia
Date: 04-1996
Virological Sampling of Inaccessible Wildlife with Drones
Publisher: MDPI AG
Date: 30-05-2018
DOI: 10.20944/PREPRINTS201805.0184.V2
Abstract: There is growing interest in characterizing the viromes of erse mammalian species, particularly in the context of disease emergence. However, little is known about virome ersity in aquatic mammals, in part due to difficulties in s ling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome ersity a meta-transcriptomic analysis was performed on 19 pooled whale blow s les collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to s le viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, ersity, and evolution.
Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses
Publisher: Microbiology Society
Date: 09-2008
DOI: 10.1099/VIR.0.2008/002055-0
Abstract: Canine parvovirus (CPV), first recognized as an emerging virus of dogs in 1978, resulted from a successful cross-species transmission. CPV emerged from the endemic feline panleukopenia virus (FPV), or from a closely related parvovirus of another host. Here we refine our current understanding of the evolution and population dynamics of FPV and CPV. By analysing nearly full-length viral sequences we show that the majority of substitutions distinguishing CPV from FPV are located in the capsid protein gene, and that this gene is under positive selection in CPV, resulting in a significantly elevated rate of molecular evolution. This provides strong phylogenetic evidence for a prominent role of the viral capsid in host adaptation. In addition, an analysis of the population dynamics of more recent CPV reveals, on a global scale, a strongly spatially sub ided CPV population with little viral movement among countries and a relatively constant population size. Such limited viral migration contrasts with the global spread of the virus observed during the early phase of the CPV pandemic, but corresponds to the more endemic nature of current CPV infections.
Virological Sampling of Inaccessible Wildlife with Drones
Publisher: MDPI AG
Date: 14-05-2018
DOI: 10.20944/PREPRINTS201805.0184.V1
Abstract: There is growing interest in characterizing the viromes of erse mammalian species, particularly in the context of disease emergence. However, little is known about virome ersity in aquatic mammals, in part due to difficulties in s ling. We characterized the respiratory virome of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome ersity a meta-transcriptomic analysis was performed on 19 pooled whale blow s les collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. Despite the relatively small number of animals surveyed, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, ersity, and evolution.
Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor
Publisher: American Society for Microbiology
Date: 15-04-2014
DOI: 10.1128/JVI.03181-13
Abstract: Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low-pathogenic (LPAI) progenitor viruses currently is poorly understood. To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages. Notably, an ultradeep-sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several in idual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI. The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high- and low-pathogenicity viruses undertaken to date and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties. IMPORTANCE The Italian H7 AI epidemic of 1999 to 2001 was one of the most important AI outbreaks described in Europe. H7 viruses have the ability to evolve into HP forms from LP precursors, although the mechanisms underlying this evolutionary transition are only poorly understood. We combined epidemiological information, whole-genome sequence data, and ultradeep sequencing approaches to provide the most complete characterization of the evolution of HPAI from LPAI viruses undertaken to date. Our analysis revealed that the LPAI viruses were the direct ancestors of the HPAI strains and identified low-frequency minority variants with HPAI mutations that were present in the LPAI s les. Spatial analysis provided key information for the design of effective control strategies for AI at both local and global scales. Overall, this work highlights the importance of implementing rapid eradication measures to prevent the emergence of novel influenza viruses with severe pathogenic properties.
Hitchhiking and the Population Genetic Structure of Avian Influenza Virus
Publisher: Springer Science and Business Media LLC
Date: 30-12-2009
Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic
Publisher: American Society for Microbiology
Date: 10-2011
DOI: 10.1128/JVI.05262-11
Abstract: That pigs may play a pivotal role in the emergence of pandemic influenza was indicated by the recent H1N1/2009 human pandemic, likely caused by a reassortant between viruses of the American triple-reassortant (TR) and Eurasian avian-like (EA) swine influenza lineages. As China has the largest human and pig populations in the world and is the only place where both TR and EA viruses have been reported to cocirculate, it is potentially the source of the H1N1/2009 pandemic virus. To examine this, the genome sequences of 405 swine influenza viruses from China were analyzed. Thirty-six TR and EA reassortant viruses were identified before and after the occurrence of the pandemic. Several of these TR-EA reassortant viruses had genotypes with most segments having the same lineage origin as the segments of the H1N1/2009 pandemic virus. However, these viruses were generated from independent reassortment events throughout our survey period and were not associated with the current pandemic. One TR-EA reassortant, which is least similar to the pandemic virus, has persisted since 2007, while all the other variants appear to be transient. Despite frequent reassortment events between TR and EA lineage viruses in China, evidence for the genesis of the 2009 pandemic virus in pigs in this region is still absent.
Phylogenetic Relationships and Differential Selection Pressures among Genotypes of Dengue-2 Virus
Publisher: Elsevier BV
Date: 06-2002
Abstract: To elucidate the processes controlling the emergence and spread of dengue-2 virus (DEN-2) we examined the evolution of viral isolates s led from both local (Viet Nam) and global populations. Our phylogenetic analysis, incorporating envelope (E) glycoprotein sequences from 147 isolates of DEN-2, provided a more complete picture of viral ersity, with a newly defined "Cosmopolitan" genotype having a near global distribution and two other genotypes restricted to Asia. By analyzing rates of synonymous and nonsynonymous substitution we determined that genotypes have experienced different selection pressures, with some evidence of positive selection in the Cosmopolitan genotype and one of the two Asian genotypes, but that the transition from sylvatic to human transmission was not accompanied by adaptive evolution of the E gene. Although there was no association between selection pressures acting on the E gene and proposed virulence differences among genotypes, some putatively selected amino acid sites have previously been implicated in changing viral pathogenicity, most notably E-390, and may also affect transmittability. These findings have implications for the future spread of DEN-2.
RNA virus genomics: a world of possibilities
Publisher: American Society for Clinical Investigation
Date: 09-2009
DOI: 10.1172/JCI38050
Cyclic Avian Mass Mortality in the Northeastern United States Is Associated with a Novel Orthomyxovirus
Publisher: American Society for Microbiology
Date: 15-01-2015
DOI: 10.1128/JVI.02019-14
Abstract: Since 1998, cyclic mortality events in common eiders ( Somateria mollissima ), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, MA, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here, we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the Quaranjavirus genus within the family Orthomyxoviridae . Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein that was demonstrated to have fusion activity this also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to Quaranfil virus and Johnston Atoll virus , the original members of the Quaranjavirus genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined. IMPORTANCE The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For ex le, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here, we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.
Genetic characterization of tick-borne flaviviruses: New insights into evolution, pathogenetic determinants and taxonomy
Publisher: Elsevier BV
Date: 04-2007
DOI: 10.1016/J.VIROL.2006.09.015
Abstract: Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages.
Nurse‐led postdischarge telephone follow‐up calls: A mixed study systematic review
Publisher: Wiley
Date: 21-06-2019
DOI: 10.1111/JOCN.14951
Abstract: To explore the quantitative and qualitative literature on the impact of nurse-led postdischarge telephone follow-up (TFU) call interventions on patient outcomes. Adverse patient outcomes such as postdischarge problems, premature contact with health systems, inability to self-manage conditions and hospital readmissions all have an impact on the health and well-being, and satisfaction of patients as well as a financial impact on healthcare systems. A mixed-study systematic review. A systematic search of CINAHL, Ebsco, PubMed, Quest and Cinch-Health databases was undertaken using the key terms "nurs*," "nurse-led," "nurse initiated," "discharge," "hospital," "telephone," "follow-up" and "telephone follow-up" to identify relevant original peer-reviewed studies published between 2010-2016. Ten articles were selected for inclusion. The selected papers were critically appraised. A sequential explanatory approach with a convergent synthesis was used to report findings following PRISMA guidelines. The findings demonstrate that nurse-led TFU interventions have the potential to improve patient outcomes. The studies suggest patient satisfaction with TFU is one of the strongest positive outcomes from the interventions. However, the results do not support improvement in patient readmission or mortality. Of the 10 studies reviewed, only two were methodologically strong limiting the conclusions that can be drawn from the current research on this topic. Telephone follow-up interventions improve patient satisfaction and have the potential to meet patient information and communication needs, improve self-management and follow-up appointment attendance and reduce postdischarge problems. Further research is required to explore patients' perceptions of the most useful content of TFU calls, the efficacy of TFU calls and nurses' perceptions and experiences of conducting TFU interventions. When conducted by a nurse, these interventions have the potential to enhance postdischarge care to patients and meet care needs. Patients perceive TFU as acceptable and are satisfied with this form of postdischarge care.
PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences
Publisher: Public Library of Science (PLoS)
Date: 13-04-2012
An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.
Publisher: Elsevier BV
Date: 10-2018
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
Publisher: Cold Spring Harbor Laboratory
Date: 03-02-2021
DOI: 10.1101/2021.02.01.21250944
Abstract: As the threat of Covid-19 continues and in the face of vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels. How timing of delivery of the second dose affects infection burden but also prospects for the evolution of viral immune escape are critical questions. Both hinge on the strength and duration (i.e. robustness) of the immune response elicited by a single dose, compared to natural and two-dose immunity. Building on an existing immuno-epidemiological model, we find that in the short-term, focusing on one dose generally decreases infections, but longer-term outcomes depend on this relative immune robustness. We then explore three scenarios of selection, evaluating how different second dose delays might drive immune escape via a build-up of partially immune in iduals. Under certain scenarios, we find that a one-dose policy may increase the potential for antigenic evolution. We highlight the critical need to test viral loads and quantify immune responses after one vaccine dose, and to r up vaccination efforts throughout the world.
Influenza Virus Reservoirs and Intermediate Hosts: Dogs, Horses, and New Possibilities for Influenza Virus Exposure of Humans
Publisher: American Society for Microbiology
Date: 15-03-2015
DOI: 10.1128/JVI.03146-14
Abstract: Influenza A virus (IAV) infections in hosts outside the main aquatic bird reservoirs occur periodically. Although most such cross-species transmission events result in limited onward transmission in the new host, sustained influenza outbreaks have occurred in poultry and in a number of mammalian species, including humans, pigs, horses, seals, and mink. Recently, two distinct strains of IAV have emerged in domestic dogs, with each circulating widely for several years. Here, we briefly outline what is known about the role of intermediate hosts in influenza emergence, summarize our knowledge of the new canine influenza viruses (CIVs) and how they provide key new information on the process of host adaptation, and assess the risk these viruses pose to human populations.
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
Publisher: American Association for the Advancement of Science (AAAS)
Date: 26-08-2022
Abstract: Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2–susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2–positive environmental s les were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.
Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses
Publisher: Public Library of Science (PLoS)
Date: 28-02-2013
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites
Publisher: Oxford University Press (OUP)
Date: 07-2022
DOI: 10.1093/VE/VEAC090
Abstract: Arthropods harbor a largely undocumented ersity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host–parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito–mite interaction. We determined the RNA virus ersity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus ersity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome ersity and ecology in the context of arthropod host–parasite–virus relationships.
Testing the Extent of Sequence Similarity Among Viroids, Satellite RNAs, and Hepatitis Delta Virus
Publisher: Springer Science and Business Media LLC
Date: 2000
Abstract: A Monte Carlo method was used to test the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus. This analysis revealed that there is insufficient sequence similarity among these pathogens to support the hypothesis that they have a common evolutionary origin. Furthermore, while definite patterns of sequence similarity were observed among some viroids, there was a clear lack of overall similarity, indicating that a monophyletic origin for even this group cannot be reliably supported from sequence data alone.
Emerging Rabbit Hemorrhagic Disease Virus 2 (RHDVb), Australia
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 12-2015
Defining compassion in a hospital setting: consensus on the characteristics that comprise compassion from researchers in the field
Publisher: Informa UK Limited
Date: 03-03-2020
Phylogeny and the origin of HIV-1
Publisher: Springer Science and Business Media LLC
Date: 04-2001
DOI: 10.1038/35074179
Social Networks Shape the Transmission Dynamics of Hepatitis C Virus
Publisher: Public Library of Science (PLoS)
Date: 23-06-2010
Mental health and substance use disorders: The reality of youth in custody
Publisher: Wiley
Date: 19-04-2019
DOI: 10.1111/INM.12597
Phylogeography of Recently Emerged DENV-2 in Southern Viet Nam
Publisher: Public Library of Science (PLoS)
Date: 27-07-2010
Pathogenicity and transmissibility of a novel respirovirus isolated from a Malayan pangolin
Publisher: Microbiology Society
Date: 12-04-2021
DOI: 10.1099/JGV.0.001586
Abstract: The identification of SARS-CoV-2-like viruses in Malayan pangolins ( Manis javanica ) has focused attention on these endangered animals and the viruses they carry. We successfully isolated a novel respirovirus from the lungs of a dead Malayan pangolin. Similar to murine respirovirus, the full-length genome of this novel virus was 15 384 nucleotides comprising six genes in the order 3′–(leader)–NP-P-M-F-HN- l -(trailer)−5’. Phylogenetic analysis revealed that this virus belongs to the genus Respirovirus and is most closely related to murine respirovirus. Notably, animal infection experiments indicated that the pangolin virus is highly pathogenic and transmissible in mice, with inoculated mice having variable clinical symptoms and a fatality rate of 70.37 %. The virus was found to replicate in most tissues with the exception of muscle and heart. Contact transmission of the virus was 100 % efficient, although the mice in the contact group displayed milder symptoms, with the virus mainly being detected in the trachea and lungs. The isolation of a novel respirovirus from the Malayan pangolin provides new insight into the evolution and distribution of this important group of viruses and again demonstrates the potential infectious disease threats faced by endangered pangolins.
A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission
Publisher: Springer Science and Business Media LLC
Date: 20-09-2005
DOI: 10.1007/S00705-005-0626-6
Abstract: The genus Flavivirus (family Flaviviridae) presently comprises around 70 single-strand positive-sense RNA viruses. These replicate in a range of vertebrate and invertebrate cells and may be mosquito-borne, tick-borne or have no-known-vector. Since transmission mode correlates strongly with phylogeny, the flaviviruses constitute a valuable model for the evolution of vector-borne disease. Attempts to resolve the higher-level taxonomic relationships of the flaviviruses through molecular phylogenetics have thus far proved inconclusive because of conflicting positions for the three main transmission groups. We conducted the most comprehensive phylogenetic study to date, involving maximum likelihood analyses of the NS3 and NS5 genes and the entire genome sequences available at present. For the first time, we use and test a variety of more robust methods of sequence alignment and appropriate models of amino acid replacement to study these highly ergent sequences, and explicitly test specific hypotheses of tree topology. We show that (i) the NS5 gene contains insufficient phylogenetic signal to choose between competing topological hypotheses, (ii) the NS3 gene and whole genome data indicate that the mosquito-borne flaviviruses represent an outgroup to the remaining flaviviruses, and (iii) that tick-borne transmission is probably a derived trait within the genus.
Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission
Publisher: Public Library of Science (PLoS)
Date: 20-06-2019
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data
Publisher: Oxford University Press (OUP)
Date: 07-2022
DOI: 10.1093/VE/VEAC082
Abstract: Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly ergent RNA viruses remain challenging, particularly from poorly characterized hosts and environmental s les. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral ‘dusk matter’: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational resource—RdRp-scan—that contains a standardized bioinformatic toolkit to identify and annotate ergent RNA viruses in metagenomic sequence data based on the detection of RNA-dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) and structural comparisons, we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10 per cent to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and ergent virus-like sequences into the ersity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence ersity detected by the RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some fell into potentially new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B, and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position that might provide new insights into the structure, function, and evolution of viral polymerases.
Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda
Publisher: Microbiology Society
Date: 11-2009
Abstract: The genus Flavivirus , which contains approximately 70 single-stranded, positive-sense RNA viruses, represents a unique model for studying the evolution of vector-borne disease, as it includes viruses that are mosquito-borne, tick-borne or have no known vector. Both theoretical work and field studies suggest the existence of a large number of undiscovered flaviviruses. Recently, the first isolation of cell fusing agent virus (CFAV) was reported from a natural mosquito population in Puerto Rico, and sequences related to CFAV have been discovered in mosquitoes from Thailand. CFAV had previously been isolated from a mosquito cell line in 1975 and represented the only known ‘insect-only’ flavivirus, appearing to replicate in insect cells alone. A second member of the ‘insect-only’ group, Kamiti River virus (KRV), was isolated from Kenyan mosquitoes in 2003. A third tentative member of the ‘insect-only’ group, Culex flavivirus (CxFV), was first isolated in 2007 from Japan and further strains have subsequently been reported from the Americas. We report the discovery, isolation and characterization of two novel ‘insect-only’ flaviviruses from Entebbe, Uganda: a novel lineage tentatively designated Nakiwogo virus (NAKV) and a new strain of CxFV. The in idual mosquitoes from which these strains were isolated, identified retrospectively by using a reference molecular phylogeny generated using voucher specimens from the region, were Mansonia africana nigerrima and Culex quinquefasciatus , respectively. This represents the first isolation, to our knowledge, of a novel insect-only flavivirus from a Mansonia species and the first isolation of a strain of CxFV from Africa.
Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence
Publisher: Public Library of Science (PLoS)
Date: 24-06-2015
Rolling of Advanced High Strength Steels
Publisher: CRC Press
Date: 12-07-2017
Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus
Publisher: American Society for Microbiology
Date: 04-2006
DOI: 10.1128/JVI.80.7.3666-3669.2006
Abstract: Human B19 erythrovirus is a ubiquitous viral pathogen, commonly infecting in iduals before adulthood. As with all autonomous parvoviruses, its small single-stranded DNA genome is replicated with host cell machinery. While the mechanism of parvovirus genome replication has been studied in detail, the rate at which B19 virus evolves is unknown. By inferring the phylogenetic history and evolutionary dynamics of temporally s led B19 sequences, we observed a surprisingly high rate of evolutionary change, at approximately 10 −4 nucleotide substitutions per site per year. This rate is more typical of RNA viruses and suggests that high mutation rates are characteristic of the Parvoviridae .
Niakha virus: A novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal
Publisher: Elsevier BV
Date: 09-2013
Evolutionary History and Phylogeography of Human Viruses
Publisher: Annual Reviews
Date: 10-2008
DOI: 10.1146/ANNUREV.MICRO.62.081307.162912
Abstract: Understanding the evolutionary history of human viruses, along with the factors that have shaped their spatial distributions, is one of the most active areas of study in the field of microbial evolution. I give an overview of our current knowledge of the genetic ersity of human viruses using comparative studies of viral populations, particularly those with RNA genomes, to highlight important generalities in the patterns and processes of viral evolution. Special emphasis is given to the major dichotomy between RNA and DNA viruses in their epidemiological dynamics and the different types of phylogeographic pattern exhibited by human viruses. I also consider a central paradox in studies of viral evolution: Although epidemiological theory predicts that RNA viruses have ancestries dating back millennia, with major ecological transitions facilitating their emergence, the genetic ersity in currently circulating viral populations has a far more recent ancestry, indicative of continual lineage turnover.
Evolution and phylodynamics of enterovirus A71
Publisher: Elsevier BV
Date: 09-2015
Recombination is associated with an outbreak of novel highly pathogenic porcine reproductive and respiratory syndrome viruses in China
Publisher: American Society for Microbiology
Date: 10-2013
DOI: 10.1128/JVI.01270-13
Abstract: In 2009 to 2010, there was a marked increase in the number of infections with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in China. Through phylogenetic analysis, we show that viruses from this outbreak originated from a single recombination event, illustrating the potential importance of this process for disease emergence.
Viral biocontrol: grand experiments in disease emergence and evolution
Publisher: Elsevier BV
Date: 02-2015
Table S5 from Copy Number Aberration Analysis to Predict Response to Neoadjuvant Anti-HER2 Therapy: Results from the NeoALTTO Phase III Clinical Trial
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/1078-0432.22481759.V1
Abstract: Table S5: Genes in the chr6q23-24 region, association with CN levels and pCR.
Unique Acquisition of Cytotoxic T-Lymphocyte Escape Mutants in Infant Human Immunodeficiency Virus Type 1 Infection
Publisher: American Society for Microbiology
Date: 15-09-2005
DOI: 10.1128/JVI.79.18.12100-12105.2005
Abstract: The role of cytotoxic T-lymphocyte (CTL) escape in rapidly progressive infant human immunodeficiency virus type 1 (HIV-1) infection is undefined. The data presented here demonstrate that infant HIV-1-specific CTL can select for viral escape variants very early in life. These variants, furthermore, may be selected specifically in the infant, despite the same CTL specificity being present in the mother. Additionally, pediatric CTL activity may be compromised both by the transmission of maternal escape variants and by mother-to-child transmission of escape variants that originally arose in the father. The unique acquisition of these CTL escape forms may help to explain the severe nature of some pediatric HIV infections.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
Publisher: American Association for the Advancement of Science (AAAS)
Date: 26-08-2022
Abstract: Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic ersity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic ersity before February 2020 likely comprised only two distinct viral lineages, denoted “A” and “B.” Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.
Guidelines for Identifying Homologous Recombination Events in Influenza A Virus
Publisher: Public Library of Science (PLoS)
Date: 03-05-2010
Human pegivirus in brain tissue of a patient with encephalitis
Publisher: Elsevier BV
Date: 02-2020
DOI: 10.1016/J.DIAGMICROBIO.2019.114898
Abstract: We describe a case of meningoencephalitis in which meta-transcriptomic (RNA) sequencing detected human pegivirus (HPgV) in brain tissue, cerebrospinal fluid, and serum in the absence of other pathogens. This is the first detection of HPgV in antemortem brain tissue, although it is uncertain whether HPgV is responsible for the observed encephalitis.
Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association
Publisher: Cold Spring Harbor Laboratory
Date: 27-08-2020
DOI: 10.1101/2020.08.27.270959
Abstract: Influenza viruses (family Orthomyxoviridae ) infect a variety of vertebrates, including birds, humans, and other mammals. Recent metatranscriptomic studies have uncovered ergent influenza viruses in hibians, fish and jawless vertebrates, suggesting that these viruses may be widely distributed. We sought to identify additional vertebrate influenza-like viruses through the analysis of publicly available RNA sequencing data. Accordingly, by data mining, we identified the complete coding segments of five ergent vertebrate influenza-like viruses. Three fell as sister lineages to influenza B virus: salamander influenza-like virus in Mexican walking fish ( Ambystoma mexicanum) and plateau tiger salamander ( Ambystoma velasci ), siamese algae-eater influenza-like virus in siamese algae-eater fish ( Gyrinocheilus aymonieri ) and chum salmon influenza-like virus in chum salmon ( Oncorhynchus keta ). Similarly, we identified two influenza-like viruses of hibians that fell as sister lineages to influenza D virus: cane toad influenza-like virus and the ornate chorus frog influenza-like virus, in the cane toad ( Rhinella marina) and ornate chorus frog ( Microhyla fissipes) , respectively. Despite their ergent phylogenetic positions, these viruses retained segment conservation and splicing consistent with transcriptional regulation in influenza B and influenza D viruses, and were detected in respiratory tissues. These data suggest that influenza viruses have been associated with vertebrates for their entire evolutionary history.
Ancient co-speciation of simian foamy viruses and primates
Publisher: Springer Science and Business Media LLC
Date: 03-2005
DOI: 10.1038/NATURE03341
Abstract: Although parasite-host co-speciation is a long-held hypothesis, convincing evidence for long-term co-speciation remains elusive, largely because of small numbers of hosts and parasites studied and uncertainty over rates of evolutionary change. Co-speciation is especially rare in RNA viruses, in which cross-species transfer is the dominant mode of evolution. Simian foamy viruses (SFVs) are ubiquitous, non-pathogenic retroviruses that infect all primates. Here we test the co-speciation hypothesis in SFVs and their primate hosts by comparing the phylogenies of SFV polymerase and mitochondrial cytochrome oxidase subunit II from African and Asian monkeys and apes. The phylogenetic trees were remarkably congruent in both branching order and ergence times, strongly supporting co-speciation. Molecular clock calibrations revealed an extremely low rate of SFV evolution, 1.7 x 10(-8) substitutions per site per year, making it the slowest-evolving RNA virus documented so far. These results indicate that SFVs might have co-speciated with Old World primates for at least 30 million years, making them the oldest known vertebrate RNA viruses.
Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction
Publisher: Microbiology Society
Date: 04-2006
Abstract: Dengue virus is a circumtropical, mosquito-borne flavivirus that infects 50–100 million people each year and is expanding in both range and prevalence. Of the four co-circulating viral serotypes (DENV-1 to DENV-4) that cause mild to severe febrile disease, DENV-2 has been implicated in the onset of dengue haemorrhagic fever (DHF) in the Americas in the early 1980s. To identify patterns of genetic change since DENV-2's reintroduction into the region, molecular evolution in DENV-2 from Puerto Rico (PR) and surrounding countries was examined over a 20 year period of fluctuating disease incidence. Structural genes (over 20 % of the viral genome), which affect viral packaging, host-cell entry and immune response, were sequenced for 91 DENV-2 isolates derived from both low- and high-prevalence years. Phylogenetic analyses indicated that DENV-2 outbreaks in PR have been caused by viruses assigned to subtype IIIb, originally from Asia. Variation amongst DENV-2 viruses in PR has since largely arisen in situ , except for a lineage-replacement event in 1994 that appears to have non-PR New World origins. Although most structural genes have remained relatively conserved since the 1980s, strong evidence was found for positive selection acting on a number of amino acid sites in the envelope gene, which have also been important in defining phylogenetic structure. Some of these changes are exhibited by the multiple lineages present in 1994, during the largest Puerto Rican outbreak of dengue, suggesting that they may have altered disease dynamics, although their functional significance will require further investigation.
What Does Virus Evolution Tell Us About Virus Origins?
Publisher: American Society for Microbiology
Date: 15-09-2011
DOI: 10.1128/JVI.05689-11
Through an ecological lens
Publisher: EMBO
Date: 18-01-2023
Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China
Publisher: Springer Science and Business Media LLC
Date: 06-02-2018
DOI: 10.1038/S41598-018-20988-9
Abstract: There have been five waves of H7N9 avian influenza virus (AIV) infection in humans since its initial emergence in China in 2013, posing a significant threat to public health. Hubei province was free local transmission during the first four waves of H7N9 AIV. However, multiple cases of human H7N9 infection were reported in Hubei during January 2017. To understand the molecular epidemiology that underlies this sudden emergence, we collected s les from 14 human cases of H7N9 influenza virus from Hubei province, along with environmental s les from different locations in Hubei. Our analysis revealed that the newly emerged human H7N9 viruses were all from persons exposed to poultry and shared the same origin as the environmental s led viruses in the Yangtze River lineage of H7N9. Notably, we also documented an earlier and distinct importation from Jiangsu province that may have established a local environmental reservoir. Our study highlights the need for continued surveillance of H7N9 in both human and avian populations in central China.
A unified call to action from Australian nursing and midwifery leaders: ensuring that Black lives matter
Publisher: Informa UK Limited
Date: 03-07-2020
A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses
Publisher: Oxford University Press (OUP)
Date: 2019
DOI: 10.1093/VE/VEZ001
Abstract: Endogenous retroviruses (ERVs) represent host genomic ‘fossils’ of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co- ergence across the vertebrate phylogeny. Endogenous foamy viruses (EFVs) have previously been discovered in mammals, hibians, and fish. Here we report a novel endogenous foamy virus, termed ERV-Spuma-Spu, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that foamy viruses have likely co- erged with their hosts over many millions of years. The discovery of ERV-Spuma-Spu fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence
Publisher: The Royal Society
Date: 31-08-2016
Abstract: Emerging diseases are a major challenge to public health. Revealing the evolutionary processes that allow novel pathogens to adapt to new hosts, also the potential barriers to host adaptation, is central to understanding the drivers of disease emergence. In particular, it is unclear how the genetics and ecology of pathogens interact to shape the likelihood of successful cross-species transmission. To better understand the determinants of host adaptation and emergence, we modelled key aspects of pathogen evolutionary dynamics at both intra- and inter-host scales, using parameter values similar to those observed in influenza virus. We considered the possibility of acquiring the necessary host adaptive mutations both before (‘off-the-shelf’ emergence) and after (‘tailor-made’ emergence) a virus is transmitted from a donor to a new recipient species. Under both scenarios, population bottlenecks at inter-host transmission act as a major barrier to host adaptation, greatly limiting the number of adaptive mutations that are able to cross the species barrier. In addition, virus emergence is hindered if the fitness valley between the donor and recipient hosts is either too steep or too shallow. Overall, our results reveal where in evolutionary parameter space a virus could adapt to and become transmissible in a new species.
Recombination between sequences of hepatitis B virus from different genotypes
Publisher: Springer Science and Business Media LLC
Date: 02-1996
DOI: 10.1007/BF02198834
Abstract: This community-based participatory research project explored the feasibility of delivering parenting and recovery supports through digital technology for mothers recovering from addictive substances. A community advisory board of key stakeholders (n = 7) served as a focus group of advisors to discuss needed supports. Data were analyzed through qualitative descriptive analysis. Results revealed themes about challenges and supports needed, and whether supports delivered through digital technology may improve recovery and parenting. Future exploration needs to examine the extent to which the use of community-guided, tailored digital support applications that supplement prescribed treatment can enhance parenting and recovery.
Evolution of major histocompatibility complex class I genes in Cetartiodactyls
Publisher: Springer Science and Business Media LLC
Date: 07-2003
DOI: 10.1007/S00251-003-0560-2
Abstract: Previous studies of cattle MHC have suggested the presence of at least four classical class I loci. Analysis of haplotypes showed that any combination of one, two or three genes may be expressed, although no gene is expressed consistently. The aim of this study was to examine the evolutionary relationships among these genes and to study their phylogenetic history in Cetartiodactyl species, including cattle and their close relatives. A secondary aim was to determine whether recombination had occurred between any of the genes. MHC class I data sets were generated from published sequences or by polymerase chain reaction from cDNA. Phylogenetic analysis revealed that MHC class I sequences from Cetartiodactyl species closely related to cattle were distributed among the main cattle gene "groups", while those from more distantly related species were either scattered (sheep, deer) or clustered in a species-specific manner (sitatunga, giraffe). A comparison between gene and species trees showed a poor match, indicating that ergence of the MHC sequences had occurred independently from that of the hosts from which they were obtained. We also found two clear instances of interlocus recombination among the cattle MHC sequences. Finally, positive natural selection was documented at positions throughout the alpha 1 and 2 domains, primarily on those amino acids directly involved in peptide binding, although two positions in the alpha 3 domain, a region generally conserved in other species, were also shown to be undergoing adaptive evolution.
Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection
Publisher: Elsevier BV
Date: 06-2005
DOI: 10.1016/J.VIROL.2005.03.018
Abstract: Between 1996 and 1998, two clades (B and C genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000, a third clade (A genotype III) of DENV-1, which had been circulating at that locality for at least 25 years, became extinct. These changes preceded the largest outbreak of dengue recorded in Myanmar, in 2001, in which more than 95% of viruses recovered from patients were DENV-1, but where the incidence of severe disease was much less than in previous years. Phylogenetic analyses of viral genomes indicated that the two new clades of DENV-1 did not arise from the, now extinct, clade A viruses nor was the extinction of this clade due to differences in the fitness of the viral populations. Since the extinction occurred during an inter-epidemic period, we suggest that it was due to a stochastic event attributable to the low rate of virus transmission in this interval.
Metagenomic Identification of Viral Sequences in Laboratory Reagents
Publisher: MDPI AG
Date: 21-10-2021
DOI: 10.3390/V13112122
Abstract: Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterise the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an in idual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (“metatranscriptomics”) we documented the presence of contaminant viral sequences in multiple ‘blank’ negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank control libraries, as well as contaminating sequences from the Totiviridae, Tombusviridae and Lentiviridae families of RNA virus. These data suggest that viral contamination of common laboratory reagents is likely commonplace and can comprise a wide variety of viruses.
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy
Publisher: MDPI AG
Date: 14-12-2020
DOI: 10.3390/V12121438
Abstract: Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely s led from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide “lockdown” (8 March–3 June). These were combined with 460 published SARS-CoV-2 sequences s led across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.
Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches
Publisher: American Society for Microbiology
Date: 09-2018
DOI: 10.1128/JVI.00768-18
Abstract: Cane toads are poisonous hibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study s les cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.
New World Bats Harbor Diverse Influenza A Viruses
Publisher: Public Library of Science (PLoS)
Date: 10-10-2013
Table S5 from Copy Number Aberration Analysis to Predict Response to Neoadjuvant Anti-HER2 Therapy: Results from the NeoALTTO Phase III Clinical Trial
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/1078-0432.22481759
Abstract: Table S5: Genes in the chr6q23-24 region, association with CN levels and pCR.
Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture
Publisher: Oxford University Press (OUP)
Date: 2019
DOI: 10.1093/VE/VEZ012
Rapid evolutionary dynamics of zucchini yellow mosaic virus
Publisher: Microbiology Society
Date: 04-2008
Abstract: Zucchini yellow mosaic virus (ZYMV) is an economically important virus of cucurbit crops. However, little is known about the rate at which this virus has evolved within members of the family Cucurbitaceae , or the timescale of its epidemiological history. Herein, we present the first analysis of the evolutionary dynamics of ZYMV. Using a Bayesian coalescent approach we show that the coat protein of ZYMV has evolved at a mean rate of 5.0×10 −4 nucleotide substitutions per site, per year. Notably, this rate is equivalent to those observed in animal RNA viruses. Using the same approach we show that the lineages of ZYMV s led here have an ancestry that dates back no more than 800 years, suggesting that human activities have played a central role in the dispersal of ZYMV. Finally, an analysis of phylogeographical structure provides strong evidence for the in situ evolution of ZYMV within in idual countries.
Virome characterization of game animals in China reveals a spectrum of emerging pathogens
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.CELL.2022.02.014
Abstract: Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, s led across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus
Publisher: Oxford University Press (OUP)
Date: 2019
DOI: 10.1093/VE/VEZ005
How accurately can we assess zoonotic risk?
Publisher: Cold Spring Harbor Laboratory
Date: 18-08-2021
DOI: 10.1101/2020.08.17.254961
Abstract: The authors have withdrawn their manuscript as a website associated with a zoonotic risk prediction tool mentioned here was not public. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Yellow fever virus exhibits slower evolutionary dynamics than dengue virus.
Publisher: American Society for Microbiology
Date: 15-01-2010
DOI: 10.1128/JVI.01738-09
Abstract: Although yellow fever has historically been one of the most important viral infections of humans, relatively little is known about the evolutionary processes that shape its genetic ersity. Similarly, there is limited information on the molecular epidemiology of yellow fever virus (YFV) in Africa even though it most likely first emerged on this continent. Through an analysis of complete E gene sequences, including a newly acquired viral collection from Central and West Africa (Senegal, Cameroon, Central African Republic, Côte d'Ivoire, Mali, and Mauritania), we show that YFV exhibits markedly lower rates of evolutionary change than dengue virus, despite numerous biological similarities between these two viruses. From this observation, along with a lack of clock-like evolutionary behavior in YFV, we suggest that vertical transmission, itself characterized by lower replication rates, may play an important role in the evolution of YFV in its enzootic setting. Despite a reduced rate of nucleotide substitution, phylogenetic patterns and estimates of times to common ancestry in YFV still accord well with the dual histories of colonialism and the slave trade, with areas of sylvatic transmission (such as Kedougou, Senegal) acting as enzootic/epidemic foci.
A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein
Publisher: Elsevier BV
Date: 06-2020
Phylogenetic profiles reveal evolutionary relationships within the “twilight zone” of sequence similarity
Publisher: Proceedings of the National Academy of Sciences
Date: 09-09-2008
Abstract: Inferring evolutionary relationships among highly ergent protein sequences is a daunting task. In particular, when pairwise sequence alignments between protein sequences fall % identity, the phylogenetic relationships among sequences cannot be estimated with statistical certainty. Here, we show that phylogenetic profiles generated with the Gestalt Domain Detection Algorithm–Basic Local Alignment Tool (GDDA-BLAST) are capable of deriving, ab initio , phylogenetic relationships for highly ergent proteins in a quantifiable and robust manner. Notably, the results from our computational case study of the highly ergent family of retroelements accord with previous estimates of their evolutionary relationships. Taken together, these data demonstrate that GDDA-BLAST provides an independent and powerful measure of evolutionary relationships that does not rely on potentially subjective sequence alignment. We demonstrate that evolutionary relationships can be measured with phylogenetic profiles, and therefore propose that these measurements can provide key insights into relationships among distantly related and/or rapidly evolving proteins.
A total infectome approach to understand the etiology of infectious disease in pigs
Publisher: Springer Science and Business Media LLC
Date: 10-05-2022
DOI: 10.1186/S40168-022-01265-4
Abstract: The global pork industry is continuously affected by infectious diseases that can result in large-scale mortality, trade restrictions, and major reductions in production. Nevertheless, the cause of many infectious diseases in pigs remains unclear, largely because commonly used diagnostic tools fail to capture the full ersity of potential pathogens and because pathogen co-infection is common. We used a meta-transcriptomic approach to systematically characterize the pathogens in 136 clinical cases representing different disease syndromes in pigs, as well as in 12 non-diseased controls. This enabled us to simultaneously determine the ersity, abundance, genomic information, and detailed epidemiological history of a wide range of potential pathogens. We identified 34 species of RNA viruses, nine species of DNA viruses, seven species of bacteria, and three species of fungi, including two novel ergent members of the genus Pneumocystis . While most of these pathogens were only apparent in diseased animals or were at higher abundance in diseased animals than in healthy animals, others were present in healthy controls, suggesting opportunistic infections. Importantly, most of the cases examined here were characterized by co-infection with more than two species of viral, bacterial, or fungal pathogens, some with highly correlated occurrence and abundance levels. Examination of clinical signs and necropsy results in the context of relevant pathogens revealed that a multiple-pathogen model was better associated with the data than a single-pathogen model was. Our data demonstrate that most of the pig diseases examined were better explained by the presence of multiple rather than single pathogens and that infection with one pathogen can facilitate infection or increase the prevalence/abundance of another. Consequently, it is generally preferable to consider the cause of a disease based on a panel of co-infecting pathogens rather than on in idual infectious agents.
The “pressure pan” evolution of human erythrovirus B19 in the Amazon, Brazil
Publisher: Elsevier BV
Date: 12-2007
DOI: 10.1016/J.VIROL.2007.07.007
Abstract: To understand the evolutionary dynamics of human parvovirus B19, we analyzed VP1 and VP2 gene sequences of B19 s led from Belém (Amazon), the city of São Paulo, Brazil and globally. Our analysis revealed a strikingly different pattern of evolutionary change for those viral lineages introduced into Belém, which exhibited a higher rate of nonsynonymous substitutions compared to those viruses s led from other locations. We propose that difference this is due to the high prevalence of B19 in Belém (up to 85%) compared to other locations (prevalences of approximately 50%), which imposes a more intense selection pressure. Hence, those B19 lineages introduced into Belém experienced an elevated rate of amino acid change, driven by positive selection, in order to generate serial re-infections in a small web of transmission, which can be thought of as an evolutionary "pressure pan".
Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand
Publisher: MDPI AG
Date: 23-06-2022
DOI: 10.3390/V14071364
Abstract: New Zealand/Aotearoa has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has been only scarcely researched. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus, and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye/tauhou (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior unders ling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were only found in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance are needed in New Zealand avifauna, particularly in Turdus populations and endemic species.
Error thresholds and the constraints to RNA virus evolution
Publisher: Elsevier BV
Date: 12-2003
Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses
Publisher: Public Library of Science (PLoS)
Date: 14-09-2007
The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand
Publisher: Elsevier BV
Date: 11-2004
DOI: 10.1016/J.VIROL.2004.08.003
Abstract: Dengue represents a major public health problem in Thailand, with all four viral serotypes co-circulating. Dengue virus serotype 4 (DENV-4) is the least frequently s led serotype, although one that is often associated with hemorrhagic fever during secondary infection. To determine the evolutionary forces shaping the genetic ersity of DENV-4, and particularly whether its changing prevalence could be attributed to instances of adaptive evolution in the viral genome, we undertook a large-scale molecular epidemiological analysis of DENV-4 in Bangkok, Thailand, using both E gene and complete coding region sequences. This analysis revealed extensive genetic ersity within a single locality at a single time, including the discovery of a new and ergent genotype of DENV-4, as well as a pattern of continual lineage turnover. We also recorded the highest average rate of evolutionary change for this serotype, at 1.072 x 10(-3) nucleotide substitutions per site, per year. However, despite this abundant genetic variation, there was no evidence for adaptive evolution in any gene, codon, or lineage of DENV-4, with the highest rate of nonsynonymous substitution observed in NS2A. Consequently, the rapid turnover of DENV-4 lineages through time is most likely the consequence of a high rate of deleterious mutation in the viral genome coupled to seasonal fluctuations in the size of the vector population.
Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds
Publisher: Wiley
Date: 18-10-2011
Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds
Publisher: Wiley
Date: 22-11-2018
DOI: 10.1111/MEC.14918
Barriers and Enablers to Successful Uptake of Continuous Positive Airway Pressure (CPAP) Treatment for Obstructive Sleep Apnoea for Aboriginal and Torres Strait Islander People
Publisher: OMICS Publishing Group
Date: 2016
Cross-validation to select Bayesian hierarchical models in phylogenetics
Publisher: Springer Science and Business Media LLC
Date: 26-05-2016
Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease
Publisher: Elsevier BV
Date: 12-2019
Is population flow an unintended consequence of alcohol management plans?
Publisher: Wiley
Date: 24-11-2016
DOI: 10.1111/JOCN.13534
Abstract: The aim of this study was to gauge whether, and to what extent, population flow occurred as a result of the implementation of alcohol management plans in Indigenous communities. Alcohol management plans involving carriage limits and dry places were introduced into 15 Queensland Indigenous communities between 2002-2004. Controls on alcohol availability were further tightened between 2008-2010, seeing the closure of eight mainly remote community taverns/canteens. A retrospective observational study was undertaken using data from the Queensland Injury Surveillance Unit. Population flow was measured by changing patterns of alcohol-related injuries in a mining region near dry Indigenous communities following the introduction of alcohol management plans and a control mining region distant from Indigenous communities with alcohol management plans. Data were analysed using descriptive and inferential statistics. Logistic regression was used for the comparison of the characteristics between the emergency department presentations. The rates of alcohol-related injury presentations per 1000 opulation were calculated and age-standardised to the Australian population. Between the five-year periods 2003-2007 and 2008-2012, alcohol-related injury presentations to the Mount Isa emergency department trebled from an age-adjusted average annual rate of 9·5/1000 in the region's population to 27·1/1000 population. In the control region, alcohol-related emergency department injury presentations did not increase to the same degree with age-adjusted average annual rates of 1·42/1000 and 2·21/1000, respectively. The 10-year pattern of emergency department presentations for alcohol-related injuries increased significantly in the Mount Isa region compared with the control region. Further research should investigate the impacts of population flow related to Indigenous community alcohol management plans. Although initiatives such as alcohol management plans have been implemented to reduce alcohol use and related consequences in Indigenous communities, there needs to be a greater consideration of the impact of these policies in nearby towns in the future.
Novel hepatitis D-like agents in vertebrates and invertebrates
Publisher: Oxford University Press (OUP)
Date: 07-2019
DOI: 10.1093/VE/VEZ021
Abstract: Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic s les from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly ergent HDV-like viruses are also present in fish, hibians, and invertebrates, with PCR and Sanger sequencing confirming the presence of the invertebrate HDV-like viruses. Notably, the novel viruses identified here share genomic features characteristic of HDV, such as a circular genome of only approximately 1.7 kb in length, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions, and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human viruses. Importantly, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV–HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the ersity and host range of HDV, but also shed light on its origin and evolutionary history.
Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population
Publisher: American Society for Microbiology
Date: 02-2017
DOI: 10.1128/JVI.01820-16
Abstract: Koala populations are in serious decline across many areas of mainland Australia, with infectious disease a contributing factor. Koala retrovirus (KoRV) is a gammaretrovirus present in most wild koala populations and captive colonies. Five subtypes of KoRV (A to E) have been identified based on amino acid sequence ergence in a hypervariable region of the receptor binding domain of the envelope protein. However, analysis of viral genetic ersity has been conducted primarily on KoRV in captive koalas housed in zoos in Japan, the United States, and Germany. Wild koalas within Australia have not been comparably assessed. Here we report a detailed analysis of KoRV genetic ersity in s les collected from 18 wild koalas from southeast Queensland. By employing deep sequencing we identified 108 novel KoRV envelope sequences and determined their phylogenetic ersity. Genetic ersity in KoRV was abundant and fell into three major groups two comprised the previously identified subtypes A and B, while the third contained the remaining hypervariable region subtypes (C, D, and E) as well as four hypervariable region subtypes that we newly define here (F, G, H, and I). In addition to the ubiquitous presence of KoRV-A, which may represent an exclusively endogenous variant, subtypes B, D, and F were found to be at high prevalence, while subtypes G, H, and I were present in a smaller number of animals. IMPORTANCE Koala retrovirus (KoRV) is thought to be a significant contributor to koala disease and population decline across mainland Australia. This study is the first to determine KoRV subtype prevalence among a wild koala population, and it significantly expands the total number of KoRV sequences available, providing a more precise picture of genetic ersity. This understanding of KoRV subtype prevalence and genetic ersity will be important for conservation efforts attempting to limit the spread of KoRV. Furthermore, KoRV is one of the only retroviruses shown to exist in both endogenous (transmitted vertically to offspring in the germ line DNA) and exogenous (horizontally transmitted between infected in iduals) forms, a ision of fundamental evolutionary importance.
The complete nucleotide sequence of a New World simian foamy virus
Publisher: Elsevier BV
Date: 12-2007
DOI: 10.1016/J.VIROL.2007.07.018
Abstract: We determined the complete nucleotide sequence of the New World simian foamy virus (FV) from spider monkey (SFVspm). Starting from a conserved region in the integrase (IN) domain of the pol gene we cloned fragments of the genome up to the 5' end of the long terminal repeat (LTR) into plasmid vectors and elucidated their nucleotide sequence. The 3' end of the genome was determined by direct nucleotide sequencing of PCR products. Each nucleotide of the genome was determined at least two times from both strands. All protein motifs described to be conserved among primate FVs were found in SFVspm. At both the nucleotide and protein levels SFVspm is the most ergent primate FV described to date, reflecting the long-term phylogenetic separation between Old World and New World primate host species (Catarrhini and Platyrrhini, respectively). The molecular probes developed for SFVspm will allow the investigation of trans-species transmissions of this New World foamy virus to humans by serological assays.
Editorial: Molecular epidemiology of dengue virus – the time for big science
Publisher: Wiley
Date: 11-1998
Long-Term Evolution of the Luteoviridae : Time Scale and Mode of Virus Speciation
Publisher: American Society for Microbiology
Date: 15-06-2010
DOI: 10.1128/JVI.02160-09
Abstract: Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic ersity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.
Patterns of Intra- and Interhost Nonsynonymous Variation Reveal Strong Purifying Selection in Dengue Virus
Publisher: American Society for Microbiology
Date: 15-10-2003
DOI: 10.1128/JVI.77.20.11296-11298.2003
Abstract: Considerable uncertainty surrounds the evolutionary rates of and selection pressures acting on arthropod-borne RNA viruses (arboviruses). In particular, it is unclear why arboviruses such as dengue virus show substantial genetic variation within in idual humans and mosquitoes yet low long-term rates of amino acid substitution. To address this question, I compared patterns of nonsynonymous variation in populations of dengue virus s led at different levels of evolutionary ergence. Although nonsynonymous variation was abundant in viral populations within in idual humans, there was a marked reduction in the frequency of nonsynonymous mutations in interhost comparisons. Moreover, intrahost genetic variation corresponded to a random pattern of mutation, and most of the sites that exhibited nonsynonymous variation within hosts were invariant at deeper phylogenetic levels. This loss of long-term nonsynonymous variation is the signature of extensive purifying selection such that more than 90% of all nonsynonymous mutations are deleterious. Consequently, although arboviruses are able to successfully adapt to erse cell types, they are characterized by a high rate of deleterious mutation.
Inferring the Rate and Time-Scale of Dengue Virus Evolution
Publisher: Oxford University Press (OUP)
Date: 2003
Abstract: Dengue is often referred to as an emerging disease because of the rapid increases in incidence and prevalence that have been observed in recent decades. To understand the rate at which genetic ersification occurs in dengue virus and to infer the time-scale of its evolution, we employed a maximum likelihood method that uses information about times of virus s ling to estimate the rate of molecular evolution in a large number of viral envelope (E) gene sequences and to place bounds around the dates of appearance of all serotypes and specific genotypes. Our analysis reveals that dengue virus generally evolves according to a molecular clock, although some serotype-specific and genotype-specific rate differences were observed, and that its origin is more recent than previously suggested, with the virus appearing approximately 1,000 years ago. Furthermore, we estimate that the zoonotic transfer of dengue from sylvatic (monkey) to sustained human transmission occurred between 125 and 320 years ago, that the current global genetic ersity in the four serotypes of dengue virus only appeared during the past century, and that the recent rise in genetic ersity can be loosely correlated both to human activities such as population growth, urbanization, and mass transport and to the emergence of dengue hemorrhagic fever as a major disease problem.
A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene
Publisher: Public Library of Science (PLoS)
Date: 27-09-2016
Phylogenetic evidence for adaptive evolution of dengue viruses in nature
Publisher: Microbiology Society
Date: 07-2002
DOI: 10.1099/0022-1317-83-7-1679
Abstract: A maximum-likelihood approach was used to analyse selection pressures acting on genes from all four serotypes of dengue virus (DEN). A number of amino acid positions were identified within the envelope (E) glycoprotein that have been subject to relatively weak positive selection in both DEN-3 and DEN-4, as well as in two of the five genotypes of DEN-2. No positive selection was detected in DEN-1. In accordance with the function of the E protein as the major antigenic determinant of DEN, the majority of these sites were located in, or near to, potential T- or B-cell epitopes. A smaller number of selected sites was located in other well-defined functional domains of the E protein, suggesting that cell tropism and virus-mediated membrane fusion may also confer fitness advantages to DEN in nature. Several positively selected amino acid substitutions were also identified in the NS2B and NS5 genes of DEN-2, although the cause of this selection is unclear, whereas the capsid, membrane and non-structural genes NS1, NS2A, NS3 and NS4 were all subject to strong functional constraints. Hence, evidence was found for localized adaptive evolution in natural isolates of DEN, revealing that selection pressures differ among serotypes, genotypes and viral proteins.
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-04-2021
Abstract: For two-dose vaccines against severe acute respiratory syndrome coronavirus 2, some jurisdictions have decided to delay the second dose to rapidly get the vaccine into more people. The consequences of deviating from manufacturer-prescribed dosing regimens are unknown but will depend on the strength of immune responses to the vaccines. Saad-Roy et al. took a modeling approach to tackling the inevitable uncertainties facing vaccine rollout. The authors found that although one-dose strategies generally reduce infections in the short term, in the long term, the outcome depends on immune robustness. A one-dose strategy may increase the potential for antigenic evolution if immune responses are suboptimal and the virus continues to replicate in some vaccinated people, potentially leading to immune-escape mutations. It is critical to gather serological data from vaccinated people and, to avoid negative outcomes, to r up vaccination efforts worldwide. Science , this issue p. 363
Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand
Publisher: Elsevier BV
Date: 06-2012
Metatranscriptomic analysis of virus diversity in urban wild birds with paretic disease
Publisher: American Society for Microbiology
Date: 31-08-2020
DOI: 10.1128/JVI.00606-20
Abstract: Wildlife naturally harbor a erse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly erse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern.
Conquering the great divide: Rural mothers of children with chronic health conditions accessing specialist medical care for their children
Publisher: Elsevier BV
Date: 06-2020
Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes
Publisher: Proceedings of the National Academy of Sciences
Date: 14-05-2013
Abstract: Dengue is the most prevalent arboviral disease of humans. The host and virus variables associated with dengue virus (DENV) transmission from symptomatic dengue cases ( n = 208) to Aedes aegypti mosquitoes during 407 independent exposure events was defined. The 50% mosquito infectious dose for each of DENV-1–4 ranged from 6.29 to 7.52 log10 RNA copies/mL of plasma. Increasing day of illness, declining viremia, and rising antibody titers were independently associated with reduced risk of DENV transmission. High early DENV plasma viremia levels in patients were a marker of the duration of human infectiousness, and blood meals containing high concentrations of DENV were positively associated with the prevalence of infectious mosquitoes 14 d after blood feeding. Ambulatory dengue cases had lower viremia levels compared with hospitalized dengue cases but nonetheless at levels predicted to be infectious to mosquitoes. These data define serotype-specific viremia levels that vaccines or drugs must inhibit to prevent DENV transmission.
The Evolutionary Biology of Dengue Virus
Publisher: Wiley
Date: 25-08-2006
Abstract: Studies of the evolution of dengue virus (DENV) have blossomed during the last 20 years, in part due to the increasing availability of viral gene sequence data. Herein I review key aspects of the evolutionary biology of DENV focusing on extent and structure of genetic ersity in DENV, the time and place of DENV origin, the major mechanisms of DENV evolution, and the evolution of DENV virulence. A central conclusion is that despite the high mutation rates common to RNA viruses in general, there are important constraints against adaptive evolution in DENV in particular. These have implications for the escape from immunological recognition and hence for vaccine design. Finally, I note that a fuller understanding of DENV evolution will require more extensive study of the sylvatic cycle, particularly in Africa, which has been largely ignored to date.
Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses
Publisher: Elsevier BV
Date: 08-2021
Plasmodium falciparum malaria in 1 st –2 nd century CE southern Italy
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.CUB.2016.10.016
Abstract: The historical record attests to the devastation malaria exacted on ancient civilizations, particularly the Roman Empire [1]. However, evidence for the presence of malaria during the Imperial period in Italy (1st-5th century CE) is based on indirect sources, such as historical, epigraphic, or skeletal evidence. Although these sources are crucial for revealing the context of this disease, they cannot establish the causative species of Plasmodium. Importantly, definitive evidence for the presence of malaria is now possible through the implementation of ancient DNA technology. As malaria is presumed to have been at its zenith during the Imperial period [1], we selected first or second molars from 58 adults from three cemeteries from this time: Isola Sacra (associated with Portus Romae, 1st-3rd century CE), Velia (1st-2nd century CE), and Vagnari (1st-4th century CE). We performed hybridization capture using baits designed from the mitochondrial (mtDNA) genomes of Plasmodium spp. on a prioritized subset of 11 adults (informed by metagenomic sequencing). The mtDNA sequences generated provided compelling phylogenetic evidence for the presence of P. falciparum in two in iduals. This is the first genomic data directly implicating P. falciparum in Imperial period southern Italy in adults.
Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics
Publisher: American Society for Microbiology
Date: 06-2019
DOI: 10.1128/JVI.00205-19
Abstract: The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral ersity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.
Surveillance of Rodent Pests for SARS-CoV-2 and Other Coronaviruses, Hong Kong
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 02-2022
Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains
Publisher: Elsevier BV
Date: 11-2004
DOI: 10.1016/J.VIROL.2004.08.029
Abstract: Outbreaks of dengue due to dengue virus type 1 (DENV-1) occurred almost simultaneously in 2001 in Myanmar and at multiple sites almost 10,000 km away in the Pacific. Phylogenetic analyses of the E protein genes of DENV-1 strains recovered from Asia and the Pacific revealed three major viral genotypes (I, II, and III) with distinct clades within each. The majority of strains from the Pacific and Myanmar, and a number of other Asian strains fell into genotype I. Genotype II comprised a smaller set of Asian and Pacific strains, while genotype III contained viruses from erse geographical localities. These analyses suggested that the continuing outbreak of dengue in the Pacific has been due to multiple, direct, introductions of dengue viruses from a variety of locations in Asia followed by local transmission. There was no evidence that the introduction of these viruses into the Pacific was associated with any adaptive changes in the E protein of the viruses.
Myxoma Virus and the Leporipoxviruses: An Evolutionary Paradigm
Publisher: MDPI AG
Date: 06-03-2015
DOI: 10.3390/V7031020
Tracking virus outbreaks in the twenty-first century
Publisher: Springer Science and Business Media LLC
Date: 13-12-2018
The evolution and emergence of hantaviruses
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.COVIRO.2014.12.007
Abstract: Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co- ergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more erse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.
Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread
Publisher: Cold Spring Harbor Laboratory
Date: 25-07-2019
DOI: 10.1101/714683
Abstract: Canine parvovirus (CPV) is a highly successful pathogen that has sustained pandemic circulation in dogs for more than 40 years. Here, integrating full-genome and deep sequencing analyses, structural information, and in vitro experimentation, we describe the macro- and micro-scale features that have accompanied CPV’s evolutionary success. Despite 40 years of viral evolution, all CPV variants are ∼99% identical in nucleotide sequence, with only a limited number ( ) of mutations becoming fixed or widespread during this time. Notably, most changes in the major capsid protein (VP2) are nonsynonymous and fall within, or adjacent to, the overlapping receptor footprint or antigenic regions, suggesting competitive selective pressures have played a key role in CPV evolution and likely constrained its evolutionary trajectory. Moreover, among the limited number of variable sites, CPV genomes exhibit complex patterns of variation that likely include parallel evolution, reversion, and recombination, making phylogenetic inference difficult. Additionally, deep sequencing of viral DNA in original clinical s les collected from dogs and other host species s led between 1978 and 2018 revealed few sub-consensus single nucleotide variants (SNVs) above ∼0.5%, and experimental passages demonstrate that substantial pre-existing genetic variation is not necessarily required for rapid host receptor driven adaptation. Together, these findings suggest that although CPV is capable of rapid host adaptation, relatively low mutation rate, pleiotropy, and/or a lack of selective challenges since its initial emergence have reduced the long-term genetic ersity accumulation and evolutionary rate. Hence, continuously high levels of inter- and intra-host ersity are not intrinsic to highly adaptable viruses. Rapid mutation rates and correspondingly high levels of standing intra-host ersity and accumulated inter-host ersity over epidemic scales are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little being known about that evolutionary processes that occur for viruses with DNA genomes. Here we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intra-host evolutionary processes of a virus in a new host animal. Our analysis reveals that successful host jumping and sustained onward transmission does not necessarily depend on a high level of intra-host ersity or result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of a virus’s biology and ecology are relevant when considering their adaptability.
Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins
Publisher: Cold Spring Harbor Laboratory
Date: 22-06-2020
DOI: 10.1101/2020.06.22.164442
Abstract: SARS-CoV-2 is having severe impact on public health at a global scale. Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. We show that CT scans of virus-positive pangolins reveal bilateral ground-glass opacities in lungs in similar manner to COVID-19 patients. The virus infected multiple organs in pangolins, with the lungs being the major target. Histological expression showed that ACE2 and TMPRSS2 are co-expressed with viral RNA. Transcriptome analysis revealed an inadequate interferon response, with different dysregulated chemokines and cytokines responses in pregnant and non-pregnant adults and fetuses. Viral RNA and protein were detected in three fetuses providing evidence for vertical virus transmission. In sum, our study identifies the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.
What Does Virus Evolution Tell Us about Virus Origins?
Publisher: American Society for Microbiology
Date: 06-2011
DOI: 10.1128/JVI.02203-10
Abstract: Despite recent advances in our understanding of erse aspects of virus evolution, particularly on the epidemiological scale, revealing the ultimate origins of viruses has proven to be a more intractable problem. Herein, I review some current ideas on the evolutionary origins of viruses and assess how well these theories accord with what we know about the evolution of contemporary viruses. I note the growing evidence for the theory that viruses arose before the last universal cellular ancestor (LUCA). This ancient origin theory is supported by the presence of capsid architectures that are conserved among erse RNA and DNA viruses and by the strongly inverse relationship between genome size and mutation rate across all replication systems, such that pre-LUCA genomes were probably both small and highly error prone and hence RNA virus-like. I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures.
Table S1, S2, S3, S4 from Copy Number Aberration Analysis to Predict Response to Neoadjuvant Anti-HER2 Therapy: Results from the NeoALTTO Phase III Clinical Trial
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/1078-0432.22481762
Abstract: Table S1: Clinicopathological characteristics of the patients. Table S2: List of 49 genes associated with CNAs in breast cancer from the COSMIC Cancer Gene Census database. Table S3: Gene ontology analysis of the genes correlated with the genome instability index. Table S4: Gene ontology analysis of the genes anti-correlated with the genome instability index.
Benign Rabbit Calicivirus in New Zealand
Publisher: American Society for Microbiology
Date: 06-2017
DOI: 10.1128/AEM.00090-17
Abstract: The Czech v351 strain of rabbit hemorrhagic disease virus (RHDV1) is used in Australia and New Zealand as a biological control agent for rabbits, which are important and damaging introduced vertebrate pests in these countries. However, nonpathogenic rabbit caliciviruses (RCVs) can provide partial immunological cross-protection against lethal RHDV infection and thus interfere with effective rabbit biocontrol. Antibodies that cross-reacted against RHDV antigens were found in wild rabbits before the release of RHDV1 in New Zealand in 1997, suggesting that nonpathogenic RCVs were already present in New Zealand. The aim of this study was to confirm the presence of nonpathogenic RCV in New Zealand and describe its geographical distribution. RCV and RHDV antibody assays were used to screen serum s les from 350 wild rabbits from 14 locations in New Zealand. The serological survey indicated that both RCV and RHDV are widespread in New Zealand wild rabbits, with antibodies detected in 10 out of 14 and 12 out of 14 populations, respectively. Two closely related RCV strains were identified in the duodenal tissue from a New Zealand wild rabbit (RCV Gore-425A and RCV Gore-425B). Both variants are most closely related to Australian RCV strains, but with 88% nucleotide identity, they are genetically distinct. Phylogenetic analysis revealed that the New Zealand RCV strains fall within the genetic ersity of the Australian RCV isolates, indicating a relatively recent movement of RCVs between Australia and New Zealand. IMPORTANCE Wild rabbits are important and damaging introduced vertebrate pests in Australia and New Zealand. Although RHDV1 is used as a biological control agent, some nonpathogenic RCVs can provide partial immunological cross-protection against lethal RHDV infection and thus interfere with its effectiveness for rabbit control. The presence of nonpathogenic RCVs in New Zealand wild rabbits has been long hypothesized, but earlier attempts to isolate a New Zealand RCV strain have been unsuccessful. Therefore, it is important to determine if such nonpathogenic viruses exist in New Zealand rabbits, especially considering the proposed introduction of new RHDV strains into New Zealand as biocontrols.
Virus genomes reveal factors that spread and sustained the Ebola epidemic
Publisher: Springer Science and Business Media LLC
Date: 04-2017
DOI: 10.1038/NATURE22040
Polymorphisms in Nef associated with different clinical outcomes in HIV type 1 subtype C-infected children
Publisher: Mary Ann Liebert Inc
Date: 02-2007
Abstract: The human immunodeficiency virus type 1 (HIV-1) negative factor, or Nef, has a variety of functions that are important in viral pathogenesis. Sequence analysis has identified nef mutations that are linked to the rate of disease progression in adults and children infected with HIV-1 subtype B. Here we have sequenced and analyzed HIV-1 subtype C nef sequences from 34 children with rapid (RP) or slow progressing (SP) disease and identified polymorphisms associated with disease stage including motifs involved in specific pathogenic functions. Unlike subtype B, insertions and deletions in the N-terminal variable region were observed exclusively in SP children (8 out of 25). Strong positive selection pressures were found in sites of known functional importance among SP sequences, whereas RP had strong negative selection across the gene. A lineage analysis of selection pressures indicated weaker pressure across the nef gene in SP sequences bearing a deletion in region 8-12, suggesting this deletion has functional importance in vivo. Together these results suggest a differential adaptation of certain Nef functions related to disease progression, some of which may be attributable to immune-imposed pressures. These data broadly reflect previous studies on subtype B, corroborate the decreased cytopathicity of SP viruses, but also highlight potential subtype differences that require further investigation.
Short report: Clinical intervention and molecular characteristics of a dengue hemorrhagic fever outbreak in Timor leste, 2005
Publisher: American Society of Tropical Medicine and Hygiene
Date: 09-2007
DOI: 10.4269/AJTMH.2007.77.534
Abstract: In response to a January 2005 report of dengue hemorrhagic fever (DHF) in Timor Leste, the World Health Organization sent a team to assist the National Hospital Guido Valadares (NHGV) in Dili with clinical case management and diagnostic support. The hospital reported 67 admissions including 8 deaths (case fatality rate approximately 12%) over the previous weeks with case histories clinically compatible with DHF. During the intervention, an additional 44 suspected dengue patients were admitted to the pediatric ward of NHGV. Among 41 patients with clinical diagnoses of dengue fever or DHF, 38 (93%) were laboratory confirmed. Although cause and effect cannot be definitely attributed, the case fatality rate decreased to 3.6% after the intervention with education about dengue management strategies.
Patterns of ‘at home’ alcohol-related injury presentations to emergency departments – An integrative literature review
Publisher: Elsevier BV
Date: 06-2017
Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants
Publisher: Oxford University Press (OUP)
Date: 07-2017
DOI: 10.1093/VE/VEX018
Potential challenges of using narrative inquiry with at-risk young people
Publisher: RCN Publishing Ltd.
Date: 29-04-2019
A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia
Publisher: MDPI AG
Date: 17-05-2018
DOI: 10.3390/V10050269
‘Canaries in the mine’. Parents of adult children with schizophrenia: An integrative review of the literature
Publisher: Wiley
Date: 20-12-2017
DOI: 10.1111/INM.12290
The paradox of HBV evolution as revealed from a 16th century mummy
Publisher: Public Library of Science (PLoS)
Date: 04-01-2018
Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis
Publisher: Springer Science and Business Media LLC
Date: 02-11-2020
DOI: 10.1038/S41598-020-75904-X
Abstract: Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the ersity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host s led. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable ersity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.
Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences
Publisher: Oxford University Press (OUP)
Date: 15-03-1997
Abstract: Genetic algorithm-based RNA secondary structure prediction was used in combination with comparative sequence analysis to construct models of folding for the distal part of the 3'-untranslated region of flaviviruses belonging to four serological groups. Elements of RNA secondary structure that are preserved among all the flaviviruses studied were revealed, despite the high degree of sequence ergence between them. At the same time, structural elements were observed that distinguish members of different serological groups and, in particular, a region of remarkable structural ergence between the tick-borne and mosquito-borne flaviviruses was found. Application of the genetic algorithm also revealed that the 3'-terminus of flaviviral genomic RNA may take on alternative conformations, which are not observed in the 3'-terminus of complementary minus strand RNA. These alternative folding patterns may have roles in the regulation of transcription and translation initiation and in the switch between them.
Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus
Publisher: Public Library of Science (PLoS)
Date: 2006
Artificial intelligence redefines RNA virus discovery
Publisher: Research Square Platform LLC
Date: 25-04-2023
DOI: 10.21203/RS.3.RS-2832379/V1
Abstract: RNA viruses are erse components of global ecosystems. The metagenomic identification of RNA viruses is currently limited to those with sequence similarity to known viruses, such that highly ergent viruses that comprise the "dark matter" of the virosphere remain challenging to detect. We developed a deep learning algorithm – LucaProt – to search for highly ergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 global meta-transcriptomes. LucaProt integrates both sequence and structural information to accurately and efficiently detect RdRP sequences. With this approach we identified 180,571 RNA viral species and 180 superclades (viral phyla/classes). This is the broadest ersity of RNA viruses described to date, including many viruses undetectable using BLAST or HMM approaches. The newly identified RNA viruses were present in erse ecological niches, including the air, hot springs and hydrothermal vents, and both virus ersity and abundance varied substantially among ecological types. We also identified the longest RNA virus genome (nido-like) observed so far, at 47,250 nucleotides, and expanded the ersity of RNA bacteriophage to more than ten phyla/classes. This study marks the beginning of a new era of virus discovery, with the potential to redefine our understanding of the global virosphere and reshape our understanding of virus evolutionary history.
Evolutionary stasis of viruses?
Publisher: Springer Science and Business Media LLC
Date: 27-02-2019
Epidemic Dynamics Revealed in Dengue Evolution
Publisher: Oxford University Press (OUP)
Date: 04-12-2009
Unbiased Characterization of the Microbiome and Virome of Questing Ticks.
Publisher: Frontiers Media SA
Date: 12-05-2021
DOI: 10.3389/FMICB.2021.627327
Abstract: Due to their vector capacity, ticks are ectoparasites of medical and veterinary significance. Modern sequencing tools have facilitated tick-associated microbiota studies, but these have largely focused on bacterial pathogens and symbionts. By combining 16S rRNA gene sequencing with total RNA-sequencing methods, we aimed to determine the complete microbiome and virome of questing, female Ixodes holocyclus recovered from coastal, north-eastern New South Wales (NSW), Australia. We present, for the first time, a robust and unbiased method for the identification of novel microbes in ticks that enabled us to identify bacteria, viruses, fungi and eukaryotic pathogens. The dominant bacterial endosymbionts were Candidatus Midichloria sp. Ixholo1 and Candidatus Midichloria sp. Ixholo2. Candidatus Neoehrlichia australis and Candidatus Neoehrlichia arcana were also recovered, confirming that these bacteria encompass I. holocyclus ’ core microbiota. In addition, seven virus species were detected—four previously identified in I. holocyclus and three novel species. Notably, one of the four previously identified virus species has pathogenic potential based on its phylogenetic relationship to other tick-associated pathogens. No known pathogenic eukaryotes or fungi were identified. This study has revealed the microbiome and virome of female I. holocyclus from the environment in north-eastern NSW. We propose that future tick microbiome and virome studies utilize equivalent methods to provide an improved representation of the microbial ersity in ticks globally.
Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 05-2021
Divergent hepaciviruses, chuvirus and deltaviruses in Australian marsupial carnivores (Dasyurids) identified through transcriptome mining
Publisher: Cold Spring Harbor Laboratory
Date: 27-06-2023
DOI: 10.1101/2023.06.27.546737
Abstract: Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (Thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the NCBI Sequence Read Archive (SRA) database to document the viral ersity within four Dasyuromorphia species. Accordingly, we identified 15 novel virus species from five DNA virus families ( Adenoviridae , Anelloviridae , Herpesviridae , Papillomaviridae and Polyomaviridae ) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus , and the delta-like virus group. Of particular note was the identification of a marsupial specific clade of delta-like viruses that may indicate an association of deltaviruses and with marsupial species dating back to their origin some 160 million years ago. In addition, we identified a highly ergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade, as well as the first detection of the Jingchuvirales in a mammalian host – a chu-like virus in Tasmanian devils – thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia
Publisher: MDPI AG
Date: 04-10-2022
DOI: 10.3390/V14102186
Abstract: Macrobrachium rosenbergii nodavirus (MrNV)—the aetiological agent of white tail disease—is a major limiting factor of crustacean aquaculture as it causes up to 100% mortality in M. rosenbergii larvae and juveniles. Despite the importance of MrNV, there have been few studies on the phylogenetic ersity and geographic range of this virus in Australian waterways. Here, we detected MrNV genomes in common carp (Cyprinus carpio) metatranscriptomes s led at five freshwater sites across the Murray-Darling Basin (MDB), Australia. We identified genetic ergence of the RNA-dependent RNA polymerase gene between MrNV sequences identified in the northern and southern rivers of the MDB. Northern viruses exhibited strong phylogenetic clustering with MrNV from China, whereas the southern viruses were more closely related to MrNV from Australia. However, all five viruses were closely related in the capsid protein, indicative of genetic reassortment of the RNA1 and RNA2 segments between Australian and introduced MrNV. In addition, we identified Macrobrachium australiense in two of the five MrNV-positive libraries, suggesting that these species may be important reservoir hosts in the MDB. Overall, this study reports the first occurrence of MrNV outside of the Queensland region in Australia and provides evidence for genetic reassortment between endemic and introduced MrNV.
Diverse Dengue Type 2 Virus Populations Contain Recombinant and Both Parental Viruses in a Single Mosquito Host
Publisher: American Society for Microbiology
Date: 04-2003
DOI: 10.1128/JVI.77.7.4463-4467.2003
Abstract: Envelope (E) protein genes s led from populations of dengue 2 (DEN-2) virus in in idual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The nucleotide sequences of the E genes in more than 70% of the clones differed from the consensus sequence for the corresponding virus population at up to 11 sites, and 24 of the 94 clones contained at least one stop codon. Virus populations recovered up to 2 years apart yielded clones with similar polymorphisms in the E gene. For one mosquito, the clones obtained fell into two genotypes. One group of sequences was closely related to those of viruses recovered from dengue patients in the same locality (Yangon, Myanmar) since 1995 and were classified as Asian 1 genotype. The second group were Cosmopolitan genotype viruses which were also circulating in Yangon in 2000 and which were related to DEN-2 viruses s led from southern China in 1999. Finally, one clone was identified as a recombinant genome composed of portions of these two “parental” genotypes. This is the first report of recombinant and parental dengue viruses in a single host.
Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Publisher: Apollo - University of Cambridge Repository
Date: 2017
DOI: 10.17863/CAM.24183
The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China
Publisher: Springer Science and Business Media LLC
Date: 10-2022
DOI: 10.1186/S13071-022-05485-3
Abstract: Ticks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic ersity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria. We collected 20,000 contemporary and historical (up to 60 years of preservation) tick s les representing a wide range of tick bio ersity across erse geographic regions in China. Metagenomic sequencing was performed on in idual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the ersity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified ergent and abundant bacteria in Haemaphysalis , Ixodes , Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia . We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co- ergence relationship between ticks and Rickettsia and Coxiella bacteria. In sum, our study provides important new information on the genetic ersity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria.
Cell Walls and the Convergent Evolution of the Viral Envelope
Publisher: American Society for Microbiology
Date: 12-2015
Abstract: Why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. The viral envelope serves several functions, including protecting the RNA or DNA molecule(s), evading recognition by the immune system, and facilitating virus entry. Despite these commonalities, viral envelopes come in a wide variety of shapes and configurations. The evolution of the viral envelope is made more puzzling by the fact that nonenveloped viruses are able to infect a erse range of hosts across the tree of life. We reviewed the entry, transmission, and exit pathways of all (101) viral families on the 2013 International Committee on Taxonomy of Viruses (ICTV) list. By doing this, we revealed a strong association between the lack of a viral envelope and the presence of a cell wall in the hosts these viruses infect. We were able to propose a new hypothesis for the existence of enveloped and nonenveloped viruses, in which the latter represent an adaptation to cells surrounded by a cell wall, while the former are an adaptation to animal cells where cell walls are absent. In particular, cell walls inhibit viral entry and exit, as well as viral transport within an organism, all of which are critical waypoints for successful infection and spread. Finally, we discuss how this new model for the origin of the viral envelope impacts our overall understanding of virus evolution.
Using Metagenomics to Characterize an Expanding Virosphere.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.CELL.2018.02.043
Abstract: We know less about viruses than any other lifeform. Fortunately, metagenomics has led to a massive expansion in the known ersity of the virosphere. Here, we discuss how metagenomics has changed our understanding of RNA viruses and present some of the remaining challenges, including characterization of the "dark matter" of ergent viral genomes.
Collecting and managing taxonomic data with NCBI-taxonomist
Publisher: Oxford University Press (OUP)
Date: 12-2020
DOI: 10.1093/BIOINFORMATICS/BTAA1027
Abstract: We present NCBI-taxonomist—a command-line tool written in Python that collects and manages taxonomic data from the National Center for Biotechnology Information (NCBI). NCBI-taxonomist does not depend on a pre-downloaded taxonomic database but can store data locally. NCBI-taxonomist has six commands to map, collect, extract, resolve, import and group taxonomic data that can be linked together to create powerful analytical pipelines. Because many lifescience databases use the same taxonomic information, the data managed by NCBI-taxonomist is not limited to NCBI and can be used to find data linked to taxonomic information present in other scientific databases. NCBI-taxonomist is implemented in Python 3 (≥3.8) and available at anpb/ncbi-taxonomist and via PyPi (roject/ncbi-taxonomist/), as a Docker container (anpb/ncbi-taxonomist/container_registry/) and Singularity (v3.5.3) image (cloud.sylabs.io/library/jpb/ncbi-taxonomist). NCBI-taxonomist is licensed under the GPLv3.
Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential
Publisher: Springer Science and Business Media LLC
Date: 10-07-2023
DOI: 10.1038/S41467-023-39835-1
Abstract: Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the ersity and abundance of viruses within in idual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 in idual bats s led from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat in iduals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia
Publisher: American Society for Microbiology
Date: 09-2017
DOI: 10.1128/JVI.00680-17
Abstract: Mosquitoes harbor a high ersity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a erse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less ersity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral ersity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus ersity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus ersity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses. IMPORTANCE Studies of virus ecology have generally focused on in idual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus ersity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a erse set of virus families. A key result was that host genetic background plays a more important role in shaping virus ersity than s ling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes.
Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome
Publisher: American Society for Microbiology
Date: 13-04-2023
DOI: 10.1128/SPECTRUM.04655-22
Abstract: This study revealed the huge capability of mosquitoes in harboring a rich ersity of RNA viruses, although relevant studies have characterized the intensively unparalleled ersity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic ersity and abundance of Wolbachia between different mosquito populations.
High Rates of Molecular Evolution in Hantaviruses
Publisher: Oxford University Press (OUP)
Date: 03-04-2008
Abstract: Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10(-7) nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of co ergence and hence shared ergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent approach to estimate the rate of nucleotide substitution from serially s led gene sequence data for hantaviruses known to infect each of the 3 rodent subfamilies: Araraquara virus (Sigmodontinae), Dobrava virus (Murinae), Puumala virus (Arvicolinae), and Tula virus (Arvicolinae). Our results reveal that hantaviruses exhibit short-term substitution rates of 10(-2) to 10(-4) substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution rate and that estimated assuming rodent-hantavirus co ergence suggests that the co ergence hypothesis may need to be reevaluated.
Viral respiratory infections among Hajj pilgrims in 2013
Publisher: Elsevier BV
Date: 14-11-2014
Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection
Publisher: American Society for Microbiology
Date: 05-2015
Abstract: Resistance following antiviral therapy is commonly observed in human influenza viruses. Although this evolutionary process is initiated within in idual hosts, little is known about the pattern, dynamics, and drivers of antiviral resistance at this scale, including the role played by reassortment. In addition, the short duration of human influenza virus infections limits the available time window in which to examine intrahost evolution. Using single-molecule sequencing, we mapped, in detail, the mutational spectrum of an H3N2 influenza A virus population s led from an immunocompromised patient who shed virus over a 21-month period. In this unique natural experiment, we were able to document the complex dynamics underlying the evolution of antiviral resistance. In idual resistance mutations appeared weeks before they became dominant, evolved independently on cocirculating lineages, led to a genome-wide reduction in genetic ersity through a selective sweep, and were placed into new combinations by reassortment. Notably, despite frequent reassortment, phylogenetic analysis also provided evidence for specific patterns of segment linkage, with a strong association between the hemagglutinin (HA)- and matrix (M)-encoding segments that matches that previously observed at the epidemiological scale. In sum, we were able to reveal, for the first time, the complex interaction between multiple evolutionary processes as they occur within an in idual host. IMPORTANCE Understanding the evolutionary forces that shape the genetic ersity of influenza virus is crucial for predicting the emergence of drug-resistant strains but remains challenging because multiple processes occur concurrently. We characterized the evolution of antiviral resistance in a single persistent influenza virus infection, representing the first case in which reassortment and the complex patterns of drug resistance emergence and evolution have been determined within an in idual host. Deep-sequence data from multiple time points revealed that the evolution of antiviral resistance reflects a combination of frequent mutation, natural selection, and a complex pattern of segment linkage and reassortment. In sum, these data show how immunocompromised hosts may help reveal the drivers of strain emergence.
Viral evolution and the emergence of SARS coronavirus
Publisher: The Royal Society
Date: 29-07-2004
Abstract: The recent appearance of severe acute respiratory syndrome coronavirus (SARS–CoV) highlights the continual threat to human health posed by emerging viruses. However, the central processes in the evolution of emerging viruses are unclear, particularly the selection pressures faced by viruses in new host species. We outline some of the key evolutionary genetic aspects of viral emergence. We emphasize that, although the high mutation rates of RNA viruses provide them with great adaptability and explain why they are the main cause of emerging diseases, their limited genome size means that they are also subject to major evolutionary constraints. Understanding the mechanistic basis of these constraints, particularly the roles played by epistasis and pleiotropy, is likely to be central in explaining why some RNA viruses are more able than others to cross species boundaries. Viral genetic factors have also been implicated in the emergence of SARS–CoV, with the suggestion that this virus is a recombinant between mammalian and avian coronaviruses. We show, however, that the phylogenetic patterns cited as evidence for recombination are more probably caused by a variation in substitution rate among lineages and that recombination is unlikely to explain the appearance of SARS in humans.
Foreword
Publisher: Cambridge University Press
Date: 26-03-2009
Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses
Publisher: American Society for Microbiology
Date: 15-01-2016
DOI: 10.1128/JVI.02036-15
Abstract: Viruses of the family Flaviviridae are important pathogens of humans and other animals and are currently classified into four genera. To better understand their ersity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to the Flaviviridae in a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the known Flaviviridae (“flavi-like” viruses) from a range of arthropod species. Although these viruses are highly ergent, they share a similar genomic plan and common ancestry with the Flaviviridae in the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic ersity of the Flaviviridae , genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide ersity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark ( Proscyllium habereri ), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that the Flaviviridae infect a far wider range of hosts and exhibit greater ersity in genome structure than previously anticipated. IMPORTANCE The family Flaviviridae of RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the bio ersity and evolution of the Flaviviridae has largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained erse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of the Flaviviridae and related viruses, harboring considerable genetic and phenotypic ersity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.
Author Correction: A new coronavirus associated with human respiratory disease in China
Publisher: Springer Science and Business Media LLC
Date: 02-04-2020
DOI: 10.1038/S41586-020-2202-3
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The impact of media sensationalism and crisis framing on stigma and negative attitudes towards methamphetamine users
Publisher: Wiley
Date: 26-04-2020
DOI: 10.1111/INM.12708
Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses
Publisher: Research Square Platform LLC
Date: 23-11-2022
DOI: 10.21203/RS.3.RS-2301793/V1
Abstract: Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the ersity and abundance of viruses within bats at the level of in idual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 in idual bats s led from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.
Invisible wounds and suicide: Moral injury and veteran mental health
Publisher: Wiley
Date: 12-03-2020
DOI: 10.1111/INM.12704
Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility
Publisher: American Society for Microbiology
Date: 26-10-2022
DOI: 10.1128/JVI.00886-22
Abstract: The evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook ex le of the coevolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype.
Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.CUB.2019.08.076
Abstract: Termitidae comprises ∼80% of all termite species [1] that play dominant decomposer roles in tropical ecosystems [2, 3]. Two major events during termite evolution were the loss of cellulolytic gut protozoans in the ancestor of Termitidae and the subsequent gain in the termitid subfamily Macrotermitinae of fungal symbionts cultivated externally in "combs" constructed within the nest [4, 5]. How these symbiotic transitions occurred remains unresolved. Phylogenetic analyses of mitochondrial data previously suggested that Macrotermitinae is the earliest branching termitid lineage, followed soon after by Sphaerotermitinae [6], which cultivates bacterial symbionts on combs inside its nests [7]. This has led to the hypothesis that comb building was an important evolutionary step in the loss of gut protozoa in ancestral termitids [8]. We sequenced genomes and transcriptomes of 55 termite species and reconstructed phylogenetic trees from up to 4,065 orthologous genes of 68 species. We found strong support for a novel sister-group relationship between the bacterial comb-building Sphaerotermitinae and fungus comb-building Macrotermitinae. This key finding indicates that comb building is a derived trait within Termitidae and that the creation of a comb-like "external rumen" involving bacteria or fungi may not have driven the loss of protozoa from ancestral termitids, as previously hypothesized. Instead, associations with gut prokaryotic symbionts, combined with dietary shifts from wood to other plant-based substrates, may have played a more important role in this symbiotic transition. Our phylogenetic tree provides a platform for future studies of comparative termite evolution and the evolution of symbiosis in this taxon.
The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus
Publisher: Oxford University Press (OUP)
Date: 16-03-2011
Mother-to-child transmission of HIV infection and CTL escape through HLA-A2-SLYNTVATL epitope sequence variation
Publisher: Elsevier BV
Date: 11-2001
DOI: 10.1016/S0165-2478(01)00272-3
Abstract: Cytotoxic T lymphocytes (CTL) play a central role in containment of HIV infection. Evasion of the immune response by CTL escape is associated with progression to disease. It is therefore hypothesised that transmitted viruses encode escape mutations within epitopes that are required for successful control of viraemia. In order to test this hypothesis, escape through the dominant HLA-A2-restricted CTL epitope SLYNTVATL (p17 Gag residues 77-85 SL9) in the setting of mother-to-child-transmission (MTCT) was investigated. Initial data from two families in which the HIV-infected mother expressed HLA-A*0201 and had transmitted the virus to other family members were consistent with this hypothesis. In addition, analysis of the gag sequence phylogeny in one family demonstrated that CTL escape variants can be successfully transmitted both horizontally and vertically. To test the hypothesis further, a larger cohort of transmitting mothers (n=8) and non-transmitters (n=14) were studied. Variation within the SL9 epitope was associated with expression of HLA-A2 (P=0.04) but overall no clear link between variation from the SL9 consensus sequence and MTCT was established. However, the high level of background ersity within p17 Gag served to obscure any possible association between escape and MTCT. In conclusion, these studies highlighted the obstacles to demonstrating CTL escape arising at this particular epitope. Alternative strategies likely to be more definitive are discussed.
Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures
Publisher: American Society for Microbiology
Date: 26-10-2022
DOI: 10.1128/JVI.00783-22
Abstract: Our knowledge of the ersity of RNA viruses infecting microbial algae—the microalgae—is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields.
S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification
Publisher: Elsevier BV
Date: 04-2016
Evolution of an Eurasian Avian-like Influenza Virus in Naive and Vaccinated Pigs
Publisher: Public Library of Science (PLoS)
Date: 31-05-2012
Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype
Publisher: Proceedings of the National Academy of Sciences
Date: 14-08-2017
Abstract: When a pathogen emerges in a host population, will it evolve to do more or less harm to its host? A single strain of myxoma virus was released as a biocontrol agent against Australian rabbit populations in 1950. The subsequent coevolution has become a textbook classic, although there has been little experimental work on this topic since the early 1980s. Here, we show that the host–pathogen arms race continued with the evolution of highly lethal viruses that cause immune collapse. The possibility that pathogens can become highly immunosuppressive in response to increases in host resistance needs to be considered where genetic and immunologic manipulations are used to enhance host resistance, as, for instance, in agriculture.
Clustered Mutations in HIV-1 Gag Are Consistently Required for Escape from Hla-B27–Restricted Cytotoxic T Lymphocyte Responses
Publisher: Rockefeller University Press
Date: 05-02-2001
Abstract: The immune response to HIV-1 in patients who carry human histocompatibility leukocyte antigen (HLA)-B27 is characterized by an immunodominant response to an epitope in p24 gag (amino acids 263–272, KRWIILGLNK). Substitution of lysine (K) or glycine (G) for arginine (R) at HIV-1 gag residue 264 (R264K and R264G) results in epitopes that bind to HLA-B27 poorly. We have detected a R264K mutation in four patients carrying HLA-B27. In three of these patients the mutation occurred late, coinciding with disease progression. In another it occurred within 1 yr of infection and was associated with a virus of syncytium-inducing phenotype. In each case, R264K was tightly associated with a leucine to methionine change at residue 268. After the loss of the cytotoxic T lymphocyte (CTL) response to this epitope and in the presence of high viral load, reversion to wild-type sequence was observed. In a fifth patient, a R264G mutation was detected when HIV-1 disease progressed. Its occurrence was associated with a glutamic acid to aspartic acid mutation at residue 260. Phylogenetic analyses indicated that these substitutions emerged under natural selection rather than by genetic drift or linkage. Outgrowth of CTL escape viruses required high viral loads and additional, possibly compensatory, mutations in the gag protein.
After the pandemic: perspectives on the future trajectory of COVID-19
Publisher: Springer Science and Business Media LLC
Date: 08-07-2021
The Evolutionary Dynamics of Human Influenza B Virus
Publisher: Springer Science and Business Media LLC
Date: 27-05-2008
17th Century Variola Virus Reveals the Recent History of Smallpox
Publisher: Elsevier BV
Date: 12-2016
Sun protective behaviors at an outdoor entertainment event in Australia
Publisher: Wiley
Date: 28-12-2018
DOI: 10.1111/NHS.12396
Abstract: An observational study was conducted to examine the use of sun protective hats, clothing, and sunglasses of people attending an outdoor entertainment event in an area of high-to-extreme ultraviolet radiation in New South Wales, Australia. Armidale is unique, as it is a highly-elevated area, almost 1000 m above sea level, and temperatures are often mild with very high-to-extreme levels of ultraviolet radiation. Four trained data collectors observed attendees as they entered the event, and recorded their use of sun protective hats, clothing, and sunglasses. While more than half of the attendees wore sun protective hats, only 14% wore sun protective clothing. Broad-brimmed hats were considered sun protective, while sun protective clothing was defined by shirts with at least three-quarter-length sleeves. Females were more likely to wear both a sun protective hat and clothing than males, and children were less protected than adults. Legislative changes are required to ensure that organizers of outdoor events have a legal responsibility to provide a safe environment for attendees, including strategies to help reduce ultraviolet radiation exposure.
Loss of Viral Control in Early HIV‐1 Infection Is Temporally Associated with Sequential Escape from CD8+T Cell Responses and Decrease in HIV–1–Specific CD4+and CD8+T C
Publisher: Oxford University Press (OUP)
Date: 15-08-2004
DOI: 10.1086/422760
The contrasting phylodynamics of human influenza B viruses
Publisher: eLife Sciences Publications, Ltd
Date: 16-01-2015
DOI: 10.7554/ELIFE.05055
Abstract: A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their in idual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.
The Recovery, Interpretation and Use of Ancient Pathogen Genomes
Publisher: Elsevier BV
Date: 10-2020
Origin and Evolution of Viruses. Esteban Domingo , Robert Webster , John Holland
Publisher: University of Chicago Press
Date: 03-2001
DOI: 10.1086/393774
Selection for Robustness in Mutagenized RNA Viruses
Publisher: Public Library of Science (PLoS)
Date: 15-06-2007
Artificial intelligence redefines RNA virus discovery
Publisher: Cold Spring Harbor Laboratory
Date: 18-04-2023
DOI: 10.1101/2023.04.18.537342
Abstract: RNA viruses are erse components of global ecosystems. The metagenomic identification of RNA viruses is currently limited to those with sequence similarity to known viruses, such that highly ergent viruses that comprise the “dark matter” of the virosphere remain challenging to detect. We developed a deep learning algorithm – LucaProt – to search for highly ergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 global meta- transcriptomes. LucaProt integrates both sequence and structural information to accurately and efficiently detect RdRP sequences. With this approach we identified 180,571 RNA viral species and 180 superclades (viral phyla/classes). This is the broadest ersity of RNA viruses described to date, including many viruses undetectable using BLAST or HMM approaches. The newly identified RNA viruses were present in erse ecological niches, including the air, hot springs and hydrothermal vents, and both virus ersity and abundance varied substantially among ecological types. We also identified the longest RNA virus genome (nido-like) observed so far, at 47,250 nucleotides, and expanded the ersity of RNA bacteriophage to more than ten phyla/classes. This study marks the beginning of a new era of virus discovery, with the potential to redefine our understanding of the global virosphere and reshape our understanding of virus evolutionary history.
Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates
Publisher: Microbiology Society
Date: 09-2007
Abstract: Equid herpesvirus 2 (EHV-2), in common with other members of the subfamily Gammaherpesvirinae , encodes homologues of cellular seven-transmembrane receptors (7TMR), namely open reading frames (ORFs) E1, 74 and E6, which each show some similarity to cellular chemokine receptors. Whereas ORF74 and E6 are members of gammaherpesvirus-conserved 7TMR gene families, E1 is currently unique to EHV-2. To investigate their genetic variability, EHV-2 7TMRs from a panel of equine gammaherpesvirus isolates were sequenced. A region of gB was sequenced to provide comparative sequence data. Phylogenetic analysis revealed six ‘genogroups’ for E1 and four for ORF74, which exhibited approximately 10–38 and 11–27 % amino acid difference between groups, respectively. In contrast, E6 was highly conserved, with two genogroups identified. The greatest variation was observed within the N-terminal domains and other extracellular regions. Nevertheless, analysis of the number of non-synonymous ( d N ) and synonymous ( d S ) substitutions per site generally supported the hypothesis that the 7TMRs are under negative selective pressure to retain functionally important residues, although some site-specific positive selection ( d N d S ) was also observed. Collectively, these data are consistent with transmembrane and cytoplasmic domains being less tolerant of mutations with adverse effects upon function. Finally, there was no evidence for genetic linkage between the different gB, E1, ORF74 and E6 genotypes, suggesting frequent intergenic recombination between different EHV-2 strains.
Reverse Engineering Field Isolates of Myxoma Virus Demonstrates that Some Gene Disruptions or Losses of Function Do Not Explain Virulence Changes Observed in the Field
Publisher: American Society for Microbiology
Date: 15-10-2017
DOI: 10.1128/JVI.01289-17
Abstract: The coevolution of myxoma virus (MYXV) and wild European rabbits in Australia and Europe is a paradigm for the evolution of a pathogen in a new host species. Genomic analyses have identified the mutations that have characterized this evolutionary process, but defining causal mutations in the pathways from virulence to attenuation and back to virulence has not been possible. Using reverse genetics, we examined the roles of six selected mutations found in Australian field isolates of MYXV that fall in known or potential virulence genes. Several of these mutations occurred in genes previously identified as virulence genes in whole-gene knockout studies. Strikingly, no single or double mutation among the mutations tested had an appreciable impact on virulence. This suggests either that virulence evolution was defined by amino acid changes other than those analyzed here or that combinations of multiple mutations, possibly involving epistatic interactions or noncoding sequences, have been critical in the ongoing evolution of MYXV virulence. In sum, our results show that single-gene knockout studies of a progenitor virus can have little power to predict the impact of in idual mutations seen in the field. The genetic determinants responsible for this canonical case of virulence evolution remain to be determined. IMPORTANCE The species jump of myxoma virus (MYXV) from the South American tapeti to the European rabbit populations of Australia and Europe is a canonical ex le of host-pathogen coevolution. Detailed molecular studies have identified multiple genes in MYXV that are critical for virulence, and genome sequencing has revealed the evolutionary history of MYXV in Australia and Europe. However, it has not been possible to categorically identify the key mutations responsible for the attenuation of or reversion to virulence during this evolutionary process. Here we use reverse genetics to examine the role of mutations in viruses isolated early and late in the Australian radiation of MYXV. Surprisingly, none of the candidate mutations that we identified as likely having roles in attenuation proved to be important for virulence. This indicates that considerable caution is warranted when interpreting the possible role of in idual mutations during virulence evolution.
A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum Lenarviricota
Publisher: Elsevier BV
Date: 10-2023
Clade Replacements in Dengue Virus Serotypes 1 and 3 Are Associated with Changing Serotype Prevalence
Publisher: American Society for Microbiology
Date: 15-12-2005
DOI: 10.1128/JVI.79.24.15123-15130.2005
Abstract: The evolution of dengue virus (DENV) is characterized by phylogenetic trees that have a strong temporal structure punctuated by dramatic changes in clade frequency. To determine the cause of these large-scale phylogenetic patterns, we examined the evolutionary history of DENV serotype 1 (DENV-1) and DENV-3 in Thailand, where gene sequence and epidemiological data are relatively abundant over a 30-year period. We found evidence for the turnover of viral clades in both serotypes, most notably in DENV-1, where a major clade replacement event took place in genotype I during the mid-1990s. Further, when this clade replacement event was placed in the context of changes in serotype prevalence in Thailand, a striking pattern emerged an increase in DENV-1 clade ersity was associated with an increase in the abundance of this serotype and a concomitant decrease in DENV-4 prevalence, while clade replacement was associated with a decline in DENV-1 prevalence and a rise of DENV-4. We postulate that intraserotypic genetic ersification proceeds at times of relative serotype abundance and that replacement events can result from differential susceptibility to cross-reactive immune responses.
Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes
Publisher: Cold Spring Harbor Laboratory
Date: 28-06-2023
DOI: 10.1101/2023.06.28.546811
Abstract: Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of disease emergence. We examined how the rapid adaptive radiation of the African cichlid fishes of Lake Tanganyika over the last 10 million years has shaped the ersity and evolution of the viruses they carry. Through metatranscriptomic analysis we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae , Metahepadnavirus , Nackednavirus , Picornaviridae , and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus evolution was not constant throughout the cichlid radiation, but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid ersification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data show that African cichlids contain a complex interacting pool of virus ersity, likely reflecting their close genetic relationships that lowers the barriers to cross-species virus transmission.
Biological consequences of deletions within the 3′-untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure
Publisher: Elsevier BV
Date: 11-1999
DOI: 10.1016/S0168-1702(99)00079-9
Abstract: It was previously reported that deletions introduced into the 3'-untranslated region (3'-UTR) of dengue type 4 (DEN 4) virus (Men, R., Bray, M., Clark, D., Chanock, R.M., Lai, C.J., 1996. DEN 4 virus mutants containing deletions in the 3'-noncoding region of the RNA genome: analysis of growth restriction in cell culture and altered viremia pattern and immunogenicity in Rhesus monkeys. J. Virol. 70, 3930-3937), tick-borne encephalitis (TBE) virus (Mandl, C.W., Holzmann, H., Meixner, T., Rauscher, S., Stadler, P.F., Allison, S.L. , Heinz, F.X., 1998. Spontaneous and engineered deletions in the 3'-noncoding region of TBE virus: construction of highly attenuated mutants of a flavivirus. J. Virol. 72, 2132-2140) and subgenomic replicons of Kunjin virus (Khromykh, A.A., Westaway, E.G., 1997. Subgenomic replicons of the flavivirus Kunjin: construction and applications. J. Virol. 71, 1497-1505) altered the infectivity of the mutants and reduced the efficiency of RNA replication. Here, these deletions were superimposed onto the models of secondary structure we constructed previously and the folding of the modified 3'-UTR sequences was simulated. The analysis showed that most of the deletions disrupted or reshaped conserved elements of secondary structure and that the biological effects of these deletions are likely to represent structural rearrangements in the 3'-UTR, rather than the loss of sequence motifs. The analysis also suggested that the overall structural integrity of the flaviviral 3'-UTR is essential for optimal performance of its promotor function, although two distinct parts can be defined: the most 3'-terminal structures and sequences which may be critical for the initiation of minus-strand RNA synthesis, and more proximal structures and sequences that possibly function as enhancers of viral RNA replication. The functional significance of certain structural elements and their possible effect on the efficiency of viral replication in different cells are also discussed.
Reagent contamination in viromics: all that glitters is not gold
Publisher: Elsevier BV
Date: 10-2019
Effective pain management as part of palliative care for persons living with HIV/AIDS in a developing country: a qualitative study
Publisher: Wiley
Date: 15-04-2016
DOI: 10.1111/JOCN.13145
Neodymium-doped nanoparticles for infrared fluorescence bioimaging: The role of the host
Publisher: AIP Publishing
Date: 13-10-2015
DOI: 10.1063/1.4932669
Abstract: The spectroscopic properties of different infrared-emitting neodymium-doped nanoparticles (LaF3:Nd3+, SrF2:Nd3+, NaGdF4: Nd3+, NaYF4: Nd3+, KYF4: Nd3+, GdVO4: Nd3+, and Nd:YAG) have been systematically analyzed. A comparison of the spectral shapes of both emission and absorption spectra is presented, from which the relevant role played by the host matrix is evidenced. The lack of a “universal” optimum system for infrared bioimaging is discussed, as the specific bioimaging application and the experimental setup for infrared imaging determine the neodymium-doped nanoparticle to be preferentially used in each case.
The COVID‐19 pandemic and mental health impacts
Publisher: Wiley
Date: 10-04-2020
DOI: 10.1111/INM.12726
Table S1, S2, S3, S4 from Copy Number Aberration Analysis to Predict Response to Neoadjuvant Anti-HER2 Therapy: Results from the NeoALTTO Phase III Clinical Trial
Publisher: American Association for Cancer Research (AACR)
Date: 31-03-2023
DOI: 10.1158/1078-0432.22481762.V1
Abstract: Table S1: Clinicopathological characteristics of the patients. Table S2: List of 49 genes associated with CNAs in breast cancer from the COSMIC Cancer Gene Census database. Table S3: Gene ontology analysis of the genes correlated with the genome instability index. Table S4: Gene ontology analysis of the genes anti-correlated with the genome instability index.
High rate of viral evolution associated with the emergence of carnivore parvovirus
Publisher: Proceedings of the National Academy of Sciences
Date: 30-12-2004
Abstract: Canine parvovirus (CPV) is an emerging DNA virus that was first observed to cause disease in canines in 1978 and has since become a ubiquitous pathogen worldwide. CPV emerged from feline panleukopenia parvovirus (FPLV) or a closely related virus, differing at several key amino acid residues. Here we characterize the evolutionary processes underlying the emergence of CPV. Although FPLV has remained an endemic infection in its host populations, we show that, since the 1970s, the newly emerged CPV has undergone an epidemic-like pattern of logistic/exponential growth, effectively doubling its population size every few years. This rapid population growth was associated with a lineage of CPV that acquired a broader host range and greater infectivity. Recombination played no role in the emergence of CPV. Rather, any preexisting variation in the donor species and the subsequent rapid adaptation of the virus to canines were likely dependent on a high rate of mutation and the positive selection of mutations in the major capsid gene. Strikingly, although these single-stranded viruses have a DNA genome and use cellular replication machinery, their rate of nucleotide substitution is closer to that of RNA viruses than to that of double-stranded DNA viruses.
Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome
Publisher: MDPI AG
Date: 25-09-2020
DOI: 10.3390/V12101073
Abstract: Viral pathogens are being increasingly described in association with mass morbidity and mortality events in reptiles. However, our knowledge of reptile viruses remains limited. Herein, we describe the meta-transcriptomic investigation of a mass morbidity and mortality event in a colony of central bearded dragons (Pogona vitticeps) in 2014. Severe, extensive proliferation of the respiratory epithelium was consistently found in affected dragons. Similar proliferative lung lesions were identified in bearded dragons from the same colony in 2020 in association with increased intermittent mortality. Total RNA sequencing identified two ergent DNA viruses: a reptile-infecting circovirus, denoted bearded dragon circovirus (BDCV), and the first exogeneous reptilian chaphamaparvovirus—bearded dragon chaphamaparvovirus (BDchPV). Phylogenetic analysis revealed that BDCV was most closely related to bat-associated circoviruses, exhibiting 70% amino acid sequence identity in the Replicase (Rep) protein. In contrast, in the nonstructural (NS) protein, the newly discovered BDchPV showed approximately 31%–35% identity to parvoviruses obtained from tilapia fish and crocodiles in China. Subsequent specific PCR assays revealed BDCV and BDchPV in both diseased and apparently normal captive reptiles, although only BDCV was found in those animals with proliferative pulmonary lesions and respiratory disease. This study expands our understanding of viral ersity in captive reptiles.
Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans
Publisher: Elsevier BV
Date: 07-2016
Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia
Publisher: Elsevier BV
Date: 07-2009
DOI: 10.1016/J.VIRUSRES.2009.02.020
Abstract: Although dengue is a common disease in South-East Asia, there is a marked absence of virological data from the Malaysian state of Sarawak located on the island of Borneo. From 1997 to 2002 we noted the co-circulation of DENV-2, DENV-3 and DENV-4 in Sarawak. To determine the origins of these Sarawak viruses we obtained the complete E gene sequences of 21 isolates. A phylogenetic analysis revealed multiple entries of DENV-2 and DENV-4 into Sarawak, such that multiple lineages co-circulate, yet with little exportation from Sarawak. Notably, all viral isolates were most closely related to those circulating in different localities in South-East Asia. In sum, our analysis reveals a frequent traffic of DENV in South-East Asia, with Sarawak representing a local sink population.
Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain
Publisher: Life Science Alliance, LLC
Date: 11-12-2019
Abstract: Host interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral restriction factors. Of these, IFITM3 potently inhibits viruses that enter cells through acidic endosomes, many of which are zoonotic and emerging viruses with bats (order Chiroptera) as their natural hosts. We previously demonstrated that microbat IFITM3 is antiviral. Here, we show that bat IFITMs are characterized by strong adaptive evolution and identify a highly variable and functionally important site—codon 70—within the conserved CD225 domain of IFITMs. Mutation of this residue in microbat IFITM3 impairs restriction of representatives of four different virus families that enter cells via endosomes. This mutant shows altered subcellular localization and reduced S-palmitoylation, a phenotype copied by mutation of conserved cysteine residues in microbat IFITM3. Furthermore, we show that microbat IFITM3 is S-palmitoylated on cysteine residues C71, C72, and C105, mutation of each cysteine in idually impairs virus restriction, and a triple C71A-C72A-C105A mutant loses all restriction activity, concomitant with subcellular re-localization of microbat IFITM3 to Golgi-associated sites. Thus, we propose that S-palmitoylation is critical for Chiropteran IFITM3 function and identify a key molecular determinant of IFITM3 S-palmitoylation.
Correction: The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations
Publisher: Public Library of Science (PLoS)
Date: 15-08-2013
DOI: 10.1371/ANNOTATION/CFF22061-44D5-4301-B853-41702D160203
Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.JCV.2015.06.093
Abstract: Although hand, foot, and mouth disease (HFMD) is a major public concern in China, the prevalence and clinical symptoms associated with the different agents of HFMD in this country remain poorly understood. We investigated the clinical and molecular characteristics of enteroviruses in patients with HFMD from Wenzhou, China. Patients with laboratory-confirmed HFMD admitted to the Yuying Children's Hospital in Wenzhou, China during 2013 were included in this study. Viral RNA sequences were lified using RT-PCR, determined by sequencing, and compared by phylogenetic analysis. A total of 955 clinically diagnosed HFMD cases were determined using PCR, with whole viral genomes obtained for each enterovirus type. 14 types of enterovirus belonging to two viral species were identified. Notably, Coxsackievirus A6 (CV-A6) was the most common species detected (77.8%), followed by EV-A71 (8.2%) and CV-A10 (8.1%). Phylogenetic analysis revealed multiple independent introductions of these viruses into Wenzhou. In addition, the enterovirus observed in Wenzhou had a recombinant history, with two or three recombination breakpoints. Although the illness associated with CV-A6 was milder than that of EV-A71, CV-A6 infection caused more widespread rash, larger blisters, and subsequent skin peeling and/or nail shedding. Our study revealed the co-circulation of 14 types of enteroviruses in a single location - Wenzhou, China - with CV-A6 virus the predominant agent of HFMD. This work highlights the need to perform larger-scale surveillance to fully understand the epidemiology of enteroviruses in China and the wider Asia-Pacific region.
Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe.
Publisher: MDPI AG
Date: 06-11-2019
DOI: 10.3390/V11111033
Abstract: Mosquitoes harbor an extensive ersity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the ersity and evolutionary history of RNA viruses s led from mosquitoes in northerly regions. Here, we compared the RNA virome of two common northern mosquito species, Culex pipiens and Culex torrentium, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we documented similar levels of virome ersity as in mosquitoes s led from the more bio erse lower latitudes. Many viruses were also related to those s led on other continents, indicative of a widespread global movement and/or long host–virus co-evolution. Although the two mosquito species investigated have overlapping geographical distributions and share many viruses, several viruses were only found at a specific location at this scale of s ling, such that local habitat and geography may play an important role in shaping viral ersity in Culex mosquitoes.
Trends in Patterns of Dengue Transmission over 4 Years in a Pediatric Cohort Study in Nicaragua
Publisher: Oxford University Press (OUP)
Date: 2010
DOI: 10.1086/648592
An Ecosystems Perspective on Virus Evolution and Emergence
Publisher: Elsevier BV
Date: 03-2020
DOI: 10.1016/J.TIM.2019.10.010
Abstract: Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host in iduals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and ersity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.
Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection
Publisher: Oxford University Press (OUP)
Date: 11-2006
DOI: 10.1534/GENETICS.105.052019
Abstract: The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic ersity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences s led longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.
Kolente virus, a rhabdovirus species isolated from Communication ticks and bats in the Republic of Guinea
Publisher: Microbiology Society
Date: 12-2013
Abstract: Kolente virus (KOLEV) is a rhabdovirus originally isolated from ticks and a bat in Guinea, West Africa, in 1985. Although tests at the time of isolation suggested that KOLEV is a novel rhabdovirus, it has remained largely uncharacterized. We assembled the complete genome sequence of the prototype strain DakAr K7292, which was found to encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs ( nt) in the P and L genes. Serologically, KOLEV exhibited a weak antigenic relationship with Barur and Fukuoka viruses in the Kern Canyon group. Phylogenetic analysis revealed that KOLEV represents a distinct and ergent lineage that shows no clear relationship to any rhabdovirus except Oita virus, although with limited phylogenetic resolution. In summary, KOLEV represents a novel species in the family Rhabdoviridae .
Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic
Publisher: Springer Science and Business Media LLC
Date: 24-06-2015
DOI: 10.1038/NATURE14612
Abstract: An epidemic of Ebola virus disease of unprecedented scale has been ongoing for more than a year in West Africa. As of 29 April 2015, there have been 26,277 reported total cases (of which 14,895 have been laboratory confirmed) resulting in 10,899 deaths. The source of the outbreak was traced to the prefecture of Guéckédou in the forested region of southeastern Guinea. The virus later spread to the capital, Conakry, and to the neighbouring countries of Sierra Leone, Liberia, Nigeria, Senegal and Mali. In March 2014, when the first cases were detected in Conakry, the Institut Pasteur of Dakar, Senegal, deployed a mobile laboratory in Donka hospital to provide diagnostic services to the greater Conakry urban area and other regions of Guinea. Through this process we s led 85 Ebola viruses (EBOV) from patients infected from July to November 2014, and report their full genome sequences here. Phylogenetic analysis reveals the sustained transmission of three distinct viral lineages co-circulating in Guinea, including the urban setting of Conakry and its surroundings. One lineage is unique to Guinea and closely related to the earliest s led viruses of the epidemic. A second lineage contains viruses probably reintroduced from neighbouring Sierra Leone on multiple occasions, while a third lineage later spread from Guinea to Mali. Each lineage is defined by multiple mutations, including non-synonymous changes in the virion protein 35 (VP35), glycoprotein (GP) and RNA-dependent RNA polymerase (L) proteins. The viral GP is characterized by a glycosylation site modification and mutations in the mucin-like domain that could modify the outer shape of the virion. These data illustrate the ongoing ability of EBOV to develop lineage-specific and potentially phenotypically important variation.
Extensive diversity and evolution of hepadnaviruses in bats in China
Publisher: Elsevier BV
Date: 2018
The potential for COVID‐19 to contribute to compassion fatigue in critical care nurses
Publisher: Wiley
Date: 18-05-2020
DOI: 10.1111/JOCN.15314
Knowledge and attitudes of mental health professionals and students regarding recovery: A systematic review
Publisher: Wiley
Date: 12-03-2020
DOI: 10.1111/INM.12712
Compassion fatigue in critical care nurses. An integrative review of the literature
Publisher: Saudi Medical Journal
Date: 11-2019
Evidence for an endogenous papillomavirus-like element in the platypus genome
Publisher: Microbiology Society
Date: 06-2012
Abstract: Papillomaviruses (PVs) infect a wide range of vertebrates and have ersified into multiple genetic types, some of which have serious consequences for human health. Although PVs have to date only been characterized as exogenous viral forms, here we report the observation of an endogenous viral element (EPVLoa) in the genome of the platypus ( Ornithorhynchus anatinus ) that is related to PVs. Further data mining for endogenous PV-like elements is therefore warranted.
Complexities of Estimating Evolutionary Rates in Viruses
Publisher: American Society for Microbiology
Date: 15-02-2016
DOI: 10.1128/JVI.02570-15
Detection and Circulation of a Novel Rabbit Hemorrhagic Disease Virus in Australia
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 2018
Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health
Publisher: Springer Science and Business Media LLC
Date: 13-06-2011
DOI: 10.1038/NRMICRO2595
The origins of SARS-CoV-2: A critical review
Publisher: Elsevier BV
Date: 09-2021
The impact of migratory flyways on the spread of avian influenza virus in North America
Publisher: Springer Science and Business Media LLC
Date: 25-05-2017
Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum
Publisher: MDPI AG
Date: 28-09-2017
DOI: 10.3390/V9100276
Widespread intra-serotype recombination in natural populations of dengue virus
Publisher: Proceedings of the National Academy of Sciences
Date: 22-06-1999
Abstract: Diversity analysis of 71 published dengue virus gene sequences revealed several strains that appeared to be mosaics comprising gene regions with conflicting evolutionary histories. Subsequent maximum likelihood breakpoint estimation identified seven recombinants, including members of three of the four dengue virus serotypes, with breakpoints in the premembrane/membrane gene, the envelope gene, and at the junction of the envelope and first nonstructural genes. Many of the in idual recombinants contain sequence representing separate genetic subtypes. The results were highly statistically significant and were confirmed by phylogenetic analysis of the regions of interest. These findings indicate that recombination may play a very significant role in shaping genetic ersity in dengue virus and, as such, have important implications for its biology and its control.
Characterizing the virome of Ixodes ricinus ticks from northern Europe.
Publisher: Springer Science and Business Media LLC
Date: 07-09-2017
DOI: 10.1038/S41598-017-11439-Y
Abstract: RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral ersity in ticks is still poorly understood, particularly in Europe. Using a bulk RNA-sequencing approach that captures the complete transcriptome, we analysed the virome of the most common tick in Europe – Ixodes ricinus . In total, RNA sequencing was performed on six libraries consisting of 33 I. ricinus nymphs and adults s led in Norway. Despite the small number of animals surveyed, our virus identification pipeline revealed nine erse and novel viral species, phylogenetically positioned within four different viral groups – bunyaviruses, luteoviruses, mononegavirales and partitiviruses – and sometimes characterized by extensive genetic ersity including a potentially novel genus of bunyaviruses. This work sheds new light on the virus ersity in I. ricinus , expands our knowledge of potential host/vector-associations and tick-transmitted viruses within several viral groups, and pushes the latitudinal limit where it is likely to find tick-associated viruses. Notably, our phylogenetic analysis revealed the presence of tick-specific virus clades that span multiple continents, highlighting the role of ticks as important virus reservoirs.
SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species
Publisher: Elsevier BV
Date: 2021
The origin and phylogeography of dog rabies virus
Publisher: Microbiology Society
Date: 11-2008
DOI: 10.1099/VIR.0.2008/003913-0
Abstract: Rabies is a progressively fatal and incurable viral encephalitis caused by a lyssavirus infection. Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies viruses (RABV). Despite the importance of rabies for human health, little is known about the spread of RABV in dog populations, and patterns of bio ersity have only been studied in limited geographical space. To address these questions on a global scale, we sequenced 62 new isolates and performed an extensive comparative analysis of RABV gene sequence data, representing 192 isolates s led from 55 countries. From this, we identified six clades of RABV in non-flying mammals, each of which has a distinct geographical distribution, most likely reflecting major physical barriers to gene flow. Indeed, a detailed analysis of phylogeographic structure revealed only limited viral movement among geographical localities. Using Bayesian coalescent methods we also reveal that the s led lineages of canid RABV derive from a common ancestor that originated within the past 1500 years. Additionally, we found no evidence for either positive selection or widespread population bottlenecks during the global expansion of canid RABV. Overall, our study reveals that the stochastic processes of genetic drift and population sub ision are the most important factors shaping the global phylogeography of canid RABV.
Living with multiple losses: Insights from patients living with pressure injury
Publisher: Elsevier BV
Date: 08-2018
Understanding the Impact of Historical Trauma Due to Colonization on the Health and Well-Being of Indigenous Young Peoples: A Systematic Scoping Review
Publisher: SAGE Publications
Date: 21-06-2020
Abstract: Introduction: Indigenous Peoples are experiencing the ongoing effects of colonization. This phenomenon, historical trauma (HT), helps to address the current ill-health disparity. Aim of this scoping review was to identify sources of evidence available to understand the impact of HT on Indigenous young peoples. Method: A scoping review was conducted on available evidence-based literature. Article quality was assessed using validated quality appraisal tools. Synthesis was conducted with predefined levels of impact. Results: Consistent with the literature, the themes and levels of impact were interrelated. Despite this, studies predominately reported a singular focus with limited discussion of protective factors. Discussion: HT continues to have a profound impact on Indigenous young peoples across Canada, Australia, New Zealand, and the United States. Protective factors for HT were evident within Indigenous research designs. Future research should ensure a multilevel focus to explore intergenerational strength and how this influences culturally congruent health care.
Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C
Publisher: Springer Science and Business Media LLC
Date: 03-2008
Prior Evidence of Putative NovelRhinovirusSpecies, Australia
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 11-2008
The Emergence of Rotavirus G12 and the Prevalence of Enteric Viruses in Hospitalized Pediatric Diarrheal Patients in Southern Vietnam
Publisher: American Society of Tropical Medicine and Hygiene
Date: 10-2011
The comparative genomics of viral emergence
Publisher: Proceedings of the National Academy of Sciences
Date: 26-01-2010
Abstract: RNA viruses are the main agents of emerging and re-emerging diseases. It is therefore important to reveal the evolutionary processes that underpin their ability to jump species boundaries and establish themselves in new hosts. Here, I discuss how comparative genomics can contribute to this endeavor. Arguably the most important evolutionary process in RNA virus evolution, abundant mutation, may even open up avenues for their control through “lethal mutagenesis.” Despite this remarkable mutational power, adaptation to erse host species remains a major adaptive challenge, such that the most common outcome of host jumps are short-term “spillover” infections. A powerful case study of the utility of genomic approaches to studies of viral evolution and emergence is provided by influenza virus and brought into sharp focus by the ongoing epidemic of swine-origin H1N1 influenza A virus (A/H1N1pdm). Research here reveals a marked lack of surveillance of influenza viruses in pigs, coupled with the possibility of cryptic transmission before the first reported human cases, such that the exact genesis of A/H1N1pdm (where, when, how) is uncertain.
Australia as a global sink for the genetic diversity of avian influenza A virus
Publisher: Public Library of Science (PLoS)
Date: 10-05-2022
DOI: 10.1371/JOURNAL.PPAT.1010150
Abstract: Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV ersity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high ersity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008
Publisher: American Society for Microbiology
Date: 04-2010
DOI: 10.1128/JVI.02385-09
Abstract: Highly pathogenic A/H5N1 avian influenza (HPAI H5N1) viruses have seriously affected the Nigerian poultry industry since early 2006. Previous studies have identified multiple introductions of the virus into Nigeria and several reassortment events between cocirculating lineages. To determine the spatial, evolutionary, and population dynamics of the multiple H5N1 lineages cocirculating in Nigeria, we conducted a phylogenetic analysis of whole-genome sequences from 106 HPAI H5N1 viruses isolated between 2006 and 2008 and representing all 25 Nigerian states and the Federal Capital Territory (FCT) reporting outbreaks. We identified a major new subclade in Nigeria that is phylogenetically distinguishable from all previously identified sublineages, as well as two novel reassortment events. A detailed analysis of viral phylogeography identified two major source populations for the HPAI H5N1 virus in Nigeria, one in a major commercial poultry area (southwest region) and one in northern Nigeria, where contact between wild birds and backyard poultry is frequent. These findings suggested that migratory birds from Eastern Europe or Russia may serve an important role in the introduction of HPAI H5N1 viruses into Nigeria, although virus spread through the movement of poultry and poultry products cannot be excluded. Our study provides new insight into the genesis and evolution of H5N1 influenza viruses in Nigeria and has important implications for targeting surveillance efforts to rapidly identify the spread of the virus into and within Nigeria.
Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
Publisher: Oxford University Press (OUP)
Date: 28-09-2015
Abstract: Determining the time scale of virus evolution is central to understanding their origins and emergence. The phylogenetic methods commonly used for this purpose can be misleading if the substitution model makes incorrect assumptions about the data. Empirical studies consider a pool of models and select that with the highest statistical fit. However, this does not allow the rejection of all models, even if they poorly describe the data. An alternative is to use model adequacy methods that evaluate the ability of a model to predict hypothetical future observations. This can be done by comparing the empirical data with data generated under the model in question. We conducted simulations to evaluate the sensitivity of such methods with nucleotide, amino acid, and codon data. These effectively detected underparameterized models, but failed to detect mutational saturation and some instances of nonstationary base composition, which can lead to biases in estimates of tree topology and length. To test the applicability of these methods with real data, we analyzed nucleotide and amino acid data sets from the genus Flavivirus of RNA viruses. In most cases these models were inadequate, with the exception of a data set of relatively closely related sequences of Dengue virus, for which the GTR+Γ nucleotide and LG+Γ amino acid substitution models were adequate. Our results partly explain the lack of consensus over estimates of the long-term evolutionary time scale of these viruses, and indicate that assessing the adequacy of substitution models should be routinely used to determine whether estimates are reliable.
The Evolution of Endogenous Viral Elements
Publisher: Elsevier BV
Date: 10-2011
Co-infecting pathogens can contribute to inflammatory responses and severe symptoms in COVID-19
Publisher: AME Publishing Company
Date: 02-2022
DOI: 10.21037/JTD-21-1284
Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses
Publisher: American Society for Microbiology
Date: 15-09-2010
DOI: 10.1128/JVI.00771-10
Abstract: The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most erse viral families described to date, the family Rhabdoviridae . We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide ergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of bio ersity in the viral world.
Molecular evolution of the insect-specific flaviviruses
Publisher: Microbiology Society
Date: 02-2012
Abstract: There has been an explosion in the discovery of ‘insect-specific’ flaviviruses and/or their related sequences in natural mosquito populations. Herein we review all ‘insect-specific’ flavivirus sequences currently available and conduct phylogenetic analyses of both the ‘insect-specific’ flaviviruses and available sequences of the entire genus Flavivirus . We show that there is no statistical support for virus–mosquito co- ergence, suggesting that the ‘insect-specific’ flaviviruses may have undergone multiple introductions with frequent host switching. We discuss potential implications for the evolution of vectoring within the family Flaviviridae . We also provide preliminary evidence for potential recombination events in the history of cell fusing agent virus. Finally, we consider priorities and guidelines for future research on ‘insect-specific’ flaviviruses, including the vast potential that exists for the study of bio ersity within a range of potential hosts and vectors, and its effect on the emergence and maintenance of the flaviviruses.
A new coronavirus associated with human respiratory disease in China
Publisher: Springer Science and Business Media LLC
Date: 03-02-2020
DOI: 10.1038/S41586-020-2008-3
Abstract: Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a s le of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae , which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
Properties and abundance of overlapping genes in viruses
Publisher: Oxford University Press (OUP)
Date: 2020
DOI: 10.1093/VE/VEAA009
Abstract: Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering & nt, and 84 per cent are & nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.
Crystal methamphetamine's impact on frontline emergency services in Victoria, Australia
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.AUEC.2019.07.004
Abstract: The use of crystal meth hetamine is a growing problem in Australia. Meth hetamine users can suffer adverse physical health effects, psychotic symptoms and meth hetamine-related aggressive behaviour. The increasing use and related harms of crystal meth hetamine is presenting serious problems for frontline emergency responders. A population-based retrospective analysis was undertaken of data collected by Ambulance Victoria describing crystal meth hetaminerelated events attended by ambulance across Victoria over six financial years from 2011/12 to 2016/17. Meth hetamine-related events attended by Victoria Ambulance paramedics significantly increased from 2011/12 to 2016/17, particularly in regional Victoria. The most frequent age group requiring ambulance attendance is 25-39 years. The proportion of events requiring police coattendance significantly increased, as did transportation to emergency department/hospital. The substantial increases in meth hetamine-related events attended by ambulance indicate the need for increased resources and support for paramedics, particularly in regional/rural areas. The large increase among young people aged 15-24 years indicates a need for policy action on prevention, harm reduction and expanded treatment services to reduce health problems and meth hetamine-related harms.
Ongoing Spillover of Hantaan and Gou Hantaviruses from Rodents Is Associated with Hemorrhagic Fever with Renal Syndrome (HFRS) in China
Publisher: Public Library of Science (PLoS)
Date: 17-10-2013
RAPIDprep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples
Publisher: MDPI AG
Date: 22-12-2022
DOI: 10.20944/PREPRINTS202212.0417.V1
Abstract: Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol & ndash the RAPIDprep assay & ndash with the aim to provide cause agnostic laboratory diagnosis of infection within 24 hours of s le collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and lification of double-stranded cDNA followed by short-read sequencing with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory s les to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library lification across different s le types, qualities and extraction kits using a single protocol without input nucleic acid quantification or quality assessment. Furthermore, we demonstrate the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift towards integration of modern genomic techniques to infectious disease investigations.
Influenza A viruses serially passaged in different MDCK cell lines exhibit limited sequence variation across their genomes, with the exception of the hemagglutinin gene
Publisher: Cold Spring Harbor Laboratory
Date: 23-02-2020
DOI: 10.1101/2020.02.20.959015
Abstract: New methods for deep sequence analysis provide an opportunity to follow the emergence and dynamics of virus mutations in real time. Although viruses are commonly grown in cell culture for research and for vaccine development, the cells used to grow the virus are often not derived from the same tissue or even the same host that the virus naturally replicates in. The selective pressures of culturing virus in vitro are still only partially understood. MDCK cells are the standard cell for growing influenza viruses yet are derived from the epithelium of the canine kidney and are also heterogenous. We passaged human H3N2, H1N1 pandemic, and canine H3N2 influenza A viruses (IAV) in different lineages of MDCK cells, as well as lines engineered to express variant Sia receptors, including α2,3- and α2,6-linkages or N -glycolylneuraminic acid (Neu5Gc) or N -acetylneuraminic acid (Neu5Ac) forms. MDCK-Type II cells had lower infection efficiency and virus production, and infection appeared more dependent on protease activation of the virus. When viruses were passaged in the different cells, they exhibited only small numbers of consensus-level mutations, and most were within the HA gene. Both human IAVs showed selection for single nucleotide minority variants in the HA stem across cell types, as well as low frequency variants in the HA receptor binding site of virus passaged in cells expressing Neu5Gc. Canine H3N2 also showed minority variants near the receptor-binding site in cells expressing Neu5Gc and also in those expressing α 2,6-linkages. The genetic variation and adaptability of viruses are fundamental properties that allow their evolutionary success in the face of differing host environments and immune responses. The growth of viruses in cell culture is widely used for their study and for preparing vaccines. However, the selection pressures that cell passaging imposes on viruses are often poorly understood. We used deep sequence analysis to define, in detail, how three different influenza A viruses respond to passaging in different lineages of canine MDCK cells that are commonly used for their growth, as well as in variant cells engineered to express different forms of their cell surface receptor, sialic acid. This analysis revealed that most mutations occur in the HA gene and few sequence changes in the virus population reached high proportions. This is relevant for understanding the selective pressures of virus growth in cell culture and how it shapes evolutionary patterns.
Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health
Publisher: American Society for Microbiology
Date: 29-06-2023
DOI: 10.1128/JVI.00434-23
Abstract: A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China.
Inferring the Timescale of Dengue Virus Evolution Under Realistic Models of DNA Substitution
Publisher: Springer Science and Business Media LLC
Date: 29-05-2007
DOI: 10.1007/S00239-006-0278-5
Abstract: Dengue virus (DENV) is the agent of the most widespread vector-borne viral disease of humans. To infer the timescale of DENV evolution with as much accuracy as possible, we compared, within a Bayesian Markov Chain Monte Carlo (MCMC) framework, estimates of phylogenetic tree length using both covarion and noncovarion models of molecular evolution, the latter also incorporating lineage-specific rate variation through a "relaxed" molecular clock. Using a data set of 32 complete genome sequences representing all four viral serotypes, we found evidence for covarion-like evolution at second codon positions in specific DENV genes, although rarely at the level of complete gene or genomes. Further, the covarion model had little effect on estimates of tree length and hence time to the Most Recent Common Ancestor (MRCA). We conclude that although covarion models can improve descriptions of the dynamics of amino acid substitution, they have little effect on estimates of the timescale of viral evolution, which in the case of DENV covers a period of no more than 2000 years.
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
Publisher: MDPI AG
Date: 25-11-2019
DOI: 10.3390/V11121092
Abstract: DNA viruses comprise a wide array of genome structures and infect erse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of s ling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of erse invertebrate species. Our analysis revealed high levels of phylogenetic ersity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nu iridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the ersity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia
Publisher: Cold Spring Harbor Laboratory
Date: 08-11-2018
DOI: 10.1101/465583
Abstract: Myxoma virus (MYXV) has been evolving in a novel host species – European rabbits – in Australia since 1950. Previous studies of viruses s led from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution. The co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural ‘experiments’ in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein
Publisher: Elsevier BV
Date: 10-2020
Evolutionary Conservation of the PA-X Open Reading Frame in Segment 3 of Influenza A Virus
Publisher: American Society for Microbiology
Date: 15-11-2012
DOI: 10.1128/JVI.01677-12
Abstract: PA-X is a fusion protein of influenza A virus encoded in part from a +1 frameshifted X open reading frame (X-ORF) in segment 3. We show that the X-ORFs of erse influenza A viruses can be ided into two groups that differ in selection pressure and likely function, reflected in the presence of an internal stop codon and a change in synonymous ersity. Notably, truncated forms of PA-X evolved convergently in swine and dogs, suggesting a strong species-specific effect.
A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19
Publisher: Cold Spring Harbor Laboratory
Date: 05-03-2020
DOI: 10.1101/2020.03.02.974139
Abstract: The unprecedented epidemic of pneumonia caused by a novel coronavirus, HCoV-19, in China and beyond has caused public health concern at a global scale. Although bats are regarded as the most likely natural hosts for HCoV-19 1,2 , the origins of the virus remain unclear. Here, we report a novel bat-derived coronavirus, denoted RmYN02, identified from a metagenomics analysis of s les from 227 bats collected from Yunnan Province in China between May and October, 2019. RmYN02 shared 93.3% nucleotide identity with HCoV-19 at the scale of the complete virus genome and 97.2% identity in the 1ab gene in which it was the closest relative of HCoV-19. In contrast, RmYN02 showed low sequence identity (61.3%) to HCoV-19 in the receptor binding domain (RBD) and might not bind to angiotensin-converting enzyme 2 (ACE2). Critically, however, and in a similar manner to HCoV-19, RmYN02 was characterized by the insertion of multiple amino acids at the junction site of the S1 and S2 subunits of the Spike (S) protein. This provides strong evidence that such insertion events can occur in nature. Together, these data suggest that HCoV-19 originated from multiple naturally occurring recombination events among those viruses present in bats and other wildlife species.
Passive Sexual Transmission of Human Immunodeficiency Virus Type 1 Variants and Adaptation in New Hosts
Publisher: American Society for Microbiology
Date: 15-07-2006
DOI: 10.1128/JVI.02014-05
Abstract: Human immunodeficiency virus type 1 (HIV-1) genetic ersity is a major obstacle for the design of a successful vaccine. Certain viral polymorphisms encode human leukocyte antigen (HLA)-associated immune escape, potentially overcoming limited vaccine protection. Although transmission of immune escape variants has been reported, the overall extent to which this phenomenon occurs in populations and the degree to which it contributes to HIV-1 viral evolution are unknown. Selection on the HIV-1 env gene at transmission favors neutralization-sensitive variants, but it is not known to what degree selection acts on the internal HIV-1 proteins to restrict or enhance the transmission of immune escape variants. Studies have suggested that HLA class I may determine susceptibility to HIV-1 infection, but a definitive role for HLA at transmission remains unproven. Comparing populations of acute seroconverters and chronically infected patients, we found no evidence of selection acting to restrict transmission of HIV-1 variants. We found that statistical associations previously reported in chronic infection between viral polymorphisms and HLA class I alleles are not present in acute infection, suggesting that the majority of viral polymorphisms in these patients are the result of transmission rather than de novo adaptation. Using four episodes of HIV-1 transmission in which the donors and recipients were both s led very close to the time of infection we found that, despite a transmission bottleneck, genetic variants of HIV-1 infection are transmitted in a frequency-dependent manner. As HIV-1 infections are seeded by unique donor-adapted viral variants, each episode is a highly in idual antigenic challenge. Host-specific, idiosyncratic HIV-1 antigenic ersity will seriously tax the efficacy of immunization based on consensus sequences.
Structure and age of genetic diversity of dengue virus type 2 in Thailand
Publisher: Microbiology Society
Date: 04-2006
Abstract: Dengue virus type 2 (DENV-2) is a common viral infection and an important health concern in South-East Asia. To determine the molecular evolution of DENV-2 in Thailand, 105 isolates of the E (envelope) gene and 10 complete genomes s led over a 27 year period were sequenced. Phylogenetic analysis of these data revealed that three genotypes of DENV-2 have circulated in Thailand, although, since 1991, only viruses assigned to Asian genotype I have been s led from the population. A broader analysis of 35 complete genomes of DENV-2 revealed that most amino acids are subject to strong selective constraints, indicative of widespread purifying selection against deleterious mutations. This was further supported by an analysis of genome-wide substitution rates, which indicated that DENV-2 fixes approximately 10 mutations per genome per year, far lower than expected from its mutational dynamics. Finally, estimates of the age of DENV-2 were remarkably consistent among genes, indicating that the current genetic ersity in this virus probably arose within the last 120 years, concordant with the first determination of the aetiology of dengue disease.
A divergent hepatitis D-like agent in birds
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2018
DOI: 10.1101/423707
Abstract: Hepatitis delta virus (HDV) is currently only found in humans, and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a ergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and subviral agents. Hepatitis delta virus (HDV) is currently only found in humans, and coinfections of HDV and Hepatitis B virus (HBV) in humans result in severe liver disease. There are a number of hypotheses for the origin of HDV, although a key component of all is that HDV only exists in humans. Here, we describe a novel deltavirus-like agent identified in wild birds. Although this agent is genetically ergent, it exhibits important similarities to HDV, such as the presence of ribosymes and self-complementarity. The discovery of an avian HDV-like agent challenges our understanding of both the origin and the co-evolutionary relationships of subviral agents with helper viruses.
Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia
Publisher: Public Library of Science (PLoS)
Date: 22-08-2023
COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic
Publisher: Wiley
Date: 22-06-2020
DOI: 10.1111/JOCN.15365
Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
Publisher: Springer Science and Business Media LLC
Date: 11-03-2015
Identification and evolution of avian endogenous foamy viruses
Publisher: Oxford University Press (OUP)
Date: 07-2019
DOI: 10.1093/VE/VEZ049
Abstract: A history of long-term co- ergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, hibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (Ciconia boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990
Publisher: Elsevier BV
Date: 06-2021
Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
Publisher: Public Library of Science (PLoS)
Date: 22-08-2008
Infectious KoRV-related retroviruses circulating in Australian bats
Publisher: Proceedings of the National Academy of Sciences
Date: 13-04-2020
Abstract: Bats are reservoirs of emerging viruses that are highly pathogenic to other mammals, including humans. Despite the ersity and abundance of bat viruses, to date they have not been shown to harbor exogenous retroviruses. Here we report the discovery and characterization of a group of koala retrovirus-related (KoRV-related) gammaretroviruses in Australian and Asian bats. These include the Hervey pteropid gammaretrovirus (HPG), identified in the scat of the Australian black flying fox ( Pteropus alecto ), which is the first reproduction-competent retrovirus found in bats. HPG is a close relative of KoRV and the gibbon ape leukemia virus (GALV), with virion morphology and Mn 2+ -dependent virion-associated reverse transcriptase activity typical of a gammaretrovirus. In vitro, HPG is capable of infecting bat and human cells, but not mouse cells, and displays a similar pattern of cell tropism as KoRV-A and GALV. Population studies reveal the presence of HPG and KoRV-related sequences in several locations across northeast Australia, as well as serologic evidence for HPG in multiple pteropid bat species, while phylogenetic analysis places these bat viruses as the basal group within the KoRV-related retroviruses. Taken together, these results reveal bats to be important reservoirs of exogenous KoRV-related gammaretroviruses.
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans
Publisher: Proceedings of the National Academy of Sciences
Date: 14-11-2011
Abstract: Populations of seasonal influenza virus experience strong annual bottlenecks that pose a considerable extinction risk. It has been suggested that an influenza source population located in tropical Southeast or East Asia seeds annual temperate epidemics. Here we investigate the seasonal dynamics and migration patterns of influenza A H3N2 virus by analysis of virus s les obtained from 2003 to 2006 from Australia, Europe, Japan, New York, New Zealand, Southeast Asia, and newly sequenced viruses from Hong Kong. In contrast to annual temperate epidemics, relatively low levels of relative genetic ersity and no seasonal fluctuations characterized virus populations in tropical Southeast Asia and Hong Kong. Bayesian phylogeographic analysis using discrete temporal and spatial characters reveal high rates of viral migration between urban centers tested. Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, this was dependent on virus input from temperate regions and these tropical regions did not maintain a source for annual H3N2 influenza epidemics. We further show that multiple lineages may seed annual influenza epidemics, and that each region may function as a potential source population. We therefore propose that the global persistence of H3N2 influenza A virus is the result of a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year. Such complex global migration dynamics may confound control efforts and contribute to the emergence and spread of antigenic variants and drug-resistant viruses.
Australian nursing students’ knowledge and attitudes towards pressure injury prevention: A cross-sectional study
Publisher: Elsevier BV
Date: 05-2018
DOI: 10.1016/J.IJNURSTU.2018.01.015
Abstract: The aim of this study was to assess student nurses' knowledge of and attitudes towards pressure injury prevention evidence-based guidelines. Pressure injuries are a substantial problem in many healthcare settings causing major harm to patients, and generating major economic costs for health service providers. Nurses have a crucial role in the prevention of pressure injuries across all health care settings. A multi-centered, cross-sectional study was conducted using a paper-based questionnaire with undergraduate nursing students enrolled in seven universities with c uses across five Australian states (Queensland, New South Wales, Western Australia, Victoria and Tasmania). Data were collected from nursing students using two validated instruments (Pressure Ulcer Knowledge Assessment Instrument and Attitude Toward Pressure Ulcer Prevention Instrument), to measure students' pressure injury prevention knowledge and attitudes. Students reported relatively low pressure injury prevention knowledge scores (51%), and high attitude scores (78%). Critical issues in this study were nursing students' lack of knowledge about preventative strategies to reduce the amount and duration of pressure/shear, and lower confidence in their capability to prevent pressure injury. Level of education and exposure to working in a greater number of different clinical units were significantly related to pressure injury prevention knowledge and attitude scores. The study findings highlight the need to implement a comprehensive approach to increasing Australian nursing students' pressure injury prevention and management knowledge, as well as ensuring that these students have adequate experiences in clinical units, with a high focus on pressure injury prevention to raise their personal capability.
Occupational exposure: rural Australian farmers’ sun-protective behaviours
Publisher: Springer Science and Business Media LLC
Date: 04-06-2019
Identification of hepatitis C virus in the common bed bug - a potential, but uncommon route for HCV infection?
Publisher: Informa UK Limited
Date: 2020
Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico
Publisher: Microbiology Society
Date: 04-2006
Abstract: The genus Flavivirus contains approximately 70 single-stranded, positive-sense RNA viruses that are mosquito-borne, tick-borne or have no known vector. Two discoveries support previous suggestions of the existence of a large number of uns led flaviviruses: (i) a new flavivirus, Kamiti River virus, was recently isolated from Kenyan mosquitoes, and (ii) sequences with high similarity to those of flaviviruses have been found integrated into the genome of Aedes mosquitoes, suggesting a past infection with a virus (or viruses) that has yet to be discovered. These sequences were related most closely to a flavivirus that infects insects alone, cell fusing agent virus (CFAV). CFAV was originally isolated in the laboratory from an Aedes aegypti cell line. To date, this virus had not been found in the wild. In the present study, over 40 isolates of a novel strain of CFAV were discovered from mature mosquitoes s led from the wild in Puerto Rico. The viral strain was present in a range of mosquito species, including Aedes aegypti , Aedes albopictus and Culex sp., from numerous locations across the island and, importantly, in mosquitoes of both sexes, suggesting vertical transmission. Here, results from viral screening, and cell culture and molecular identification of the infected mosquitoes are presented. Experimental-infection tests were also conducted by using the original CFAV strain and a highly efficient reverse-transcription mechanism has been documented, in which initiation of copying occurs at the 3′ terminus of either the genomic RNA or the intermediate of replication, potentially elucidating the mechanism by which flaviviral sequences may have integrated into mosquito genomes.
Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry
Publisher: Springer Science and Business Media LLC
Date: 26-06-2015
Immune Selection for Altered Antigen Processing Leads to Cytotoxic T Lymphocyte Escape in Chronic HIV-1 Infection
Publisher: Rockefeller University Press
Date: 05-04-2004
DOI: 10.1084/JEM.20031982
Abstract: Mutations within cytotoxic T lymphocyte (CTL) epitopes impair T cell recognition, but escape mutations arising in flanking regions that alter antigen processing have not been defined in natural human infections. In human histocompatibility leukocyte antigen (HLA)-B57+ HIV-infected persons, immune selection pressure leads to a mutation from alanine to proline at Gag residue 146 immediately preceding the NH2 terminus of a dominant HLA-B57–restricted epitope, ISPRTLNAW. Although N-extended wild-type or mutant peptides remained well-recognized, mutant virus–infected CD4 T cells failed to be recognized by the same CTL clones. The A146P mutation prevented NH2-terminal trimming of the optimal epitope by the endoplasmic reticulum aminopeptidase I. These results demonstrate that allele-associated sequence variation within the flanking region of CTL epitopes can alter antigen processing. Identifying such mutations is of major relevance in the construction of vaccine sequences.
Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures
Publisher: Cold Spring Harbor Laboratory
Date: 15-05-2022
DOI: 10.1101/2022.05.14.491972
Abstract: Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the ersity within, and effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions on virus evolution. We assessed the ersity of RNA viruses in eight microalgal cultures including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimised to detect highly ergent RNA viruses, we identified ten RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae and Partitiviridae , greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae , commonly associated with microalgal hosts, were also identified. This study highlights that a great ersity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterisation and to investigate the effects of viral infections on microalgal physiology, biology and growth, considering their environmental and industrial roles. In comparison to animals or plants, our knowledge of the ersity of RNA viruses infecting microbial algae – the microalgae – is minimal. Yet describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economical levels because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte and euglena major clades of algae. This work identified ten new ergent RNA virus species, belonging to RNA virus families as erse as the double-stranded Totiviridae, Endornaviridae, Partitiviridae and the single-stranded Marnaviridae . By expanding the known ersity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.
Comparative Analysis of the Complete Genome Sequence of the California MSW Strain of Myxoma Virus Reveals Potential Host Adaptations
Publisher: American Society for Microbiology
Date: 15-11-2013
DOI: 10.1128/JVI.01923-13
Abstract: Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit, Sylvilagus bachmani . We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the M156R , M154L , M153R , M152R , and M151R genes and part of the M150R gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes, M008.1L/R and M152R , with major virulence functions in European rabbits, and a sixth gene, M000.5L/R , was absent. The loss of these gene functions suggests that S. bachmani is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of M008.1L/R and M152R in infections of European rabbits.
Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry
Publisher: Elsevier BV
Date: 11-2011
DOI: 10.1016/J.VACCINE.2011.09.127
Abstract: Highly pathogenic avian influenza (HPAI) H5N1 (clade 2.2) was introduced into Egypt in early 2006. Despite the control measures taken, including mass vaccination of poultry, the virus rapidly spread among commercial and backyard flocks. Since the initial outbreaks, the virus in Egypt has evolved into a third order clade (clade 2.2.1) and erged into antigenically and genetically distinct subclades. To better understand the dynamics of HPAI H5N1 evolution in countries that differ in vaccination policy, we undertook an in-depth analysis of those virus strains circulating in Egypt between 2006 and 2010, and compared countries where vaccination was adopted (Egypt and Indonesia) to those where it was not (Nigeria, Turkey and Thailand). This study incorporated 751 sequences (Egypt n=309, Indonesia n=149, Nigeria n=106, Turkey n=87, Thailand n=100) of the complete haemagglutinin (HA) open reading frame, the major antigenic determinant of influenza A virus. Our analysis revealed that two main Egyptian subclades (termed A and B) have co-circulated in domestic poultry since late 2007 and exhibit different profiles of positively selected codons and rates of nucleotide substitution. The mean evolutionary rate of subclade A H5N1 viruses was 4.07×10(-3) nucleotide substitutions per site, per year (HPD 95%, 3.23-4.91), whereas subclade B possessed a markedly higher substitution rate (8.87×10(-3) 95% HPD 7.0-10.72×10(-3)) and a stronger signature of positive selection. Although the direct association between H5N1 vaccination and virus evolution is difficult to establish, we found evidence for a difference in the evolutionary dynamics of H5N1 viruses among countries where vaccination was or was not adopted. In particular, both evolutionary rates and the number of positively selected sites were higher in virus populations circulating in countries applying avian influenza vaccination for H5N1, compared to viruses circulating in countries which had never used vaccination. We therefore urge a greater consideration of the potential consequences of inadequate vaccination on viral evolution.
Unrecognized diversity of mammalian orthoreoviruses in North American bats
Publisher: Elsevier BV
Date: 06-2022
DOI: 10.1016/J.VIROL.2022.03.012
Abstract: Bats have recently been identified as potential reservoir hosts for mammalian orthoreoviruses (MRVs) throughout Europe and China. Here we present the first evolutionary and biological characterization of bat-borne MRVs in North America, including phylogenomic analysis, in vitro relative infectivity in bat and other mammalian cell cultures, host cell receptor specificity, and epifluorescence microscopy of viral factory formation. Through genetic and phylogenetic comparisons, we show that two ergent MRV serotype 2 (T2) strains - isolated from a silver-haired bat (Lasionycteris noctivagans) and a big brown bat (Eptesicus fuscus) from Pennsylvania, USA - provide an evolutionary link to an MRV strain (T2W) recovered from an 8-week-old infant who died in Winnipeg, Manitoba, Canada in 1997. Although these findings suggest North American bats may represent a previously unrecognized source for the cross-species transmission of MRVs to other animals, including humans, the ecology and epidemiology of MRVs in wildlife remain enigmatic.
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2023
Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens
Publisher: Cold Spring Harbor Laboratory
Date: 12-11-2021
DOI: 10.1101/2021.11.10.467646
Abstract: Game animals are wildlife species often traded and consumed as exotic food, and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1725 game animals, representing 16 species and five mammalian orders, s led across China. From this we identified 71 mammalian viruses, with 45 described for the first time. Eighteen viruses were considered as potentially high risk to humans and domestic animals. Civets ( Paguma larvata ) carried the highest number of potentially high risk viruses. We identified the transmission of Bat coronavirus HKU8 from a bat to a civet, as well as cross-species jumps of coronaviruses from bats to hedgehogs and from birds to porcupines. We similarly identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence. 1725 game animals from five mammalian orders were surveyed for viruses 71 mammalian viruses were discovered, 18 with a potential risk to humans Civets harbored the highest number of potential ‘high risk’ viruses A species jump of an alphacoronavirus from bats to a civet was identified H9N2 influenza virus was detected in a civet and an Asian badger Humans viruses were also identified in game animals
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Amount: $534,100.00
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Amount: $595,000.00
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View Funded ActivityAustralian Laureate Fellowships - Grant ID: FL170100022
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Amount: $3,402,903.00
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Amount: $630,000.00
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