ORCID Profile
0000-0002-5629-0196
Current Organisations
University of Sydney
,
University of Melbourne
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Microbial Ecology | Host-Parasite Interactions | Virology | Microbiology
Poultry | Expanding Knowledge in the Biological Sciences | Disease Distribution and Transmission (incl. Surveillance and Response) |
Publisher: Springer International Publishing
Date: 2017
Publisher: Elsevier BV
Date: 07-2017
Publisher: Public Library of Science (PLoS)
Date: 30-09-2015
Publisher: Springer Science and Business Media LLC
Date: 04-11-2010
DOI: 10.1007/S00705-010-0839-1
Abstract: The primary hosts for influenza A viruses are waterfowl, although gulls and shorebirds are also important in global avian influenza dynamics. Avian influenza virus genes are separated phylogenetically into two geographic clades, American and Eurasian, which is caused by the geographic separation of the host species between these two regions. We surveyed a gregarious and cosmopolitan species, the Great Black-backed Gull (Larus marinus), in Newfoundland, Canada, for the presence of avian influenza viruses. We have isolated and determined the complete genome sequence of an H13N2 virus, A/Great Black-backed Gull/Newfoundland/296/2008(H13N2), from one of these birds. Phylogenetic analysis revealed that this virus contained two genes in the American gull clade (PB1, HA), two genes in the American avian clade (PA, NA), and four genes in the Eurasian gull clade (PB2, NP, M, NS). We analyzed bird band recovery information and found the first evidence of trans-Atlantic migration from Newfoundland to Europe (UK, Spain and Portugal) for this species. Thus, great black-backed gulls could be important for movement of avian influenza viruses across the Atlantic Ocean and within North America.
Publisher: Springer Science and Business Media LLC
Date: 18-10-2023
Publisher: Elsevier BV
Date: 2015
Publisher: Elsevier BV
Date: 08-2020
Publisher: Cambridge University Press (CUP)
Date: 02-03-2017
DOI: 10.1017/S0950268817000346
Abstract: Hantaviruses are globally distributed and cause severe human disease. Puumala hantavirus (PUUV) is the most common species in Northern Europe, and the only hantavirus confirmed to circulate in Sweden, restricted to the northern regions of the country. In this study, we aimed to further add to the natural ecology of PUUV in Sweden by investigating prevalence, and spatial and host species infection patterns. Specifically, we wanted to ascertain whether PUUV was present in the natural reservoir, the bank vole ( Myodes glareolus ) further south than Dalälven river, in south-central Sweden, and whether PUUV can be detected in other rodent species in addition to the natural reservoir. In total, 559 animals were collected at Grimsö (59°43′N 15°28′E), Sala (59°55′N 16°36′E) and Bogesund (59°24′N 18°14′E) in south-central Sweden between May 2013 and November 2014. PUUV ELISA-reactive antibodies were found both in 2013 (22/295) and in 2014 (18/264), and nine s les were confirmed as PUUV-specific by focus reduction neutralization test. Most of the PUUV-specific s les were from the natural host, the bank vole, but also from other rodent hosts, indicating viral spill-over. Finally, we showed that PUUV is present in more highly populated central Sweden.
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.
Publisher: American Chemical Society (ACS)
Date: 22-09-2020
Publisher: Springer Science and Business Media LLC
Date: 14-05-2014
Publisher: Elsevier BV
Date: 08-2021
DOI: 10.1016/J.VIROL.2021.05.010
Abstract: Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All s les were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid ergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast unders ling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.JVIROMET.2017.11.004
Abstract: Surveillance of wild birds is critical in monitoring for highly pathogenic avian influenza A viruses (AIVs). However, a successful surveillance regime requires proper treatment of s les in the field - rapid placement of s les in -80°C and subsequent maintenance of cold-chain. Given the logistical difficulties of this, many avian taxa and/or geographic locations are not s led, or, when s led may result in false negatives due to poor s le treatment in the field. Here, we assessed the utility of RNAlater
Publisher: Wiley
Date: 06-02-2017
DOI: 10.1111/MEC.13967
Publisher: Wiley
Date: 28-11-2019
DOI: 10.1111/MEC.15306
Abstract: The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. V ire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat-borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in v ire bats by interrogating factors that affect the structure, ersity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology.
Publisher: Wildlife Disease Association
Date: 2014
DOI: 10.7589/2012-10-247
Abstract: Influenza A viruses infect a wide range of hosts, including many species of birds. Avian influenza A virus (AIV) infection appears to be most common in Anseriformes (ducks, geese, and swans) and some Charadriiformes (shorebirds and gulls), but many other birds also serve as hosts of AIV. Here, we evaluated the role of seabirds as hosts for AIV. We tested 3,160 swab s les from 13 seabird species between May 2008 and December 2011 in Newfoundland and Labrador, Canada. We also tested 156 serum s les for evidence of previous infection of AIV in Common Murres (Uria aalge) and Atlantic Puffins (Fratercula arctica). Avian influenza A virus was detected in breeding Common Murres and nonbreeding Thick-billed Murres (Uria lomvia), and Common Murres also had high antibody prevalence (44%). From these findings, combined with other studies showing AIV infection in murres, we conclude that murres are important for the ecology of AIV. For other species (Razorbill, Alca torda Leach's Storm-Petrel, Oceanodroma leucorhoa Black-legged Kittiwake, Rissa tridactyla Atlantic Puffin) with good coverage (>100 s les) we did not detect AIV. However, serology indicates infection does occur in Atlantic Puffins, with 22% antibody prevalence found. The possibility of virus spread through dense breeding colonies and the long distance movements of these hosts make a more thorough evaluation of the role for seabirds as hosts of AIV important.
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.
Publisher: Oxford University Press (OUP)
Date: 05-08-2019
Abstract: Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.
Publisher: Springer Science and Business Media LLC
Date: 26-06-2010
DOI: 10.1007/S11262-010-0504-5
Abstract: Influenza A viruses infect a range of host species, including various mammals and more than 100 species of birds. For avian influenza viruses (AIV), prevalence varies between different groups of birds, with waterfowl showing the highest prevalence. We have sequenced the complete genome of A/Thick-billed Murre/Newfoundland/031/2007(H11N2), an AIV identified in the pelagic seabird, Thick-billed Murre (Uria lomvia). This represents the first complete genome sequence of an AIV from this host species, and only the second complete genome sequence from a seabird in the alcid group. All of the virus segments fall within the American avian lineage. Several of the segments show a close relationship to AIV identified in other marine host species, and also a strong geographic association with other AIV sequences from the northeastern coast of North America from recent years. The identification of this virus, and the growing number of AIV identified in seabird species, indicates these marine birds could be underappreciated host species. This has potential consequences for global influenza dynamics because of the seasonal distributions and migratory patterns of this group of birds.
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.
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.VIROL.2014.04.009
Abstract: Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of s led gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics.
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.
Publisher: Springer Science and Business Media LLC
Date: 25-06-2019
Publisher: Springer Science and Business Media LLC
Date: 16-08-2023
Publisher: Public Library of Science (PLoS)
Date: 15-06-2011
Publisher: Wiley
Date: 03-2023
DOI: 10.1111/IRV.13118
Publisher: Wiley
Date: 16-07-2023
DOI: 10.1111/MEC.17078
Abstract: Rodent virus communities (viromes) are overrepresented with zoonotic viruses, and as such are a key host system for the study of zoonotic viruses. However, the extent of viral ersity beyond characterized zoonotic viruses, and the factors that modulate the viromes of rodents remain opaque. In this issue of Molecular Ecology, Raghwani et al. (2023) use rodents as a model to understand the role of seasonality in dictating virome abundance and composition—a factor known to play an important role in most animal one‐host, one‐pathogen systems. These data are not only highly relevant to rodents, but have broad applications across understanding and disentangling animal virome ecology.
Publisher: Research Square Platform LLC
Date: 31-01-2023
DOI: 10.21203/RS.3.RS-2434849/V1
Abstract: Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, replacing the dominant clade 2.3.4.4 H5N8 virus. H5N1 viruses have spread rapidly to four continents, causing increasing reports of mass mortality in wild birds and poultry. The ecological and virological properties required for future mitigation strategies are unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the source of resurgent H5 HPAI and reveal significant shifts in virus ecology and evolution. Outbreak data indicates key resurgent events in 2016/17 and 2020/21 that contributed to the panzootic spread of H5N1 in 2021/22, including an increase in virus diffusion velocity and persistence in wild birds. Genomic analysis reveals that the 2016/17 epizootics originated in Asia, where HPAI H5 reservoirs are documented as persistent. However, in 2020/21, 2.3.4.4b H5N8 viruses emerged in domestic poultry in Africa, featuring several novel mutations altering the HA structure, receptor binding, and antigenicity. The new H5N1 virus emerged from H5N8 through reassortment in wild birds along the Adriatic flyway around the Mediterranean Sea. It was characterized by extensive reassortment with low pathogenic avian influenza in domestic and wild birds as it spread globally. In contrast, earlier outbreaks of H5N8 were caused by a more stable genetic constellation, highlighting dynamic changes in HPAI H5 genomic evolution. These results suggest a shift in the epicenter of HPAI H5 beyond Asia to new regions in Africa, the Middle East, Europe, and North and South America. The persistence of HPAI H5 with resurgence potential in domestic birds indicates that elimination strategies remain a high priority.
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1093/VE/VEY025
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.COVIRO.2017.10.006
Abstract: Low pathogenic influenza A virus (LPIAV) prevalence and subtype distribution differs between and across bird taxa. A crucial factor in the epidemiology of these viruses and virus subtypes is the ability to transmit between and within different host taxa and in iduals. Successful viral transmission depends on availability of susceptible hosts and exposure of host to virus. Exposure to viruses and susceptibility to virus infection and/or disease are shaped by both host and virus traits. In this review we have identified key host and virus traits that can affect LPIAV transmission, both in terms of exposure and susceptibility. Furthermore we highlight current challenges in assessment of these traits and identify methodological considerations for future studies.
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.
Publisher: The Royal Society
Date: 22-04-2014
Abstract: Data on long-term circulation of pathogens in wildlife populations are seldom collected, and hence understanding of spatial–temporal variation in prevalence and genotypes is limited. Here, we analysed a long-term surveillance series on influenza A virus (IAV) in mallards collected at an important migratory stopover site from 2002 to 2010, and characterized seasonal dynamics in virus prevalence and subtype ersity. Prevalence dynamics were influenced by year, but retained a common pattern for all years whereby prevalence was low in spring and summer, but increased in early autumn with a first peak in August, and a second more pronounced peak during October–November. A total of 74 haemagglutinin (HA)/neuraminidase (NA) combinations were isolated, including all NA and most HA (H1–H12) subtypes. The most common subtype combinations were H4N6, H1N1, H2N3, H5N2, H6N2 and H11N9, and showed a clear linkage between specific HA and NA subtypes. Furthermore, there was a temporal structuring of subtypes within seasons based on HA phylogenetic relatedness. Dissimilar HA subtypes tended to have different temporal occurrence within seasons, where the subtypes that dominated in early autumn were rare in late autumn, and vice versa. This suggests that build-up of herd immunity affected IAV dynamics in this system.
Publisher: Elsevier BV
Date: 11-2022
DOI: 10.1016/J.VIROL.2022.09.001
Abstract: Canine distemper virus (CDV) causes a highly contagious systemic infection in an array of animal species. In this study we report an outbreak of distemper in ferrets in two research facilities in Australia, caused by a novel lineage of CDV. While the CDV strain caused mainly mild symptoms in ferrets, histopathology results presented a typical profile of distemper pathology, with multi-system virus replication. Through the development of a discriminatory PCR, paired with full genome sequencing, we revealed that the outbreak was caused by a novel lineage of CDV. The novel CDV lineage was highly ergent, with less than 93% similarity across the H gene to other described lineages, including the vaccine strain, and erged approximately 140-400 years ago. Enhanced surveillance to determine the prevalence of CDV in ferrets, dogs and other at-risk species is critical to better understand the presence and ersity of CDV in Australia currently.
Publisher: Microbiology Society
Date: 08-2020
DOI: 10.1099/JGV.0.001369
Abstract: Neuraminidase inhibitors (NAIs) are the gold standard treatment for influenza A virus (IAV). Oseltamivir is mostly used, followed by zanamivir (ZA). NAIs are not readily degraded in conventional wastewater treatment plants and can be detected in aquatic environments. Waterfowl are natural IAV hosts and replicating IAVs could thus be exposed to NAIs in the environment and develop resistance. Avian IAVs form the genetic basis for new human IAVs, and a resistant IAV with pandemic potential poses a serious public health threat, as NAIs constitute a pandemic preparedness cornerstone. Resistance development in waterfowl IAVs exposed to NAIs in the water environment has previously been investigated in an in vivo mallard model and resistance development was demonstrated in several avian IAVs after the exposure of infected ducks to oseltamivir, and in an H1N1 IAV after exposure to ZA. The N1 and N2 types of IAVs have different characteristics and resistance mutations, and so the present study investigated the exposure of an N2-type IAV (H4N2) in infected mallards to 1, 10 and 100 µg l −1 of ZA in the water environment. Two neuraminidase substitutions emerged, H274N (ZA IC 50 increased 5.5-fold) and E119G (ZA IC 50 increased 110-fold) at 10 and 100 µg l −1 of ZA, respectively. Reversion towards wild-type was observed for both substitutions in experiments with removed drug pressure, indicating reduced fitness of both resistant viruses. These results corroborate previous findings that the development of resistance to ZA in the environment seems less likely to occur than the development of resistance to oseltamivir, adding information that is useful in planning for prudent drug use and pandemic preparedness.
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.
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.
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.
Publisher: Springer Science and Business Media LLC
Date: 12-09-2013
Abstract: Newcastle disease virus (NDV) is the causative agent of the Newcastle disease, a severe disease in birds associated with substantial economic losses to the poultry industry worldwide. Sweden is situated along the Western European waterfowl flyway and applies a non-vaccination policy combined with directives of immediate euthanisation of NDV infected flocks. During the last decades there have been several outbreaks with NDV in poultry in Sweden. However, less is known about the virus prevalence in the wild bird population including waterfowl, a well-established reservoir of avian paramyxovirus type 1 (APMV-1), the paramyxovirus serotype that include pathogenic NDV. The survey constituted of 2332 s les from Mallards ( Anas platyrhynchos ), trapped in the southern part of Sweden during autumn migration in 2010. These s les were screened for APMV-1 by real-time reverse transcription PCR, and viral strains from positive s les were isolated and characterized by sequence analysis of the fusion gene and by phylogenetic analysis. Twenty of these s les were positive for APMV-1, hence a virus prevalence of 0.9% (95% Confidence Interval [95% CI]=0.54%, 1.35%). The highest APMV-1 prevalence was detected in juvenile Mallards s led in November (n=887, prevalence 1.24% ([95% CI])=0.67%, 2.24%). Sequence analysis and evaluation of phylogenetic relatedness indicated that isolated APMV-1 strains were lentogenic, and phylogenetically most closely related to genotype Ib strains within the clade of class II viruses. The s ling system employed enabled us to follow APMV-1 infections and the shedding of one particular viral strain in one in idual bird over several days. Furthermore, combining previous screening results with the APMV-1 detections in this study showed that more than 50% of Mallards that tested positive for APMV-1 RNA were co-infected with influenza A virus.
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.
Publisher: Cold Spring Harbor Laboratory
Date: 03-05-2023
DOI: 10.1101/2023.05.02.539182
Abstract: The current avian influenza panzootic is unprecedented and catastrophic for birds. With a focus on the implications of this panzootic for poultry, there is limited attention on wild birds. We highlight shortcomings and geographic biases in reporting leading to a severe underappreciation of wildlife mortality. We estimate the scale of mortality amongst wild birds is in the millions rather than tens-of-thousands reported, through comparison of notification data to accounts literature. The outbreaks amongst wild birds are causing population and species level concerns which may drive extinctions and jeopardise decades of conservation efforts.
Publisher: Cold Spring Harbor Laboratory
Date: 23-12-2020
Publisher: American Society for Microbiology
Date: 09-2015
DOI: 10.1128/AAC.00886-15
Abstract: Influenza A virus (IAV) has its natural reservoir in wild waterfowl, and new human IAVs often contain gene segments originating from avian IAVs. Treatment options for severe human influenza are principally restricted to neuraminidase inhibitors (NAIs), among which oseltamivir is stockpiled in preparedness for influenza pandemics. There is evolutionary pressure in the environment for resistance development to oseltamivir in avian IAVs, as the active metabolite oseltamivir carboxylate (OC) passes largely undegraded through sewage treatment to river water where waterfowl reside. In an in vivo mallard ( Anas platyrhynchos ) model, we tested if low-pathogenic avian influenza A(H7N9) virus might become resistant if the host was exposed to low levels of OC. Ducks were experimentally infected, and OC was added to their water, after which infection and transmission were maintained by successive introductions of uninfected birds. Daily fecal s les were tested for IAV excretion, genotype, and phenotype. Following mallard exposure to 2.5 μg/liter OC, the resistance-related neuraminidase (NA) I222T substitution, was detected within 2 days during the first passage and was found in all viruses sequenced from subsequently introduced ducks. The substitution generated 8-fold and 2.4-fold increases in the 50% inhibitory concentration (IC 50 ) for OC ( P 0.001) and zanamivir ( P = 0.016), respectively. We conclude that OC exposure of IAV hosts, in the same concentration magnitude as found in the environment, may result in amino acid substitutions, leading to changed antiviral sensitivity in an IAV subtype that can be highly pathogenic to humans. Prudent use of oseltamivir and resistance surveillance of IAVs in wild birds are warranted.
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
Publisher: Public Library of Science (PLoS)
Date: 23-04-2013
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.MOLIMM.2018.01.012
Abstract: The vertebrate innate immune system provides hosts with a rapid, non-specific response to a wide range of invading pathogens. However, the speed and duration of innate responses will be influenced by the co-evolutionary dynamics of specific host-pathogen combinations. Here, we show that low pathogenic avian influenza virus (LPAI) subtype H1N1 elicits a strong but extremely transient innate immune response in its main wildlife reservoir, the mallard (Anas platyrhynchos). Using a series of experimental and methodological improvements over previous studies, we followed the expression of retinoic acid inducible gene 1 (RIG-I) and myxovirus resistance gene (Mx) in mallards semi-naturally infected with low pathogenic H1N1. One day post infection, both RIG-I and Mx were significantly upregulated in all investigated tissues. By two days post infection, the expression of both genes had generally returned to basal levels, and remained so for the remainder of the experiment. This is despite the fact that birds continued to actively shed viral particles throughout the study period. We additionally show that the spleen plays a particularly active role in the innate immune response to LPAI. Waterfowl and avian influenza viruses have a long co-evolutionary history, suggesting that the mallard innate immune response has evolved to provide a minimum effective response to LPAIs such that the viral infection is brought under control while minimising the damaging effects of a sustained immune response.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2018
DOI: 10.1038/S41598-018-24407-X
Abstract: We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird s les collected during 2016–17. Coronaviruses were detected in 141 s les (15.3%) from species of ducks, shorebirds and herons and from multiple s ling locations. Sequencing of selected positive s les found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive s les. Sequencing of the relatively conserved Orf1 PCR licons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.
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.
Publisher: Public Library of Science (PLoS)
Date: 03-03-2016
Publisher: Canadian Science Publishing
Date: 10-2013
Abstract: The island of Newfoundland, Canada, is at the eastern edge of North America and has migratory bird connections with the continental mainland as well as across the North Atlantic Ocean. Here, we report a 4-year avian influenza virus (AIV) epidemiological study in ducks in the St. John’s region of Newfoundland. The overall prevalence of AIV detection in ducks during this study was 7.2%, with American Black Ducks contributing the vast majority of the collected s les and the AIV positives. The juvenile ducks showed a significantly higher AIV detection rate (10.6%) compared with adults (3.4%). Seasonally, AIV prevalence rates were higher in the autumn (8.4%), but positives were still detected in the winter (4.6%). Preliminary serology tests showed a high incidence of previous AIV infection (20/38, 52.6%). A total of 43 viruses were characterized for their HA–NA or HA subtypes, which revealed a large ersity of AIV subtypes and little recurrence of subtypes from year to year. Investigation of the movement patterns of ducks in this region showed that it is a largely non-migratory duck population, which may contribute to the observed pattern of high AIV subtype turnover. Phylogenetic analysis of 4 H1N1 and one H5N4 AIVs showed these viruses were highly similar to other low pathogenic AIV sequences from waterfowl in North America and assigned all gene segments into American-avian clades. Notably, the H1N1 viruses, which were identified in consecutive years, possessed homologous genomes. Such detection of homologous AIV genomes across years is rare, but indicates the role of the environmental reservoir in viral perpetuation.
Publisher: Wiley
Date: 22-11-2018
DOI: 10.1111/MEC.14918
Publisher: Cold Spring Harbor Laboratory
Date: 16-02-2023
DOI: 10.1101/2023.02.15.528752
Abstract: The rapid destruction of natural wetland habitats over past decades has been partially offset by an increase in artificial wetlands. However, these also include wastewater treatment plants, which may pose a pollution risk to the wildlife using them. We studied two long-distance Arctic-breeding migratory shorebird species, curlew sandpiper ( Calidris ferruginea , n=70) and red-necked stint ( Calidris ruficollis , n=100), while on their Australian non-breeding grounds using a natural wetland versus an artificial wetland at a wastewater treatment plant (WTP). We compared pollutant exposure (elements and per- and poly-fluoroalkyl substances/PFASs), disease (avian influenza), physiological status (oxidative stress) of the birds at the two locations from 2011-2020, and population survival from 1978-2019. Our results indicated no significant differences in blood pellet pollutant concentrations between the habitats except mercury (WTP median: 224 ng/g, range: 19-873 ng/g natural wetland: 160 ng/g, 22-998 ng/g) and perfluorooctanesulfonic acid (WTP median: 52 ng/g, range: .01-1280 ng/g natural wetland: 14 ng/g, .01-379 ng/g) which were higher at the WTP, and selenium which was lower at the WTP (WTP median: 5000 ng/g, range: 1950-34400 ng/g natural wetland: 19200 ng/g, 4130-65200 ng/g). We also measured higher blood o,o’-dityrosine (an indicator of protein damage) at the WTP. No significant differences were found for adult survival, but survival of immature birds at the WTP appeared to be lower which could be due to higher dispersal to other wetlands. Interestingly, we found active avian influenza infections were higher in the natural habitat, while seropositivity was higher in the WTP, seemingly not directly related to pollutant exposure. Overall, we found negligible differences in pollutant exposure, health and survival of the shorebirds in the two habitats. Our findings suggest that appropriately managed wastewater treatment wetlands may provide a suitable alternative habitat to these migratory species, curbing the decline of shorebird populations from widespread habitat loss.
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.
Publisher: Oxford University Press (OUP)
Date: 07-2022
DOI: 10.1093/VE/VEAC074
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002–9) from mallards (Anas platyrhynchos) s led in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly lify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2–3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Publisher: Springer Science and Business Media LLC
Date: 02-07-2015
Publisher: Public Library of Science (PLoS)
Date: 07-11-2012
Publisher: Cold Spring Harbor Laboratory
Date: 12-2021
DOI: 10.1101/2021.11.30.470533
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, 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. A result of the ever-growing poultry industry is a dramatic global increase in the incidence of high pathogenicity avian influenza virus outbreaks. In contrast, wild birds are believed to be the main reservoir for low pathogenic avian influenza A virus. Due to intensive research and surveillance of AIV in waterfowl in the Northern Hemisphere, we have a better understanding of AIV ecology and evolution in that region compared to the Southern Hemisphere, which are characterised by different patterns of avian migration and ecological conditions. We analysed 333 unique AIV genomes collected from wild birds in Australia to understand how Australia fits into global AIV dynamics and how viruses are maintained and dispersed within the continent of Australia. We show that the Southern Hemisphere experiences differing evolutionary dynamics to those seen in Northern Hemisphere with Australia representing a global sink for AIV.
Publisher: MDPI AG
Date: 21-08-2020
DOI: 10.20944/PREPRINTS202008.0478.V1
Abstract: The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly to most parts of the world, causing high numbers of deaths and significant social and economic impacts. SARS-CoV-2 is a novel coronavirus with a suggested zoonotic origin and with the potential for cross-species transmission among animals. Antarctica can be considered the only continent free of SARS-CoV-2 although at the end of the 2019-2020 tourist season, at least one SARS-CoV-2 positive tourist visited the Antarctic Peninsula. Therefore, concerns have been expressed regarding the potential human introduction of this virus to the continent through the activities of research or tourism with potential effects including those related to human health, but also the potential for virus transmission to Antarctic wildlife. This reverse-zoonotic transmission risk to Antarctic wildlife is assessed considering the available information on host susceptibility, dynamics of the infection in humans, and contact interactions between humans and Antarctic wildlife. Measures to reduce the risk are proposed as well as the identification of knowledge gaps related to this issue.
Publisher: Cold Spring Harbor Laboratory
Date: 24-11-2021
DOI: 10.1101/2021.11.24.469925
Abstract: Avian influenza A virus (AIV) is ubiquitous in waterfowl, and detected annually at high prevalence in waterfowl during the Northern Hemipshere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-2009) from Mallards ( Anas platyrhynchos ) s led in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into in three distinct lineages, structured by year of isolation. Specifically, across the eight years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigentic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly lify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
Publisher: Springer Science and Business Media LLC
Date: 29-10-2018
Publisher: Cold Spring Harbor Laboratory
Date: 18-12-2022
DOI: 10.1101/2022.12.18.520670
Abstract: Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, replacing the dominant clade 2.3.4.4 H5N8 virus. H5N1 viruses have spread rapidly to four continents, causing increasing reports of mass mortality in wild birds and poultry. The ecological and virological properties required for future mitigation strategies are unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the source of resurgent H5 HPAI and reveal significant shifts in virus ecology and evolution. Outbreak data indicates key resurgent events in 2016/17 and 2020/21 that contributed to the panzootic spread of H5N1 in 2021/22, including an increase in virus diffusion velocity and persistence in wild birds. Genomic analysis reveals that the 2016/17 epizootics originated in Asia, where HPAI H5 reservoirs are documented as persistent. However, in 2020/21, 2.3.4.4b H5N8 viruses emerged in domestic poultry in Africa, featuring several novel mutations altering the HA structure, receptor binding, and antigenicity. The new H5N1 virus emerged from H5N8 through reassortment in wild birds along the Adriatic flyway around the Mediterranean Sea. It was characterized by extensive reassortment with low pathogenic avian influenza in domestic and wild birds as it spread globally. In contrast, earlier outbreaks of H5N8 were caused by a more stable genetic constellation, highlighting dynamic changes in HPAI H5 genomic evolution. These results suggest a shift in the epicenter of HPAI H5 beyond Asia to new regions in Africa, the Middle East, Europe, and North and South America. The persistence of HPAI H5 with resurgence potential in domestic birds indicates that elimination strategies remain a high priority.
Publisher: American Society for Microbiology
Date: 06-2019
DOI: 10.1128/JVI.00271-19
Abstract: Approximately 99% of all viruses are still to be described, and in our changing world, any one of these unknown viruses could potentially expand their host range and cause epidemic disease in wildlife, agricultural animals, or humans. Avian avulavirus 1 causes outbreaks in wild birds and poultry and is thus well described. However, for many avulavirus species, only a single specimen has been described, and their viral ecology and epidemiology are unknown. Through the detection of avian avulaviruses in penguins from Antarctica, we have been able to expand upon our understanding of three avian avulavirus species (avian avulaviruses 17 to 19) and report a potentially novel avulavirus species. Importantly, we show that penguins appear to play a key role in the epidemiology of avian avulaviruses, and we encourage additional s ling of this avian group.
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 10-2019
Publisher: Springer Science and Business Media LLC
Date: 07-09-2023
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2019
DOI: 10.1101/2019.12.11.873513
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. However, there is 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 test the idea that penguins have limited microbial ersity we determined the 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 therefore reject the theory 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.
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.
Publisher: Elsevier BV
Date: 07-2020
Publisher: Wildlife Disease Association
Date: 10-2016
DOI: 10.7589/2015-12-342
Abstract: Avian cholera, caused by the bacterium Pasteurella multocida , is an endemic disease globally, often causing annual epizootics in North American wild bird populations with thousands of mortalities. From December 2006 to March 2007, an avian cholera outbreak caused mortality in marine birds off the coast of Atlantic Canada, largely centered 300-400 km off the coast of the island of Newfoundland. Scavenging gulls ( Larus spp.) were the primary species detected however, mortality was also identified in Black-legged Kittiwakes ( Rissa tridactyla ) and one Common Raven ( Corvus corax ), a nonmarine species. The most common gross necropsy findings in the birds with confirmed avian cholera were acute fibrinous and necrotizing lesions affecting the spleen, air sacs, and pericardium, and nonspecific hepatomegaly and splenomegaly. The etiologic agent, P. multocida serotype 1, was recovered from 77 of 136 carcasses examined, and confirmed or probable avian cholera was diagnosed in 85 cases. Mortality observed in scavenging gull species was disproportionately high relative to their abundance, particularly when compared to nonscavenging species. The presence of feather shafts in the ventricular lumen of the majority of larid carcasses diagnosed with avian cholera suggests scavenging of birds that died from avian cholera as a major mode of transmission. This documentation of an outbreak of avian cholera in a North American pelagic environment affecting primarily scavenging gulls indicates that offshore marine environments may be a component of avian cholera dynamics.
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.
Publisher: Cold Spring Harbor Laboratory
Date: 06-02-2023
DOI: 10.1101/2023.02.06.527378
Abstract: There is an ongoing and profound burden of lineage 2.3.4.4b high pathogenicity avian influenza (HPAI) H5 on wild birds and poultry, globally. Herein we report the continued absence of HPAI in Australia from September – December 2022, in inbound migratory birds. Given the ever changing phenotype of this virus, worldwide studies on the occurence, or here absence of the virus, are of critical importance to understand the virus’ dispersal and incursion risk and development of response strategies.
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2023
Publisher: Cold Spring Harbor Laboratory
Date: 24-02-2023
DOI: 10.1101/2023.02.23.529812
Abstract: Anthropogenic pollution may disrupt wildlife immune function and increase susceptibility to, and ability to withstand, infection. Of particular concern is avian influenza virus (AIV), which in its low-pathogenic form is endemic in many wild bird populations, notably waterfowl and shorebirds, and in its high-pathogenic form poses a threat to wildlife, livestock and people. Many pollutants have immunomodulative properties, yet little is known about how these pollutants affect AIV infection risk specifically. We examined concentrations of known immunomodulatory compounds, per- and polyfluoroalkyl substances (PFASs), and assessed their influence on AIV infection in three reservoir species, red-necked stint ( Calidris ruficollis , n=121), pacific black duck ( Anas superciliosa , n=57) and grey teal ( Anas gracilis , n= 62). Using data on viral prevalence (cloacal/oropharyngeal swabs) and seroprevalence (AIV anti-nucleoprotein antibodies), we found no significant effect of PFASs pollution (total PFASs .01 – 470 ng/g in red-necked stint, .01 – 600 ng/g in pacific black duck and 0.3 – 200 ng/g in grey teal) on infection status in our three species. This may be due to relatively low pollutant concentrations, but we cannot rule out possible population culling through a synergy of pollution and infection stressors. We therefore recommend further studies on infection incidence in more polluted populations or species.
Publisher: Elsevier BV
Date: 08-2013
DOI: 10.1016/J.VIROL.2013.05.004
Abstract: Influenza A viruses (IAV) can dramatically alter both genotype and phenotype at a rapid rate as a product of co-infection and reassortment. Avian IAV exhibit high levels of phylogenetic incongruence, suggesting high levels of reassortment in the virus reservoir. Using a natural-experimental system, we reconstructed relationships amongst 92 viruses across 15 subtypes from 10 Mallards in an autumn season. Phylogenetic analyses estimated that 56% of the isolated viruses were reassorted. Network analysis demonstrated different patterns of reassortment and limited exchange of segments between primary and secondary infections. No clear patterns of linkage between segments were found, and patterns within a season were likely the consequence of continued introduction of new constellations, high viral load and ersity in the wild bird reservoir, and co-infections. This is the first IAV study to implement multiple tools available for elucidating factors governing reassortment patterns in naturally infected Mallards.
Publisher: Public Library of Science (PLoS)
Date: 17-02-2016
Publisher: Springer Science and Business Media LLC
Date: 11-07-2022
DOI: 10.1007/S10682-022-10190-9
Abstract: Seasonal long-distance migratory behaviour of trillions of animals may in part have evolved to reduce parasite infection risk, and the fitness costs that may come with these infections. This may apply to a ersity of vertebrate migration strategies that can sometimes be observed within species and may often be age-dependent. Herein we review some common age-related variations in migration strategy, discussing why in some animal species juveniles preferentially forego or otherwise rearrange their migrations as compared to adults, potentially as an either immediate (proximate) or anticipatory (ultimate) response to infection risk and disease. We notably focus on the phenomenon of “oversummering”, where juveniles abstain from migration to the breeding grounds. This strategy is particularly prevalent amongst migratory shorebirds and has thus far received little attention as a strategy to reduce parasite infection rate, while comparative intra-specific research approaches have strong potential to elucidate the drivers of differential behavioural strategies.
Publisher: Microbiology Society
Date: 12-2017
DOI: 10.1099/JGV.0.000977
Abstract: Neuraminidase inhibitors are a cornerstone of influenza pandemic preparedness before vaccines can be mass-produced and thus a neuraminidase inhibitor-resistant pandemic is a serious threat to public health. Earlier work has demonstrated the potential for development and persistence of oseltamivir resistance in influenza A viruses exposed to environmentally relevant water concentrations of the drug when infecting mallards, the natural influenza reservoir that serves as the genetic base for human pandemics. As zanamivir is the major second-line neuraminidase inhibitor treatment, this study aimed to assess the potential for development and persistence of zanamivir resistance in an
Publisher: Public Library of Science (PLoS)
Date: 30-01-2014
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.
Location: Australia
Start Date: 06-2020
End Date: 05-2023
Amount: $419,016.00
Funder: Australian Research Council
View Funded Activity