ORCID Profile
0000-0001-6665-7492
Current Organisations
University of Sydney
,
Uppsala University Hospital
,
Public Health Agency of Sweden
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Publisher: American Society for Microbiology
Date: 02-05-2018
Publisher: Oxford University Press (OUP)
Date: 17-11-2020
Abstract: Whether type-specific human papillomavirus (HPV) infection influences the risk of acquiring infections with other HPV types is unclear. We studied concurrent HPV infections in 17-year-old girls from 2 birth cohorts the first vaccine-eligible cohort in Norway and a prevaccination cohort. Urine s les were collected and tested for 37 HPV genotypes. This study was restricted to unvaccinated girls from the prevaccination cohort (n = 5245) and vaccinated girls from the vaccine-eligible cohort (n = 4904). Risk of HPV infection was modelled using mixed-effect logistic regression. Expected frequencies of concurrent infection with each pairwise combination of the vaccine types and high-risk types (6/11/16/18/31/33/35/39/45/51/52/56/58/59) were compared to observed frequencies. Infection with multiple HPV types was more common among unvaccinated girls than vaccinated girls (9.2% vs 3.7%). HPV33 and HPV51 was the only HPV pair that was detected together more often than expected among both unvaccinated (P = .002) and vaccinated girls (P & .001). No HPV pairs were observed significantly less often than expected. HPV33 and HPV51 tended to be involved in coinfection among both unvaccinated and vaccinated girls. The introduction of HPV vaccination does not seem to have had an effect on the tendency of specific HPV types to cluster together.
Publisher: Springer Science and Business Media LLC
Date: 29-08-2018
Publisher: Informa UK Limited
Date: 09-05-2018
Publisher: Springer Science and Business Media LLC
Date: 06-08-2018
Publisher: Springer Science and Business Media LLC
Date: 14-08-2019
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.
Publisher: Springer Science and Business Media LLC
Date: 07-03-2019
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.
Publisher: Elsevier BV
Date: 2020
Publisher: Cold Spring Harbor Laboratory
Date: 08-09-2021
DOI: 10.1101/2021.09.04.21263123
Abstract: The Nordic countries, defined here as Norway, Sweden, Denmark, Finland and Iceland, are known for their comparable demographics and political systems. Since these countries implemented different COVID-19 intervention strategies, they provide a natural laboratory for examining how COVID-19 policies and mitigation strategies affected the propagation, evolution and spread of the SARS-CoV-2 virus. We explored how the duration, the size and number of transmission clusters, defined as country-specific monophyletic groups in a SARS-CoV-2 phylogenetic tree, differed between the Nordic countries. We found that Sweden had the largest number of COVID-19 transmission clusters followed by Denmark, Norway, Finland and Iceland. Moreover, Sweden and Denmark had the largest, and most enduring, transmission clusters followed by Norway, Finland and Iceland. In addition, there was a significant positive association between transmission cluster size and duration, suggesting that the size of transmission clusters could be reduced by rapid and effective contact tracing. Thus, these data indicate that to reduce the general burden of COVID-19 there should be a focus on limiting dense gatherings and their subsequent contacts to keep the number, size and duration of transmission clusters to a minimum. Our results further suggest that although geographical connectivity, population density and openness influence the spread and the size of SARS-CoV-2 transmission clusters, country-specific intervention strategies had the largest single impact.
Publisher: Springer Science and Business Media LLC
Date: 11-03-2014
Publisher: Microbiology Society
Date: 19-11-2021
DOI: 10.1099/JGV.0.001674
Abstract: Sandfly-borne phleboviruses are distributed widely throughout the Mediterranean Basin, presenting a threat to public health in areas where they circulate. However, the true ersity and distribution of pathogenic and apathogenic sandfly-borne phleboviruses remains a key issue to be studied. In the Balkans, most published data rely on serology-based studies although virus isolation has occasionally been reported. Here, we report the discovery of two novel sandfly-borne phleboviruses, provisionally named Zaba virus (ZABAV) and Bregalaka virus (BREV), which were isolated in Croatia and North Macedonia, respectively. This constitutes the first isolation of phleboviruses in both countries. Genetic analysis based on complete coding sequences indicated that ZABAV and BREV are distinct from each other and belong to the genus Phlebovirus, family Phenuiviridae . Phylogenetic and amino acid modelling of viral polymerase shows that ZABAV and BREV are new members of the Salehabad phlebovirus species and the Adana phlebovirus species, respectively. Moreover, sequence-based vector identification suggests that ZABAV is mainly transmitted by Phlebotomus neglectus and BREV is mainly transmitted by Phlebotomus perfiliewi . BREV neutralizing antibodies were detected in 3.3% of human sera with rates up to 16.7% in certain districts, demonstrating that BREV frequently infects humans in North Macedonia. In vitro viral growth kinetics experiments demonstrated viral replication of both viruses in mammalian and mosquito cells. In vivo experimental studies in mice suggest that ZABAV and BREV exhibit characteristics making them possible human pathogens.
Publisher: Proceedings of the National Academy of Sciences
Date: 21-11-2016
Abstract: We used population genomic analyses to reconstruct the recent history and dispersal of a major clade of Mycobacterium tuberculosis in central Asia and beyond. Our results indicate that the fall of the Soviet Union and the ensuing collapse of public health systems led to a rise in M. tuberculosis drug resistance. We also show that armed conflict and population displacement is likely to have aided the export of this clade from central Asia to war-torn Afghanistan and beyond.
Publisher: Cold Spring Harbor Laboratory
Date: 05-05-2020
DOI: 10.1101/2020.05.04.075515
Abstract: Ticks (order: Ixodida) are a highly erse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick ( Ixodes uriae ), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circumpolar region millions of years ago and has remained isolated in these regions ever since. Such a profound biographic sub ision provides a unique opportunity to determine whether viruses associated with ticks exhibit the same evolutionary patterns as their hosts. To test this, we collected Ix. uriae specimens near a Gentoo penguin ( Pygoscelis papua ) colony at Neko harbour, Antarctica, and from migratory birds - the Razorbill ( Alca torda ) and the Common murre ( Uria aalge ) - on Bonden island, northern Sweden. Through meta-transcriptomic next- generation sequencing we identified 16 RNA viruses, seven of which were novel. Notably, we detected the same species, Ronne virus, and two closely related species, Bonden virus and Piguzov virus, in both hemispheres indicating that there have been at least two cross- circumpolar dispersal events. Similarly, we identified viruses discovered previously in other locations several decades ago, including Gadgets Gully virus, Taggert virus and Okhotskiy virus. By identifying the same or closely related viruses in geographically disjunct s ling locations we therefore provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of the Ix. uriae hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both the local and global scales. As host populations erge, so may those microorganisms, including viruses, that are dependent on those hosts. To examine this key issue in host-microbial evolution we compared the co-phylogenies of the seabird tick, Ixodes uriae , and their RNA viruses s led from the far northern and southern hemispheres. Despite the huge geographic distance between them, phylogeographic analysis reveals that the same viruses were found both within and between the northern and southern circumpolar regions, most likely reflecting transfer by virus-infected migratory birds. In contrast, genomic data suggested that the Ix. uriae populations were phylogenetically distinct between the northern and southern hemispheres. This work emphasises the importance of migratory birds and ticks as vectors and sources of virus dispersal and introduction at both the local and global scales.
Publisher: Microbiology Society
Date: 03-2017
DOI: 10.1099/JGV.0.000704
Publisher: Informa UK Limited
Date: 2020
Publisher: American Society for Microbiology
Date: 02-11-2016
Abstract: The unexpected emergence of Zika virus (ZIKV) in the Pacific Islands and Latin America and its association with congenital Zika virus syndrome (CZVS) (which includes microcephaly) and Guillain-Barré syndrome (GBS) have stimulated wide-ranging research. High densities of susceptible Aedes spp., immunologically naive human populations, global population growth with increased urbanization, and escalation of global transportation of humans and commercial goods carrying vectors and ZIKV undoubtedly enhanced the emergence of ZIKV. However, flavivirus mutations accumulate with time, increasing the likelihood that genetic viral differences are determinants of change in viral phenotype. Based on comparative ZIKV complete genome phylogenetic analyses and temporal estimates, we identify amino acid substitutions that may be associated with increased viral epidemicity, CZVS, and GBS. Reverse genetics, vector competence, and seroepidemiological studies will test our hypothesis that these amino acid substitutions are determinants of epidemic and neurotropic ZIKV emergence.
Publisher: Wiley
Date: 29-02-2020
DOI: 10.1111/ZPH.12696
Publisher: Elsevier BV
Date: 2019
Publisher: MDPI AG
Date: 11-07-2022
DOI: 10.3390/MICROORGANISMS10071393
Abstract: The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick s les that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.
Publisher: Public Library of Science (PLoS)
Date: 03-08-2020
Publisher: Elsevier BV
Date: 12-2019
Publisher: Wiley
Date: 07-2015
DOI: 10.1111/APM.12412
Abstract: Tick-borne encephalitis (TBE) is the most important viral tick-borne disease in Europe and can cause severe disease in humans. In Norway, human cases have been reported only from the southern coast. The aim of this study was to investigate the prevalence of tick-borne encephalitis virus (TBEV) in questing Ixodes ricinus ticks from the north-western part of Norway. A total of 4509 ticks were collected by flagging in May and June 2014. A subpopulation of 2220 nymphs and 162 adult ticks were analysed by real-time PCR and positive s les were confirmed by pyrosequencing. The estimated prevalence of TBEV was 3.08% among adult ticks from Sekken in Møre og Romsdal County and 0.41% among nymphs from both Hitra and Frøya in Sør-Trøndelag County. This study indicates that TBEV might be more widespread than the distribution of reported human cases suggests.
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.
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.
Publisher: Public Library of Science (PLoS)
Date: 09-06-2022
DOI: 10.1371/JOURNAL.PONE.0269105
Abstract: Male sex and advanced age are associated with severe symptoms of COVID-19. Sex and age also exhibit substantial associations with genome-wide DNA methylation (DNAm) differences in humans. Using a random s le of Illumina EPIC-based genome-wide methylomes from peripheral whole blood of 1,976 parents, participating in The Norwegian Mother, Father and Child Cohort Study (MoBa), we explored whether DNAm in genes linked to SARS-CoV-2 host cell entry and to severe COVID-19 were associated with sex and age. This was carried out by testing 1,572 DNAm sites (CpGs) located near 45 genes for associations with age and sex. We found that DNAm in 281 and 231 of 1,572 CpGs were associated (p FDR .01) with sex and aging, respectively. CpGs linked to SARS-CoV-2 host cell entry genes were all associated with age and sex, except for the ACE2 receptor gene (located on the X-chromosome), which was only associated with sex (p FDR .01). Furthermore, we examined whether 1,487 autosomal CpGs associated with host-cell entry and severe COVID-19 were more or less associated with sex and age than what would be expected from the same number of randomly s led genome-wide CpGs. We found that the CpGs associated with host-cell entry and severe COVID-19 were not more or less associated with sex (R 2 = 0.77, p = 0.09) than the CpGs s led from random genomic regions age was actually found to be significantly less so (R 2 = 0.36, p = 0.04). Hence, while we found wide-spread associations between sex and age at CpGs linked to genes implicated with SARS-CoV-2 host cell entry and severe COVID-19, the effect from the sum of these CpGs was not stronger than that from randomly s led CpGs for age it was significantly less so. These findings could suggest that advanced age and male sex may not be unsurmountable barriers for the SARS-CoV-2 virus to evolve increased infectiousness.
Publisher: Frontiers Media SA
Date: 24-03-2020
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.
Publisher: American Society for Microbiology
Date: 15-08-2019
DOI: 10.1128/JVI.00620-19
Abstract: This study shows that only a single introduction of SINV into a new geographical area is required for spread and establishment, provided that the requisite vector(s) and reservoir(s) of epizootological and epidemiological importance are present. Furthermore, we present the first report of recombination between two strains of SINV in nature. Our study increases the knowledge on new introductions and dispersal of arboviruses in general and of SINV in particular.
Publisher: Elsevier BV
Date: 12-2017
Publisher: Cold Spring Harbor Laboratory
Date: 18-11-2020
DOI: 10.1101/2020.11.18.20233767
Abstract: Many countries have attempted to mitigate and control COVID-19 through the implementation of 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. To assess the duration of chains of virus transmission within in idual countries and the extent to which countries export viruses to their geographic neighbours. To address core questions in genomic epidemiology and public health we analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, within countries of northern Europe. To this end, we examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the pandemic. The Nordic countries differed markedly in the invasiveness of control strategies implemented. In particular, Sweden did not initially employ any strict population movement limitations and experienced markedly different transmission chain dynamics, which were more numerous and tended to have more cases, a set of features that increased with time during the first eight months of 2020. Together with Denmark, Sweden was also characterised as a net exporter of SARS-CoV-2. Hence, Sweden effectively constituted an epidemiological and evolutionary ‘refugia’ that enabled the virus to maintain active transmission and spread to other geographic localities. In sum, our analysis reveals the utility of genomic surveillance where active transmission chain monitoring is a key metric.
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.
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.
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.JHEP.2016.01.001
Abstract: On-going risk behaviour can lead to hepatitis C virus (HCV) reinfection following successful treatment. We aimed to assess the incidence of persistent HCV reinfection in a population of people who inject drugs (PWID) who had achieved sustained virological response (SVR) seven years earlier. In 2004-2006 we conducted a multicentre treatment trial comprising HCV genotype 2 or 3 patients in Sweden, Norway and Denmark (NORTH-C). Six months of abstinence from injecting drug use (IDU) was required before treatment. All Norwegian patients who had obtained SVR (n=161) were eligible for participation in this long-term follow-up study assessing virological and behavioural characteristics. Follow-up data were available in 138 of 161 (86%) in iduals. Persistent reinfection was identified in 10 of 94 (11%) in iduals with a history of IDU prior to treatment (incidence rate 1.7/100 person-years (PY) 95% CI 0.8-3.1) and in 10 of 37 (27%) in iduals who had relapsed to IDU after treatment (incidence rate 4.9/100 PY 95% CI 2.3-8.9). Although relapse to IDU perfectly predicted reinfection, no baseline factor was associated with reinfection. Relapse to IDU was associated with age <30 years (vs. ⩾40 years) at treatment (adjusted odds ratio [aOR] 7.03 95% CI 1.78-27.8) and low education level (aOR 3.64 95% CI 1.44-9.18). Over time, persistent HCV reinfection was common among in iduals who had relapsed to IDU after treatment. Reinfection should be systematically addressed and prevented when providing HCV care for PWID.
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.ANTIVIRAL.2019.104676
Abstract: Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV placement in relation to Aedes-borne dengue viruses (DENV) and Culex-borne flaviviruses. We hypothesized that this incongruence reflects interspecies recombination resulting in ZIKV evasion of cross-protective T-cell immunity. We investigated ZIKV phylogenetic incongruence in relation to: DENV T-cell epitope maps experimentally identified ex vivo, published B-cell epitope loci, and CD8
Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2020
DOI: 10.1101/2020.09.08.20184580
Abstract: The first imported case of severe haemorrhagic fever in Sweden was reported in 1990. Despite extensive diagnostic study, no aetiological agent was identified. Following retrospective investigation with total RNA-sequencing of plasma and urine s les collected during between 7–36 days from onset of symptoms, we identified dengue virus 3 (DENV-3) and a human pegivirus (HPgV). We conclude that the patient most likely suffered from haemorrhagic symptoms due to a severe dengue infection.
Publisher: Microbiology Society
Date: 09-2014
Abstract: The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of ersification of the genus has long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years. However, it has been argued that the tick-borne Powassan flavivirus was introduced into North America some time between the opening and closing of the Beringian land bridge that connected Asia and North America 15 000–11 000 years ago, indicating an even older origin for Flavivirus . To determine the temporal origin of Flavivirus , we performed Bayesian relaxed molecular clock dating on a dataset with high coverage of the presently available Flavivirus ersity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000 (64 000–110 000) or 120 000 (87 000–159 000) years ago, depending on the circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
Publisher: Springer Science and Business Media LLC
Date: 04-08-2010
Abstract: Tick-borne Anaplasma phagocytophilum and Rickettsia spp. are considered to be emerging human pathogens, but only limited data are available on their occurrence in Sweden. Two real-time PCR assays followed by nested PCR and sequence analysis were carried out to investigate the prevalence of A. phagocytophilum and spotted fever rickettsiae in ticks from seven areas in Sweden. In 139 pooled s les, representing a total of 1245 Ixodes ricinus ticks (204 larvae, 963 nymphs, 38 males, 40 females), the overall positive mean infection prevalence was 1.3-15.0% for A. phagocytophilum and 1.5-17.3% for R. helvetica. A. phagocytophilum was only detected in nymphs (1.7-19.4%), whereas R. helvetica was detected in all three tick stages. Support for vertical and transstadial transmission was only obtained for R. helvetica . Both agents showed similar infection rates across study areas, although infection rates were greater in coastal areas. The results show that both pathogens occurred in all seven locations, indicating that they are prevalent in Sweden and should be considered etiological agents in patients recently bitten by ticks.
Publisher: Springer Science and Business Media LLC
Date: 10-02-2017
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.TTBDIS.2011.11.003
Abstract: A total of 887 adult Ixodes ricinus ticks (469 females and 418 males) from 29 different localities in Sweden were screened for Rickettsia, Anaplasma, and Coxiella DNA using PCR and then subjected to gene sequencing. Rickettsial DNA was detected in 9.5-9.6% of the ticks. Most of the positive ticks were infected with Rickettsia helvetica. One tick harbored another spotted fever rickettsia, closely related to or identical with R. sibirica not previously found in I. ricinus nor in Sweden. Six of the ticks (0.7%) were infected with an Anaplasma sp., presumably A. phagocytophilum. Coxiella burnetii DNA was not detected in any of the ticks. The detection of R. helvetica and A. phagocytophilum in several of the localities s led suggests that these potentially human-pathogenic agents are common in Sweden.
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/VE/VEAC027
Abstract: Intraspecies (homologous) phylogenetic incongruence, or ‘tree conflict’ between different loci within the same genome of mosquito-borne flaviviruses (MBFV), was first identified in dengue virus (DENV) and subsequently in Japanese encephalitis virus (JEV), St Louis encephalitis virus, and Zika virus (ZIKV). Recently, the first evidence of phylogenetic incongruence between interspecific members of the MBFV was reported in ZIKV and its close relative, Spondweni virus. Uniquely, these hybrid proteomes were derived from four incongruent trees involving an Aedes-associated DENV node (1 tree) and three different Culex-associated flavivirus nodes (3 trees). This analysis has now been extended across a wider spectrum of viruses within the MBFV lineage targeting the breakpoints between phylogenetic incongruent loci originally identified in ZIKV. Interspecies phylogenetic incongruence at these breakpoints was identified in 10 of 50 viruses within the MBFV lineage, representing emergent Aedes and Culex-associated viruses including JEV, West Nile virus, yellow fever virus, and insect-specific viruses. Thus, interspecies phylogenetic incongruence is widespread amongst the flaviviruses and is robustly associated with the specific breakpoints that coincide with the interspecific phylogenetic incongruence previously identified, inferring they are ‘hotspots’. The incongruence amongst the emergent MBFV group was restricted to viruses within their respective associated epidemiological boundaries. This MBFV group was RY-coded at the third codon position (‘wobble codon’) to remove transition saturation. The resulting ‘wobble codon’ trees presented a single topology for the entire genome that lacked any robust evidence of phylogenetic incongruence between loci. Phylogenetic interspecific incongruence was therefore observed for exactly the same loci between amino acid and the RY-coded ‘wobble codon’ alignments and this incongruence represented either a major part, or the entire genomes. Maximum likelihood codon analysis revealed positive selection for the incongruent lineages. Positive selection could result in the same locus producing two opposing trees. These analyses for the clinically important MBFV suggest that robust interspecific phylogenetic incongruence resulted from amino acid selection. Convergent or parallel evolutions are evolutionary processes that would explain the observation, whilst interspecific recombination is unlikely.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 05-10-2018
Abstract: Repeated emergence, not international dissemination, is behind the rise of multidrug-resistant lineage 4 tuberculosis.
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2022
DOI: 10.1101/2022.02.24.481848
Abstract: We identified a novel Betacoronavirus from bank voles ( Myodes glareolus ) in Grimsö, Sweden. Repeated detection over three years and an overall prevalence of 3.4% suggests the virus commonly occurs in bank voles. Furthermore, phylogenetic analyses indicate the virus belongs to a highly ergent Embecovirus lineage predominantly associated with bank voles.
Publisher: Oxford University Press (OUP)
Date: 03-01-2022
DOI: 10.1093/OFID/OFAB665
Abstract: We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic tree, differed among the Nordic countries of Norway, Sweden, Denmark, Finland, and Iceland. Our results suggest that although geographical connectivity, population density, and openness influence the spread and the size of SARS-CoV-2 transmission clusters, the different country-specific intervention strategies had the largest impact. We also found a significant positive association between the size and duration of transmission clusters in the Nordic countries, suggesting that the rapid deployment of contact tracing is a key response measure in reducing virus transmission.
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.
Start Date: 2016
End Date: 2019
Funder: European Commission
View Funded ActivityStart Date: 2019
End Date: 2021
Funder: Märta Lundqvists Stiftelse
View Funded ActivityStart Date: 2016
End Date: 2020
Funder: Svenska Forskningsrådet Formas
View Funded ActivityStart Date: 2017
End Date: 2021
Funder: Vetenskapsrådet
View Funded ActivityStart Date: 2021
End Date: 2024
Funder: Vetenskapsrådet
View Funded Activity