Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units
Identifieur interne : 000086 ( Main/Exploration ); précédent : 000085; suivant : 000087Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units
Auteurs : Anita C. Schürch [Pays-Bas] ; Debby Schipper [Pays-Bas] ; Maarten A. Bijl [Pays-Bas] ; Jim Dau [États-Unis] ; Kimberlee B. Beckmen [États-Unis] ; Claudia M. E. Schapendonk [Pays-Bas] ; V. Stalin Raj [Pays-Bas] ; Albert D. M. E. Osterhaus [Pays-Bas] ; Bart L. Haagmans [Pays-Bas] ; Morten Tryland [Norvège] ; Saskia L. Smits [Pays-Bas]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (
Url:
DOI: 10.1371/journal.pone.0105227
PubMed: 25140520
PubMed Central: 4139337
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000008
- to stream Pmc, to step Curation: 000008
- to stream Pmc, to step Checkpoint: 000055
- to stream Ncbi, to step Merge: 000203
- to stream Ncbi, to step Curation: 000203
- to stream Ncbi, to step Checkpoint: 000203
- to stream Main, to step Merge: 000083
- to stream Main, to step Curation: 000086
Le document en format XML
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Schürch</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Schipper, Debby" sort="Schipper, Debby" uniqKey="Schipper D" first="Debby" last="Schipper">Debby Schipper</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Bijl, Maarten A" sort="Bijl, Maarten A" uniqKey="Bijl M" first="Maarten A." last="Bijl">Maarten A. Bijl</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Dau, Jim" sort="Dau, Jim" uniqKey="Dau J" first="Jim" last="Dau">Jim Dau</name><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Alaska Department of Fish and Game, Kotzebue, Alaska, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Alaska Department of Fish and Game, Kotzebue, Alaska</wicri:regionArea><placeName><region type="state">Alaska</region></placeName></affiliation></author><author><name sortKey="Beckmen, Kimberlee B" sort="Beckmen, Kimberlee B" uniqKey="Beckmen K" first="Kimberlee B." last="Beckmen">Kimberlee B. Beckmen</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>Alaska Department of Fish and Game, Division of Wildlife Conservation, Fairbanks, Alaska, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Alaska Department of Fish and Game, Division of Wildlife Conservation, Fairbanks, Alaska</wicri:regionArea><placeName><region type="state">Alaska</region></placeName></affiliation></author><author><name sortKey="Schapendonk, Claudia M E" sort="Schapendonk, Claudia M E" uniqKey="Schapendonk C" first="Claudia M. E." last="Schapendonk">Claudia M. E. Schapendonk</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Raj, V Stalin" sort="Raj, V Stalin" uniqKey="Raj V" first="V. Stalin" last="Raj">V. Stalin Raj</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Osterhaus, Albert D M E" sort="Osterhaus, Albert D M E" uniqKey="Osterhaus A" first="Albert D. M. E." last="Osterhaus">Albert D. M. E. Osterhaus</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Viroclinics Biosciences, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Viroclinics Biosciences, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Haagmans, Bart L" sort="Haagmans, Bart L" uniqKey="Haagmans B" first="Bart L." last="Haagmans">Bart L. Haagmans</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Tryland, Morten" sort="Tryland, Morten" uniqKey="Tryland M" first="Morten" last="Tryland">Morten Tryland</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Research Group for Arctic Infection Biology, Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø, Norway</addr-line></nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>Research Group for Arctic Infection Biology, Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø</wicri:regionArea><wicri:noRegion>Tromsø</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Genøk - Centre for Biosafety, Tromsø, Norway</addr-line></nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>Genøk - Centre for Biosafety, Tromsø</wicri:regionArea><wicri:noRegion>Tromsø</wicri:noRegion></affiliation></author><author><name sortKey="Smits, Saskia L" sort="Smits, Saskia L" uniqKey="Smits S" first="Saskia L." last="Smits">Saskia L. Smits</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Viroclinics Biosciences, Rotterdam, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Viroclinics Biosciences, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (<italic>Rangifer tarandus granti</italic>) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family <italic>Coronaviridae</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Das Neves, C" uniqKey="Das Neves C">C das Neves</name></author><author><name sortKey="Mork, T" uniqKey="Mork T">T Mork</name></author><author><name sortKey="Thiry, J" uniqKey="Thiry J">J Thiry</name></author><author><name sortKey="Godfroid, J" uniqKey="Godfroid J">J Godfroid</name></author><author><name sortKey="Rimstad, E" uniqKey="Rimstad E">E Rimstad</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Evans, Al" uniqKey="Evans A">AL Evans</name></author><author><name sortKey="Das Neves, Cg" uniqKey="Das Neves C">CG das Neves</name></author><author><name 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Schürch</name></region><name sortKey="Bijl, Maarten A" sort="Bijl, Maarten A" uniqKey="Bijl M" first="Maarten A." last="Bijl">Maarten A. Bijl</name><name sortKey="Haagmans, Bart L" sort="Haagmans, Bart L" uniqKey="Haagmans B" first="Bart L." last="Haagmans">Bart L. Haagmans</name><name sortKey="Osterhaus, Albert D M E" sort="Osterhaus, Albert D M E" uniqKey="Osterhaus A" first="Albert D. M. E." last="Osterhaus">Albert D. M. E. Osterhaus</name><name sortKey="Osterhaus, Albert D M E" sort="Osterhaus, Albert D M E" uniqKey="Osterhaus A" first="Albert D. M. E." last="Osterhaus">Albert D. M. E. Osterhaus</name><name sortKey="Raj, V Stalin" sort="Raj, V Stalin" uniqKey="Raj V" first="V. Stalin" last="Raj">V. Stalin Raj</name><name sortKey="Schapendonk, Claudia M E" sort="Schapendonk, Claudia M E" uniqKey="Schapendonk C" first="Claudia M. E." last="Schapendonk">Claudia M. E. Schapendonk</name><name sortKey="Schipper, Debby" sort="Schipper, Debby" uniqKey="Schipper D" first="Debby" last="Schipper">Debby Schipper</name><name sortKey="Smits, Saskia L" sort="Smits, Saskia L" uniqKey="Smits S" first="Saskia L." last="Smits">Saskia L. Smits</name><name sortKey="Smits, Saskia L" sort="Smits, Saskia L" uniqKey="Smits S" first="Saskia L." last="Smits">Saskia L. Smits</name></country><country name="États-Unis"><region name="Alaska"><name sortKey="Dau, Jim" sort="Dau, Jim" uniqKey="Dau J" first="Jim" last="Dau">Jim Dau</name></region><name sortKey="Beckmen, Kimberlee B" sort="Beckmen, Kimberlee B" uniqKey="Beckmen K" first="Kimberlee B." last="Beckmen">Kimberlee B. Beckmen</name></country><country name="Norvège"><noRegion><name sortKey="Tryland, Morten" sort="Tryland, Morten" uniqKey="Tryland M" first="Morten" last="Tryland">Morten Tryland</name></noRegion><name sortKey="Tryland, Morten" sort="Tryland, Morten" uniqKey="Tryland M" first="Morten" last="Tryland">Morten Tryland</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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