Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units
Identifieur interne : 000008 ( Pmc/Curation ); précédent : 000007; suivant : 000009Metagenomic 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
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Schürch</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Schipper, Debby" sort="Schipper, Debby" uniqKey="Schipper D" first="Debby" last="Schipper">Debby Schipper</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Bijl, Maarten A" sort="Bijl, Maarten A" uniqKey="Bijl M" first="Maarten A." last="Bijl">Maarten A. 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Haagmans</name><affiliation wicri:level="1"><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></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></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></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="1"><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></affiliation><affiliation wicri:level="1"><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></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25140520</idno><idno type="pmc">4139337</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139337</idno><idno type="RBID">PMC:4139337</idno><idno type="doi">10.1371/journal.pone.0105227</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000008</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000008</idno><idno type="wicri:Area/Pmc/Curation">000008</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000008</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units</title><author><name sortKey="Schurch, Anita C" sort="Schurch, Anita C" uniqKey="Schurch A" first="Anita C." last="Schürch">Anita C. Schürch</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Schipper, Debby" sort="Schipper, Debby" uniqKey="Schipper D" first="Debby" last="Schipper">Debby Schipper</name><affiliation wicri:level="1"><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></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="1"><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></affiliation></author><author><name sortKey="Dau, Jim" sort="Dau, Jim" uniqKey="Dau J" first="Jim" last="Dau">Jim Dau</name><affiliation wicri:level="1"><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></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="1"><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></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="1"><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></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="1"><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></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="1"><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></affiliation><affiliation wicri:level="1"><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></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="1"><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></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></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></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="1"><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></affiliation><affiliation wicri:level="1"><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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25140520</article-id><article-id pub-id-type="pmc">4139337</article-id><article-id pub-id-type="publisher-id">PONE-D-14-17550</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0105227</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Sequence Assembly Tools</subject></subj-group></subj-group></subj-group><subj-group><subject>Microbiology</subject><subj-group><subject>Virology</subject></subj-group></subj-group><subj-group><subject>Veterinary Science</subject><subj-group><subject>Veterinary Diseases</subject><subj-group><subject>Veterinary Virology</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units</article-title><alt-title alt-title-type="running-head">New Viruses Detected in Alaskan Caribou</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Schürch</surname><given-names>Anita C.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Schipper</surname><given-names>Debby</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bijl</surname><given-names>Maarten A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dau</surname><given-names>Jim</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Beckmen</surname><given-names>Kimberlee B.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Schapendonk</surname><given-names>Claudia M. E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Raj</surname><given-names>V. Stalin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Osterhaus</surname><given-names>Albert D. M. E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Haagmans</surname><given-names>Bart L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tryland</surname><given-names>Morten</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Smits</surname><given-names>Saskia L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Viroclinics Biosciences, Rotterdam, The Netherlands</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Alaska Department of Fish and Game, Kotzebue, Alaska, United States of America</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Alaska Department of Fish and Game, Division of Wildlife Conservation, Fairbanks, Alaska, United States of America</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Research Group for Arctic Infection Biology, Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø, Norway</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Genøk - Centre for Biosafety, Tromsø, Norway</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Attoui</surname><given-names>Houssam</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>The Pirbright Institute, United Kingdom</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>s.smits@erasmusmc.nl</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>I have read the journal's policy and the authors of this manuscript have the following competing interests: Drs A.D.M.E. Osterhaus and S.L. Smits are partly employed by Viroclinics Biosciences B.V., Rotterdam, The Netherlands. This does not alter our adherence to PLOS ONE policies on sharing data and materials.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: MT SLS BLH ADMEO. Performed the experiments: CMES VSR DS MT SLS. Analyzed the data: AS MT SLS BLH ADMEO MAB. Contributed reagents/materials/analysis tools: MT JD KB SLS. Contributed to the writing of the manuscript: AS SLS MT BLH.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>20</day><month>8</month><year>2014</year></pub-date><volume>9</volume><issue>8</issue><elocation-id>e105227</elocation-id><history><date date-type="received"><day>18</day><month>4</month><year>2014</year></date><date date-type="accepted"><day>18</day><month>7</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><license><license-p>This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.</license-p></license></permissions><abstract><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></abstract><funding-group><funding-statement>This work was partially funded by the European Community's Seventh Framework Program (FP7/2007–2013) under the project “European Management Platform for Emerging and Reemerging Infectious disease Entities” European Commission agreement no. 223498 and the Virgo Consortium, funded by the Dutch government project number FES0908, and by the Netherlands Genomics Initiative (NGI) project number 050-060-452. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="11"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. Nucleotide sequence accession numbers: The L1 nucleotide sequence of RtPV4, VP2 and NS1 sequences of caribou parvovirus, partial helicase sequence of caribou nidovirus, and the large T antigen sequence of caribou polyomavirus were deposited in the GenBank sequence database under accession numbers KJ719447-451, respectively.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The authors confirm that all data underlying the findings are fully available without restriction. Nucleotide sequence accession numbers: The L1 nucleotide sequence of RtPV4, VP2 and NS1 sequences of caribou parvovirus, partial helicase sequence of caribou nidovirus, and the large T antigen sequence of caribou polyomavirus were deposited in the GenBank sequence database under accession numbers KJ719447-451, respectively.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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