The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates
Identifieur interne : 000541 ( Ncbi/Merge ); précédent : 000540; suivant : 000542The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates
Auteurs : Joel O. WertheimSource :
- PLoS ONE [ 1932-6203 ] ; 2010.
Abstract
In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.
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DOI: 10.1371/journal.pone.0011184
PubMed: 20567599
PubMed Central: 2887442
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates</title><author><name sortKey="Wertheim, Joel O" sort="Wertheim, Joel O" uniqKey="Wertheim J" first="Joel O." last="Wertheim">Joel O. Wertheim</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20567599</idno><idno type="pmc">2887442</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887442</idno><idno type="RBID">PMC:2887442</idno><idno type="doi">10.1371/journal.pone.0011184</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000B10</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B10</idno><idno type="wicri:Area/Pmc/Curation">000B10</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B10</idno><idno type="wicri:Area/Pmc/Checkpoint">000875</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000875</idno><idno type="wicri:Area/Ncbi/Merge">000541</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates</title><author><name sortKey="Wertheim, Joel O" sort="Wertheim, Joel O" uniqKey="Wertheim J" first="Joel O." last="Wertheim">Joel O. Wertheim</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pybus, Og" uniqKey="Pybus O">OG Pybus</name></author><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drummond, Aj" uniqKey="Drummond A">AJ Drummond</name></author><author><name sortKey="Pybus, Og" uniqKey="Pybus O">OG Pybus</name></author><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name></author><author><name sortKey="Forsberg, R" uniqKey="Forsberg R">R Forsberg</name></author><author><name sortKey="Rodrigo, Ag" uniqKey="Rodrigo A">AG Rodrigo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beveridge, Wib" uniqKey="Beveridge W">WIB 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Goldstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zimmer, Sm" uniqKey="Zimmer S">SM Zimmer</name></author><author><name sortKey="Burke, Ds" uniqKey="Burke D">DS Burke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Gj" uniqKey="Smith G">GJ Smith</name></author><author><name sortKey="Bahl, J" uniqKey="Bahl J">J Bahl</name></author><author><name sortKey="Vijaykrishna, D" uniqKey="Vijaykrishna D">D Vijaykrishna</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fitch, Wm" uniqKey="Fitch W">WM Fitch</name></author><author><name sortKey="Leiter, Jm" uniqKey="Leiter J">JM Leiter</name></author><author><name sortKey="Li, Xq" uniqKey="Li X">XQ Li</name></author><author><name sortKey="Palese, P" uniqKey="Palese P">P 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sortKey="Drummond, Aj" uniqKey="Drummond A">AJ Drummond</name></author><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beklemishev, Ab" uniqKey="Beklemishev A">AB Beklemishev</name></author><author><name sortKey="Blinov, Vm" uniqKey="Blinov V">VM Blinov</name></author><author><name sortKey="Vasilenko, Sk" uniqKey="Vasilenko S">SK Vasilenko</name></author><author><name sortKey="Golovin, S" uniqKey="Golovin S">S Golovin</name></author><author><name sortKey="Gutorov, Vv" uniqKey="Gutorov V">VV Gutorov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beklemishev, Ab" uniqKey="Beklemishev A">AB Beklemishev</name></author><author><name sortKey="Blinov, Vm" uniqKey="Blinov V">VM Blinov</name></author><author><name sortKey="Vasilenko, Sk" uniqKey="Vasilenko S">SK Vasilenko</name></author><author><name sortKey="Golovin, S" uniqKey="Golovin S">S 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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">20567599</article-id><article-id pub-id-type="pmc">2887442</article-id><article-id pub-id-type="publisher-id">10-PONE-RA-16751</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0011184</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Evolutionary Biology/Microbial Evolution and Genomics</subject><subject>Virology/Emerging Viral Diseases</subject><subject>Virology/Virus Evolution and Symbiosis</subject></subj-group></article-categories><title-group><article-title>The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates</article-title><alt-title alt-title-type="running-head">Influenza Divergence Times</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wertheim</surname><given-names>Joel O.</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Department of Pathology, University of California San Diego, San Diego, California, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Poon</surname><given-names>Art F. Y.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">BC Centre for Excellence in HIV/AIDS, Canada</aff><author-notes><corresp id="cor1">* E-mail: <email>jwertheim@ucsd.edu</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: JOW. Performed the experiments: JOW. Analyzed the data: JOW. Wrote the paper: JOW.</p></fn></author-notes><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>17</day><month>6</month><year>2010</year></pub-date><volume>5</volume><issue>6</issue><elocation-id>e11184</elocation-id><history><date date-type="received"><day>3</day><month>3</month><year>2010</year></date><date date-type="accepted"><day>7</day><month>4</month><year>2010</year></date></history><permissions><copyright-statement>Joel O. Wertheim.</copyright-statement><copyright-year>2010</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><p>In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.</p></abstract><counts><page-count count="4"></page-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Wertheim, Joel O" sort="Wertheim, Joel O" uniqKey="Wertheim J" first="Joel O." last="Wertheim">Joel O. Wertheim</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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