Identifying Changes in Selective Constraints: Host Shifts in Influenza
Identifieur interne : 000440 ( Ncbi/Merge ); précédent : 000439; suivant : 000441Identifying Changes in Selective Constraints: Host Shifts in Influenza
Auteurs : Asif U. Tamuri ; Mario Dos Reis ; Alan J. Hay ; Richard A. GoldsteinSource :
- PLoS Computational Biology [ 1553-734X ] ; 2009.
Abstract
The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.
Url:
DOI: 10.1371/journal.pcbi.1000564
PubMed: 19911053
PubMed Central: 2770840
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identifying Changes in Selective Constraints: Host Shifts in Influenza</title><author><name sortKey="Tamuri, Asif U" sort="Tamuri, Asif U" uniqKey="Tamuri A" first="Asif U." last="Tamuri">Asif U. Tamuri</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19911053</idno><idno type="pmc">2770840</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770840</idno><idno type="RBID">PMC:2770840</idno><idno type="doi">10.1371/journal.pcbi.1000564</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000A41</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A41</idno><idno type="wicri:Area/Pmc/Curation">000A41</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A41</idno><idno type="wicri:Area/Pmc/Checkpoint">000A45</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000A45</idno><idno type="wicri:Area/Ncbi/Merge">000440</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identifying Changes in Selective Constraints: Host Shifts in Influenza</title><author><name sortKey="Tamuri, Asif U" sort="Tamuri, Asif U" uniqKey="Tamuri A" first="Asif U." last="Tamuri">Asif U. Tamuri</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author><author><name sortKey="Bean, Wj" uniqKey="Bean W">WJ Bean</name></author><author><name sortKey="Gorman, Ot" uniqKey="Gorman O">OT Gorman</name></author><author><name sortKey="Chambers, Tm" uniqKey="Chambers T">TM Chambers</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schafer, Jr" uniqKey="Schafer J">JR Schafer</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author><author><name sortKey="Bean, Wj" uniqKey="Bean W">WJ Bean</name></author><author><name sortKey="Suss, J" uniqKey="Suss J">J Suss</name></author><author><name sortKey="Senne, D" 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sortKey="Kishino, H" uniqKey="Kishino H">H Kishino</name></author><author><name sortKey="Yano, Ta" uniqKey="Yano T">TA Yano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z Yang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Comput Biol</journal-id><journal-id journal-id-type="iso-abbrev">PLoS Comput. Biol</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">ploscomp</journal-id><journal-title-group><journal-title>PLoS Computational Biology</journal-title></journal-title-group><issn pub-type="ppub">1553-734X</issn><issn pub-type="epub">1553-7358</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">19911053</article-id><article-id pub-id-type="pmc">2770840</article-id><article-id pub-id-type="publisher-id">09-PLCB-RA-0610R2</article-id><article-id pub-id-type="doi">10.1371/journal.pcbi.1000564</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Computational Biology/Comparative Sequence Analysis</subject><subject>Computational Biology/Evolutionary Modeling</subject><subject>Evolutionary Biology/Microbial Evolution and Genomics</subject><subject>Infectious Diseases/Viral Infections</subject><subject>Molecular Biology/Molecular Evolution</subject><subject>Virology/Virus Evolution and Symbiosis</subject></subj-group></article-categories><title-group><article-title>Identifying Changes in Selective Constraints: Host Shifts in Influenza</article-title><alt-title alt-title-type="running-head">Changes in Selective Constraints: Influenza</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tamuri</surname><given-names>Asif U.</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>dos Reis</surname><given-names>Mario</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Hay</surname><given-names>Alan J.</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Goldstein</surname><given-names>Richard A.</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>National Institute for Medical Research, London, United Kingdom</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Fraser</surname><given-names>Christophe</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Imperial College London, United Kingdom</aff><author-notes><corresp id="cor1">* E-mail: <email>Richard.Goldstein@nimr.mrc.ac.uk</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: MdR AJH RAG. Performed the experiments: AUT RAG. Analyzed the data: AUT MdR RAG. Contributed reagents/materials/analysis tools: MdR. Wrote the paper: MdR AJH RAG.</p></fn></author-notes><pub-date pub-type="collection"><month>11</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>13</day><month>11</month><year>2009</year></pub-date><volume>5</volume><issue>11</issue><elocation-id>e1000564</elocation-id><history><date date-type="received"><day>27</day><month>5</month><year>2009</year></date><date date-type="accepted"><day>15</day><month>10</month><year>2009</year></date></history><permissions><copyright-statement>Tamuri et al.</copyright-statement><copyright-year>2009</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>The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.</p></abstract><abstract abstract-type="summary"><title>Author Summary</title><p>Influenza A's natural reservoir is waterfowl. Sometimes avian virus genomic segments are able to shift to a human host, either <italic>in toto</italic> or by combining with those that underwent a previous host shift event. Such host shift events can cause worldwide pandemics in their immunologically naive hosts. In order for these host shifts to establish a stable lineage, the virus has to adapt to the new host. Identifying the changes that have occurred in the past can provide important clues about how this process happens, and how surveillance for new influenza threats should be targeted. Unfortunately, it is difficult to determine whether an amino acid has changed due to adaptation to the new host or whether the change occurred through random drift. Here we describe a novel phylogenetic approach to identifying locations where the nature of the selective pressure exerted on the location has changed corresponding to the host shift event. We identify a set of locations on a number of the genomic segments. The approach we describe is of wide applicability when the timing of the change of selective constraints is known in advance.</p></abstract><counts><page-count count="14"></page-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name><name sortKey="Tamuri, Asif U" sort="Tamuri, Asif U" uniqKey="Tamuri A" first="Asif U." last="Tamuri">Asif U. Tamuri</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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