Identifying Changes in Selective Constraints: Host Shifts in Influenza
Identifieur interne : 001089 ( Main/Exploration ); précédent : 001088; suivant : 001090Identifying 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
Affiliations:
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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. 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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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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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Ou
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