Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
Identifieur interne : 000E96 ( Main/Exploration ); précédent : 000E95; suivant : 000E97Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
Auteurs : Emily Hm Wong [République populaire de Chine] ; David K. Smith [République populaire de Chine] ; Raul Rabadan [États-Unis] ; Malik Peiris [République populaire de Chine] ; Leo Lm Poon [République populaire de Chine]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2010.
Abstract
The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.
Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through
Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes.
Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.
Url:
DOI: 10.1186/1471-2148-10-253
PubMed: 20723216
PubMed Central: 2933640
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus</title><author><name sortKey="Wong, Emily Hm" sort="Wong, Emily Hm" uniqKey="Wong E" first="Emily Hm" last="Wong">Emily Hm Wong</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Smith, David K" sort="Smith, David K" uniqKey="Smith D" first="David K" last="Smith">David K. Smith</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Rabadan, Raul" sort="Rabadan, Raul" uniqKey="Rabadan R" first="Raul" last="Rabadan">Raul Rabadan</name><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University College of Physicians and Surgeons, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University College of Physicians and Surgeons, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Poon, Leo Lm" sort="Poon, Leo Lm" uniqKey="Poon L" first="Leo Lm" last="Poon">Leo Lm Poon</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20723216</idno><idno type="pmc">2933640</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933640</idno><idno type="RBID">PMC:2933640</idno><idno type="doi">10.1186/1471-2148-10-253</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000905</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000905</idno><idno type="wicri:Area/Pmc/Curation">000905</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000905</idno><idno type="wicri:Area/Pmc/Checkpoint">000962</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000962</idno><idno type="wicri:Area/Ncbi/Merge">000558</idno><idno type="wicri:Area/Ncbi/Curation">000558</idno><idno type="wicri:Area/Ncbi/Checkpoint">000558</idno><idno type="wicri:Area/Main/Merge">000F03</idno><idno type="wicri:Area/Main/Curation">000E96</idno><idno type="wicri:Area/Main/Exploration">000E96</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus</title><author><name sortKey="Wong, Emily Hm" sort="Wong, Emily Hm" uniqKey="Wong E" first="Emily Hm" last="Wong">Emily Hm Wong</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Smith, David K" sort="Smith, David K" uniqKey="Smith D" first="David K" last="Smith">David K. Smith</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Rabadan, Raul" sort="Rabadan, Raul" uniqKey="Rabadan R" first="Raul" last="Rabadan">Raul Rabadan</name><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University College of Physicians and Surgeons, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University College of Physicians and Surgeons, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Poon, Leo Lm" sort="Poon, Leo Lm" uniqKey="Poon L" first="Leo Lm" last="Poon">Leo Lm Poon</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20<sup>th </sup>century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.</p></sec><sec><title>Results</title><p>Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through <italic>in toto </italic>transfer of an avian influenza virus.</p><p>Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes.</p></sec><sec><title>Conclusions</title><p>Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cox, Nj" uniqKey="Cox N">NJ Cox</name></author><author><name sortKey="Subbarao, K" uniqKey="Subbarao K">K Subbarao</name></author></analytic></biblStruct><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="Webby, Rj" uniqKey="Webby R">RJ Webby</name></author><author><name sortKey="Webster, Rg" 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Kh" uniqKey="Phillippy K">KH Phillippy</name></author><author><name sortKey="Sherman, Pm" uniqKey="Sherman P">PM Sherman</name></author><author><name sortKey="Muertter, Rn" uniqKey="Muertter R">RN Muertter</name></author><author><name sortKey="Edgar, R" uniqKey="Edgar R">R Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dos Reis, M" uniqKey="Dos Reis M">M dos Reis</name></author><author><name sortKey="Wernisch, L" uniqKey="Wernisch L">L Wernisch</name></author><author><name sortKey="Savva, R" uniqKey="Savva R">R Savva</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Venables, Wn" uniqKey="Venables W">WN Venables</name></author><author><name sortKey="Ripley, Bd" uniqKey="Ripley B">BD Ripley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benzecri, J" uniqKey="Benzecri J">J Benzecri</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>État de New York</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wong, Emily Hm" sort="Wong, Emily Hm" uniqKey="Wong E" first="Emily Hm" last="Wong">Emily Hm Wong</name></noRegion><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><name sortKey="Poon, Leo Lm" sort="Poon, Leo Lm" uniqKey="Poon L" first="Leo Lm" last="Poon">Leo Lm Poon</name><name sortKey="Smith, David K" sort="Smith, David K" uniqKey="Smith D" first="David K" last="Smith">David K. Smith</name></country><country name="États-Unis"><region name="État de New York"><name sortKey="Rabadan, Raul" sort="Rabadan, Raul" uniqKey="Rabadan R" first="Raul" last="Rabadan">Raul Rabadan</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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