Phylodynamics and Molecular Evolution of Influenza A Virus Nucleoprotein Genes in Taiwan between 1979 and 2009
Identifieur interne : 000C21 ( Main/Exploration ); précédent : 000C20; suivant : 000C22Phylodynamics and Molecular Evolution of Influenza A Virus Nucleoprotein Genes in Taiwan between 1979 and 2009
Auteurs : Jih-Hui Lin [Taïwan] ; Shu-Chun Chiu [Taïwan] ; Ju-Chien Cheng [Taïwan] ; Hui-Wen Chang [Taïwan] ; Kuang-Liang Hsiao [Taïwan] ; Yung-Cheng Lin [Taïwan] ; Ho-Sheng Wu [Taïwan] ; Marco Salemi [États-Unis] ; Hsin-Fu Liu [Taïwan]Source :
- PLoS ONE [ 1932-6203 ] ; 2011.
Abstract
Many studies concentrate on variation in the hemagglutinin glycoprotein (HA) because of its significance in host immune response, the evolution of this virus is even more complex when other genome segments are considered. Recently, it was found that cytotoxic T lymphocytes (CTL) play an important role in immunity against influenza and most CTL epitopes of human influenza viruses were remarkably conserved. The NP gene has evolved independently in human and avian hosts after 1918 flu pandemic and it has been assigned a putative role as a determinant of host range.
Phylodynamic patterns of the genes encoding nucleoprotein (NP) of influenza A viruses isolated from 1979–2009 were analyzed by applying the Bayesian Markov Chain Monte Carlo framework to better understand the evolutionary mechanisms of these Taiwanese isolates. Phylogenetic analysis of the NP gene showed that all available H3 worldwide isolates collected so far were genetically similar and divided into two major clades after the year 2004. We compared the deduced amino acid sequences of the NP sequences from human, avian and swine hosts to investigate the emergence of potential adaptive mutations. Overall, selective pressure on the NP gene of human influenza A viruses appeared to be dominated by purifying selection with a mean dN/dS ratio of 0.105. Site-selection analysis of 488 codons, however, also revealed 3 positively selected sites in addition to 139 negatively selected ones.
The demographic history inferred by Bayesian skyline plot showed that the effective number of infections underwent a period of smooth and steady growth from 1998 to 2001, followed by a more recent rise in the rate of spread. Further understanding the correlates of interspecies transmission of influenza A virus genes from other host reservoirs to the human population may help to elucidate the mechanisms of variability among influenza A virus.
Url:
DOI: 10.1371/journal.pone.0023454
PubMed: 21858124
PubMed Central: 3155553
Affiliations:
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America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, Immunology and Laboratory Medicine, College of Medicine & Emerging Pathogens Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Liu, Hsin Fu" sort="Liu, Hsin Fu" uniqKey="Liu H" first="Hsin-Fu" last="Liu">Hsin-Fu Liu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung</wicri:regionArea><wicri:noRegion>Keelung</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Medical Research, Mackay Memorial Hospital, New Taipei City</wicri:regionArea><wicri:noRegion>New Taipei City</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>Institute of Public Health, National Yang-Ming University, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Public Health, National Yang-Ming University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21858124</idno><idno type="pmc">3155553</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155553</idno><idno type="RBID">PMC:3155553</idno><idno type="doi">10.1371/journal.pone.0023454</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000B29</idno><idno type="wicri:explorRef" 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wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Center for Research and Diagnostics, Centers for Disease Control, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung</wicri:regionArea><wicri:noRegion>Keelung</wicri:noRegion></affiliation></author><author><name sortKey="Chiu, Shu Chun" sort="Chiu, Shu Chun" uniqKey="Chiu S" first="Shu-Chun" last="Chiu">Shu-Chun Chiu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Center for Research and Diagnostics, Centers for Disease Control, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Ju Chien" sort="Cheng, Ju Chien" uniqKey="Cheng J" first="Ju-Chien" last="Cheng">Ju-Chien Cheng</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung</wicri:regionArea><wicri:noRegion>Taichung</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Hui Wen" sort="Chang, Hui Wen" uniqKey="Chang H" first="Hui-Wen" last="Chang">Hui-Wen Chang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Center for Research and Diagnostics, Centers for Disease Control, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Hsiao, Kuang Liang" sort="Hsiao, Kuang Liang" uniqKey="Hsiao K" first="Kuang-Liang" last="Hsiao">Kuang-Liang Hsiao</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung</wicri:regionArea><wicri:noRegion>Keelung</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Yung Cheng" sort="Lin, Yung Cheng" uniqKey="Lin Y" first="Yung-Cheng" last="Lin">Yung-Cheng Lin</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung</wicri:regionArea><wicri:noRegion>Keelung</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Ho Sheng" sort="Wu, Ho Sheng" uniqKey="Wu H" first="Ho-Sheng" last="Wu">Ho-Sheng Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Center for Research and Diagnostics, Centers for Disease Control, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Salemi, Marco" sort="Salemi, Marco" uniqKey="Salemi M" first="Marco" last="Salemi">Marco Salemi</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>Department of Pathology, Immunology and Laboratory Medicine, College of Medicine & Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, Immunology and Laboratory Medicine, College of Medicine & Emerging Pathogens Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Liu, Hsin Fu" sort="Liu, Hsin Fu" uniqKey="Liu H" first="Hsin-Fu" last="Liu">Hsin-Fu Liu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung</wicri:regionArea><wicri:noRegion>Keelung</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Medical Research, Mackay Memorial Hospital, New Taipei City</wicri:regionArea><wicri:noRegion>New Taipei City</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>Institute of Public Health, National Yang-Ming University, Taipei, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Public Health, National Yang-Ming University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Many studies concentrate on variation in the hemagglutinin glycoprotein (HA) because of its significance in host immune response, the evolution of this virus is even more complex when other genome segments are considered. Recently, it was found that cytotoxic T lymphocytes (CTL) play an important role in immunity against influenza and most CTL epitopes of human influenza viruses were remarkably conserved. The NP gene has evolved independently in human and avian hosts after 1918 flu pandemic and it has been assigned a putative role as a determinant of host range.</p></sec><sec><title>Methods and Findings</title><p>Phylodynamic patterns of the genes encoding nucleoprotein (NP) of influenza A viruses isolated from 1979–2009 were analyzed by applying the Bayesian Markov Chain Monte Carlo framework to better understand the evolutionary mechanisms of these Taiwanese isolates. Phylogenetic analysis of the NP gene showed that all available H3 worldwide isolates collected so far were genetically similar and divided into two major clades after the year 2004. We compared the deduced amino acid sequences of the NP sequences from human, avian and swine hosts to investigate the emergence of potential adaptive mutations. Overall, selective pressure on the NP gene of human influenza A viruses appeared to be dominated by purifying selection with a mean d<sub>N</sub>/d<sub>S</sub> ratio of 0.105. Site-selection analysis of 488 codons, however, also revealed 3 positively selected sites in addition to 139 negatively selected ones.</p></sec><sec><title>Conclusions</title><p>The demographic history inferred by Bayesian skyline plot showed that the effective number of infections underwent a period of smooth and steady growth from 1998 to 2001, followed by a more recent rise in the rate of spread. Further understanding the correlates of interspecies transmission of influenza A virus genes from other host reservoirs to the human population may help to elucidate the mechanisms of variability among influenza A virus.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name></author><author><name sortKey="Pybus, Og" uniqKey="Pybus O">OG Pybus</name></author><author><name sortKey="Nelson, Mi" uniqKey="Nelson M">MI Nelson</name></author><author><name sortKey="Viboud, C" uniqKey="Viboud C">C Viboud</name></author><author><name sortKey="Taubenberger, Jk" uniqKey="Taubenberger J">JK Taubenberger</name></author></analytic></biblStruct><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="Gammelin, M" 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Liang" uniqKey="Hsiao K" first="Kuang-Liang" last="Hsiao">Kuang-Liang Hsiao</name><name sortKey="Lin, Jih Hui" sort="Lin, Jih Hui" uniqKey="Lin J" first="Jih-Hui" last="Lin">Jih-Hui Lin</name><name sortKey="Lin, Yung Cheng" sort="Lin, Yung Cheng" uniqKey="Lin Y" first="Yung-Cheng" last="Lin">Yung-Cheng Lin</name><name sortKey="Liu, Hsin Fu" sort="Liu, Hsin Fu" uniqKey="Liu H" first="Hsin-Fu" last="Liu">Hsin-Fu Liu</name><name sortKey="Liu, Hsin Fu" sort="Liu, Hsin Fu" uniqKey="Liu H" first="Hsin-Fu" last="Liu">Hsin-Fu Liu</name><name sortKey="Liu, Hsin Fu" sort="Liu, Hsin Fu" uniqKey="Liu H" first="Hsin-Fu" last="Liu">Hsin-Fu Liu</name><name sortKey="Wu, Ho Sheng" sort="Wu, Ho Sheng" uniqKey="Wu H" first="Ho-Sheng" last="Wu">Ho-Sheng Wu</name></country><country name="États-Unis"><region name="Floride"><name sortKey="Salemi, Marco" sort="Salemi, Marco" uniqKey="Salemi M" first="Marco" last="Salemi">Marco Salemi</name></region></country></tree></affiliations></record>Pour manipuler ce 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