Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
Identifieur interne : 001575 ( Main/Exploration ); précédent : 001574; suivant : 001576Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
Auteurs : Edward C. Holmes ; Elodie Ghedin ; Naomi Miller ; Jill Taylor ; Yiming Bao ; Kirsten St George ; Bryan T. Grenfell ; Steven L. Salzberg ; Claire M. Fraser ; David J. Lipman ; Jeffery K. TaubenbergerSource :
- PLoS Biology [ 1544-9173 ] ; 2005.
Abstract
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002–2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003–2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.
Url:
DOI: 10.1371/journal.pbio.0030300
PubMed: 16026181
PubMed Central: 1180517
Affiliations:
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Holmes</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Miller, Naomi" sort="Miller, Naomi" uniqKey="Miller N" first="Naomi" last="Miller">Naomi Miller</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Taylor, Jill" sort="Taylor, Jill" uniqKey="Taylor J" first="Jill" last="Taylor">Jill Taylor</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Bao, Yiming" sort="Bao, Yiming" uniqKey="Bao Y" first="Yiming" last="Bao">Yiming Bao</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="St George, Kirsten" sort="St George, Kirsten" uniqKey="St George K" first="Kirsten" last="St George">Kirsten St George</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Grenfell, Bryan T" sort="Grenfell, Bryan T" uniqKey="Grenfell B" first="Bryan T" last="Grenfell">Bryan T. Grenfell</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Fraser, Claire M" sort="Fraser, Claire M" uniqKey="Fraser C" first="Claire M" last="Fraser">Claire M. Fraser</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Lipman, David J" sort="Lipman, David J" uniqKey="Lipman D" first="David J" last="Lipman">David J. Lipman</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Taubenberger, Jeffery K" sort="Taubenberger, Jeffery K" uniqKey="Taubenberger J" first="Jeffery K" last="Taubenberger">Jeffery K. Taubenberger</name><affiliation><nlm:aff id="aff5"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Biology</title><idno type="ISSN">1544-9173</idno><idno type="eISSN">1545-7885</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002–2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003–2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.</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="Cox, Nj" uniqKey="Cox N">NJ Cox</name></author><author><name sortKey="Subbarao, K" uniqKey="Subbarao K">K 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Rimmelzwaan</name></author><author><name sortKey="Osterhaus, Ad" uniqKey="Osterhaus A">AD Osterhaus</name></author><author><name sortKey="Grenfell, Bt" uniqKey="Grenfell B">BT Grenfell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gulati, U" uniqKey="Gulati U">U Gulati</name></author><author><name sortKey="Wu, W" uniqKey="Wu W">W Wu</name></author><author><name sortKey="Gulati, S" uniqKey="Gulati S">S Gulati</name></author><author><name sortKey="Kumari, K" uniqKey="Kumari K">K Kumari</name></author><author><name sortKey="Waner, Jl" uniqKey="Waner J">JL Waner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swofford, Dl" uniqKey="Swofford D">DL Swofford</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Bao, Yiming" sort="Bao, Yiming" uniqKey="Bao Y" first="Yiming" last="Bao">Yiming Bao</name><name sortKey="Fraser, Claire M" sort="Fraser, Claire M" uniqKey="Fraser C" first="Claire M" last="Fraser">Claire M. Fraser</name><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name><name sortKey="Grenfell, Bryan T" sort="Grenfell, Bryan T" uniqKey="Grenfell B" first="Bryan T" last="Grenfell">Bryan T. Grenfell</name><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C" last="Holmes">Edward C. Holmes</name><name sortKey="Lipman, David J" sort="Lipman, David J" uniqKey="Lipman D" first="David J" last="Lipman">David J. Lipman</name><name sortKey="Miller, Naomi" sort="Miller, Naomi" uniqKey="Miller N" first="Naomi" last="Miller">Naomi Miller</name><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name><name sortKey="St George, Kirsten" sort="St George, Kirsten" uniqKey="St George K" first="Kirsten" last="St George">Kirsten St George</name><name sortKey="Taubenberger, Jeffery K" sort="Taubenberger, Jeffery K" uniqKey="Taubenberger J" first="Jeffery K" last="Taubenberger">Jeffery K. Taubenberger</name><name sortKey="Taylor, Jill" sort="Taylor, Jill" uniqKey="Taylor J" first="Jill" last="Taylor">Jill Taylor</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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