Genetic Structure of Human A/H1N1 and A/H3N2 Influenza Virus on Corsica Island: Phylogenetic Analysis and Vaccine Strain Match, 2006-2010.
Identifieur interne : 000244 ( Hal/Corpus ); précédent : 000243; suivant : 000245Genetic Structure of Human A/H1N1 and A/H3N2 Influenza Virus on Corsica Island: Phylogenetic Analysis and Vaccine Strain Match, 2006-2010.
Auteurs : Alessandra Falchi ; Jean Pierre Amoros ; Christophe Arena ; Jean Arrighi ; François Casabianca ; Laurent Andreoletti ; Clément Turbelin ; Antoine Flahault ; Thierry Blanchon ; Thomas Hanslik ; Laurent VaresiSource :
- PLoS ONE [ 1932-6203 ] ; 2011.
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Abstract
BACKGROUND: The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA) genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS: Nasopharyngeal samples from 371 patients with influenza-like illness (ILI) were collected by General Practitioners (GPs) of the Sentinelles Network through a randomised selection routine. RESULTS: Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009). Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope) model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION: The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.
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DOI: 10.1371/journal.pone.0024471
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<author><name sortKey="Hanslik, Thomas" sort="Hanslik, Thomas" uniqKey="Hanslik T" first="Thomas" last="Hanslik">Thomas Hanslik</name>
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<idno type="DOI">10.1371/journal.pone.0024471</idno>
<series><title level="j">PLoS ONE</title>
<idno type="ISSN">1932-6203</idno>
<imprint><date type="datePub">2011</date>
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<profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>A VIRUS</term>
<term>ANTIGENIC DISTANCE</term>
<term>EPIDEMIC</term>
<term>H1N1</term>
<term>HA GENE</term>
<term>HEMAGGLUTININ</term>
<term>MAXIMUM-LIKELIHOOD</term>
<term>POSITIVE SELECTION</term>
<term>RT-PCR</term>
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<front><div type="abstract" xml:lang="en"> <p>BACKGROUND: The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA) genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS: Nasopharyngeal samples from 371 patients with influenza-like illness (ILI) were collected by General Practitioners (GPs) of the Sentinelles Network through a randomised selection routine. RESULTS: Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009). Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope) model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION: The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.</p>
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</front>
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<hal api="V3"> <titleStmt> <title xml:lang="en">Genetic Structure of Human A/H1N1 and A/H3N2 Influenza Virus on Corsica Island: Phylogenetic Analysis and Vaccine Strain Match, 2006-2010.</title>
<author role="aut"> <persName> <forename type="first">Alessandra</forename>
<surname>Falchi</surname>
</persName>
<idno type="halauthorid">647168</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Jean Pierre</forename>
<surname>Amoros</surname>
</persName>
<idno type="halauthorid">647169</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Christophe</forename>
<surname>Arena</surname>
</persName>
<idno type="halauthorid">647170</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Jean</forename>
<surname>Arrighi</surname>
</persName>
<idno type="halauthorid">647171</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">François</forename>
<surname>Casabianca</surname>
</persName>
<idno type="halauthorid">513833</idno>
</author>
<author role="aut"> <persName> <forename type="first">Laurent</forename>
<surname>Andreoletti</surname>
</persName>
<idno type="halauthorid">647172</idno>
<affiliation ref="#struct-7569"></affiliation>
<affiliation ref="#struct-202715"></affiliation>
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<author role="aut"> <persName> <forename type="first">Clément</forename>
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<author role="aut"> <persName> <forename type="first">Antoine</forename>
<surname>Flahault</surname>
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<idno type="halauthorid">119515</idno>
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<author role="aut"> <persName> <forename type="first">Thierry</forename>
<surname>Blanchon</surname>
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<idno type="halauthorid">209496</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Thomas</forename>
<surname>Hanslik</surname>
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<idno type="halauthorid">647173</idno>
<affiliation ref="#struct-3065"></affiliation>
<affiliation ref="#struct-81173"></affiliation>
<affiliation ref="#struct-159445"></affiliation>
</author>
<author role="crp"> <persName> <forename type="first">Laurent</forename>
<surname>Varesi</surname>
</persName>
<email type="md5">74b1a662ede18074441b5d1f082c9171</email>
<email type="domain">univ-corse.fr</email>
<idno type="halauthorid">647174</idno>
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</author>
<editor role="depositor"> <persName> <forename>Laurent</forename>
<surname>Varesi</surname>
</persName>
<email type="md5">74b1a662ede18074441b5d1f082c9171</email>
<email type="domain">univ-corse.fr</email>
</editor>
<funder>Corsican Economic Development Agency; FEDER</funder>
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<editionStmt> <edition n="v1" type="current"> <date type="whenSubmitted">2020-05-28 18:51:34</date>
<date type="whenModified">2020-05-29 16:17:41</date>
<date type="whenReleased">2020-05-28 18:51:55</date>
<date type="whenProduced">2011</date>
<date type="whenEndEmbargoed">2020-05-28</date>
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<name key="165471"> <persName> <forename>Laurent</forename>
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<author role="aut"> <persName> <forename type="first">Jean Pierre</forename>
<surname>Amoros</surname>
</persName>
<idno type="halauthorid">647169</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Christophe</forename>
<surname>Arena</surname>
</persName>
<idno type="halauthorid">647170</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Jean</forename>
<surname>Arrighi</surname>
</persName>
<idno type="halauthorid">647171</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">François</forename>
<surname>Casabianca</surname>
</persName>
<idno type="halauthorid">513833</idno>
</author>
<author role="aut"> <persName> <forename type="first">Laurent</forename>
<surname>Andreoletti</surname>
</persName>
<idno type="halauthorid">647172</idno>
<affiliation ref="#struct-7569"></affiliation>
<affiliation ref="#struct-202715"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Clément</forename>
<surname>Turbelin</surname>
</persName>
<idno type="halauthorid">610637</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Antoine</forename>
<surname>Flahault</surname>
</persName>
<idno type="halauthorid">119515</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Thierry</forename>
<surname>Blanchon</surname>
</persName>
<idno type="halauthorid">209496</idno>
<affiliation ref="#struct-3065"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Thomas</forename>
<surname>Hanslik</surname>
</persName>
<idno type="halauthorid">647173</idno>
<affiliation ref="#struct-3065"></affiliation>
<affiliation ref="#struct-81173"></affiliation>
<affiliation ref="#struct-159445"></affiliation>
</author>
<author role="crp"> <persName> <forename type="first">Laurent</forename>
<surname>Varesi</surname>
</persName>
<email type="md5">74b1a662ede18074441b5d1f082c9171</email>
<email type="domain">univ-corse.fr</email>
<idno type="halauthorid">647174</idno>
<affiliation ref="#struct-843"></affiliation>
</author>
</analytic>
<monogr> <idno type="halJournalId" status="VALID">28700</idno>
<idno type="issn">1932-6203</idno>
<idno type="eissn">1932-6203</idno>
<title level="j">PLoS ONE</title>
<imprint> <publisher>Public Library of Science</publisher>
<biblScope unit="volume">6</biblScope>
<biblScope unit="issue">9</biblScope>
<biblScope unit="pp">e24471</biblScope>
<date type="datePub">2011</date>
<date type="dateEpub">2011-09-14</date>
</imprint>
</monogr>
<idno type="doi">10.1371/journal.pone.0024471</idno>
<idno type="prodinra">205479</idno>
<idno type="pubmed">21935413</idno>
<idno type="wos">000295039700023</idno>
</biblStruct>
</sourceDesc>
<profileDesc> <langUsage> <language ident="en">English</language>
</langUsage>
<textClass> <keywords scheme="author"> <term xml:lang="en">A VIRUS</term>
<term xml:lang="en">MAXIMUM-LIKELIHOOD</term>
<term xml:lang="en">POSITIVE SELECTION</term>
<term xml:lang="en">ANTIGENIC DISTANCE</term>
<term xml:lang="en">HA GENE</term>
<term xml:lang="en">RT-PCR</term>
<term xml:lang="en">HEMAGGLUTININ</term>
<term xml:lang="en">H1N1</term>
<term xml:lang="en">EPIDEMIC</term>
<term xml:lang="fr">EVOLUTION</term>
</keywords>
<classCode scheme="halDomain" n="sdv.gen.gpo">Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]</classCode>
<classCode scheme="halTypology" n="ART">Journal articles</classCode>
</textClass>
<abstract xml:lang="en"> <p>BACKGROUND: The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA) genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS: Nasopharyngeal samples from 371 patients with influenza-like illness (ILI) were collected by General Practitioners (GPs) of the Sentinelles Network through a randomised selection routine. RESULTS: Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009). Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope) model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION: The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.</p>
</abstract>
</profileDesc>
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