Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study
Identifieur interne : 000404 ( Hal/Corpus ); précédent : 000403; suivant : 000405Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study
Auteurs : Hervé Pascalis ; Sarah Temmam ; David A. Wilkinson ; Najla Dsouli ; Magali Turpin ; Xavier Lamballerie ; Koussay DellagiSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
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- mix :
Abstract
BACKGROUND/OBJECTIVES: Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. METHODOLOGY: We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. PRINCIPAL FINDINGS: We found that i) Reunion pH1N1 sequences stemmed from global "clade 7" but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. CONCLUSIONS: Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.
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DOI: 10.1371/journal.pone.0043742
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Hôpitaux de Marseille</orgName> <orgName type="acronym">APHM</orgName> <desc> <address> <addrLine>Direction générale AP-HM80, rue Brochier13 354 Marseille Cedex 5</addrLine> <country key="FR"></country> </address> <ref type="url">http://fr.ap-hm.fr/</ref> </desc> </org></tutelle></tutelles></hal:affiliation></affiliation></author><author><name sortKey="Dellagi, Koussay" sort="Dellagi, Koussay" uniqKey="Dellagi K" first="Koussay" last="Dellagi">Koussay Dellagi</name><affiliation><hal:affiliation type="laboratory" xml:id="struct-234808" status="VALID"> <orgName>Cyclotron Réunion Océan Indien</orgName> <orgName type="acronym">CYROI</orgName> <desc> <address> <addrLine>GIP-CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde</addrLine> <country key="RE"></country> </address> <ref type="url">http://www.cyroi.fr</ref> </desc> <listRelation> <relation active="#struct-300316" type="direct"></relation> <relation active="#struct-351465" type="direct"></relation> </listRelation> <tutelles><tutelle active="#struct-300316" type="direct"><org type="institution" xml:id="struct-300316" status="VALID"> <orgName>Université de La Réunion</orgName> <orgName type="acronym">UR</orgName> <desc> <address> <addrLine>15, avenue René Cassin - CS92003 -97744 Saint Denis Cedex 9</addrLine> <country key="RE"></country> </address> <ref type="url">http://www.univ-reunion.fr</ref> </desc> </org></tutelle><tutelle active="#struct-351465" type="direct"><org type="institution" xml:id="struct-351465" status="VALID"> <orgName>Centre Hospitalier Universitaire de La Réunion</orgName> <orgName type="acronym">CHU La Réunion</orgName> <desc> <address> <country key="RE"></country> </address> <ref type="url">http://www.chu-reunion.fr/</ref> </desc> </org></tutelle></tutelles></hal:affiliation></affiliation></author></analytic><idno type="DOI">10.1371/journal.pone.0043742</idno><series><title level="j">PLoS ONE</title><idno type="ISSN">1932-6203</idno><imprint><date type="datePub">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Adolescent</term><term>Adult</term><term>Child</term><term>Cohort Studies</term><term>Evolution</term><term>Female</term><term>Follow-Up Studies</term><term>Genetic Variation</term><term>Genome</term><term>H1N1 Subtype</term><term>Human</term><term>Humans</term><term>Indian Ocean</term><term>Influenza</term><term>Influenza A Virus</term><term>Male</term><term>Middle Aged</term><term>Molecular</term><term>Pandemics</term><term>Preschool</term><term>Viral</term><term>Young Adult</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"> <p>BACKGROUND/OBJECTIVES: Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. METHODOLOGY: We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. PRINCIPAL FINDINGS: We found that i) Reunion pH1N1 sequences stemmed from global "clade 7" but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. CONCLUSIONS: Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.</p> </div></front></TEI><hal api="V3"> <titleStmt> <title xml:lang="en">Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study</title> <author role="aut"> <persName> <forename type="first">Hervé</forename> <surname>Pascalis</surname> </persName> <email type="md5">8899ded9d7780cd22f21d19b29bd6467</email> <email type="domain">ird.fr</email> <idno type="idhal" notation="string">herve-pascalis</idno> <idno type="idhal" notation="numeric">174648</idno> <idno type="halauthorid">960771</idno> <idno type="ORCID">https://orcid.org/0000-0002-6822-7311</idno> <idno type="ResearcherId">http://www.researcherid.com/rid/M-9410-2019</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Sarah</forename> <surname>Temmam</surname> </persName> <idno type="halauthorid">754146</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-726"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">David A</forename> <surname>Wilkinson</surname> </persName> <email type="md5">2d3e050241e2bc3becaffee035a966ea</email> <email type="domain">univ-reunion.fr</email> <idno type="halauthorid">960770</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-174264"></affiliation> <affiliation ref="#struct-300316"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Najla</forename> <surname>Dsouli</surname> </persName> <idno type="halauthorid">602835</idno> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Magali</forename> <surname>Turpin</surname> </persName> <idno type="halauthorid">1294399</idno> <affiliation ref="#struct-174264"></affiliation> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Xavier</forename> <forename type="middle">de</forename> <surname>Lamballerie</surname> </persName> <idno type="halauthorid">1294248</idno> <affiliation ref="#struct-86891"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Koussay</forename> <surname>Dellagi</surname> </persName> <email type="md5">940bb26a1ba1137e182e1d2325436662</email> <email type="domain">ird.fr</email> <idno type="halauthorid">645823</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <editor role="depositor"> <persName> <forename>Réunion</forename> <surname>Univ</surname> </persName> <email type="md5">fcc6f146feaf44b21f9d6255bbfcdc9f</email> <email type="domain">univ-reunion.fr</email> </editor> </titleStmt> <editionStmt> <edition n="v1" type="current"> <date type="whenSubmitted">2018-06-19 09:10:31</date> <date type="whenModified">2020-03-17 02:52:49</date> <date type="whenReleased">2018-06-19 13:59:05</date> <date type="whenProduced">2012</date> <date type="whenEndEmbargoed">2018-06-19</date> <ref type="file" target="https://hal.univ-reunion.fr/hal-01285448/document"> <date notBefore="2018-06-19"></date> </ref> <ref type="file" subtype="greenPublisher" n="1" target="https://hal.univ-reunion.fr/hal-01285448/file/Molecular_evolutionary_analysis_pH1N1_influenza_virus.PDF"> <date notBefore="2018-06-19"></date> </ref> <ref type="externalLink" target="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428279/pdf"></ref> </edition> <respStmt> <resp>contributor</resp> <name key="313340"> <persName> <forename>Réunion</forename> <surname>Univ</surname> </persName> <email type="md5">fcc6f146feaf44b21f9d6255bbfcdc9f</email> <email type="domain">univ-reunion.fr</email> </name> </respStmt> </editionStmt> <publicationStmt> <distributor>CCSD</distributor> <idno type="halId">hal-01285448</idno> <idno type="halUri">https://hal.univ-reunion.fr/hal-01285448</idno> <idno type="halBibtex">pascalis:hal-01285448</idno> <idno type="halRefHtml">PLoS ONE, Public Library of Science, 2012, 7 (8), pp.e43742. ⟨10.1371/journal.pone.0043742⟩</idno> <idno type="halRef">PLoS ONE, Public Library of Science, 2012, 7 (8), pp.e43742. ⟨10.1371/journal.pone.0043742⟩</idno> <availability status="restricted"> <licence target="http://creativecommons.org/licenses/by/">Attribution</licence> </availability> </publicationStmt> <seriesStmt> <idno type="stamp" n="UNIV-REUNION">Université de la Réunion</idno> <idno type="stamp" n="BIOENVIS">Fédération de Recherche BioEnviS, BioEnvironnement et Santé (Université de Lyon)</idno> <idno type="stamp" n="PIMIT" corresp="UNIV-REUNION">UMR PIMIT - Processus Infectieux en Milieu Insulaire Tropical</idno> <idno type="stamp" n="UNIV-AMU">Aix Marseille Université</idno> <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno> <idno type="stamp" n="INRA">INRA - Institut national de la recherche agronomique</idno> <idno type="stamp" n="COPANFLU" corresp="INSERM">Cohorte des 1000 ménages pour le suivi de la pandémie de grippe H1N1</idno> <idno type="stamp" n="TEST-AMU">Espace de test AMU</idno> <idno type="stamp" n="UNIV-LYON1">Université Claude Bernard - Lyon I</idno> <idno type="stamp" n="AGREENIUM">Archive ouverte en agrobiosciences</idno> <idno type="stamp" n="IRD">IRD - Institut de recherche pour le développement</idno> <idno type="stamp" n="PAPANGUE">Papangue</idno> <idno type="stamp" n="UDL">UDL</idno> <idno type="stamp" n="UNIV-LYON">Université de Lyon</idno> <idno type="stamp" n="INRAE">Institut National de Recherche en Agriculture, Alimentation et Environnement</idno> </seriesStmt> <notesStmt> <note type="audience" n="2">International</note> <note type="popular" n="0">No</note> <note type="peer" n="1">Yes</note> </notesStmt> <sourceDesc> <biblStruct> <analytic> <title xml:lang="en">Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study</title> <author role="aut"> <persName> <forename type="first">Hervé</forename> <surname>Pascalis</surname> </persName> <email type="md5">8899ded9d7780cd22f21d19b29bd6467</email> <email type="domain">ird.fr</email> <idno type="idhal" notation="string">herve-pascalis</idno> <idno type="idhal" notation="numeric">174648</idno> <idno type="halauthorid">960771</idno> <idno type="ORCID">https://orcid.org/0000-0002-6822-7311</idno> <idno type="ResearcherId">http://www.researcherid.com/rid/M-9410-2019</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Sarah</forename> <surname>Temmam</surname> </persName> <idno type="halauthorid">754146</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-726"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">David A</forename> <surname>Wilkinson</surname> </persName> <email type="md5">2d3e050241e2bc3becaffee035a966ea</email> <email type="domain">univ-reunion.fr</email> <idno type="halauthorid">960770</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-174264"></affiliation> <affiliation ref="#struct-300316"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Najla</forename> <surname>Dsouli</surname> </persName> <idno type="halauthorid">602835</idno> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-174264"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Magali</forename> <surname>Turpin</surname> </persName> <idno type="halauthorid">1294399</idno> <affiliation ref="#struct-174264"></affiliation> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Xavier</forename> <forename type="middle">de</forename> <surname>Lamballerie</surname> </persName> <idno type="halauthorid">1294248</idno> <affiliation ref="#struct-86891"></affiliation> </author> <author role="aut"> <persName> <forename type="first">Koussay</forename> <surname>Dellagi</surname> </persName> <email type="md5">940bb26a1ba1137e182e1d2325436662</email> <email type="domain">ird.fr</email> <idno type="halauthorid">645823</idno> <affiliation ref="#struct-234808"></affiliation> <affiliation ref="#struct-67872"></affiliation> <affiliation ref="#struct-174264"></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">7</biblScope> <biblScope unit="issue">8</biblScope> <biblScope unit="pp">e43742</biblScope> <date type="datePub">2012</date> </imprint> </monogr> <idno type="doi">10.1371/journal.pone.0043742</idno> <idno type="pubmed">22952752</idno> <idno type="pubmedcentral">PMC3428279</idno> </biblStruct> </sourceDesc> <profileDesc> <langUsage> <language ident="en">English</language> </langUsage> <textClass> <keywords scheme="author"> <term xml:lang="en">H1N1 Subtype</term> <term xml:lang="en">Indian Ocean</term> <term xml:lang="en">Influenza A Virus</term> <term xml:lang="en">Humans</term> <term xml:lang="en">Adolescent</term> <term xml:lang="en">Adult</term> <term xml:lang="en">Child</term> <term xml:lang="en">Preschool</term> <term xml:lang="en">Cohort Studies</term> <term xml:lang="en">Evolution</term> <term xml:lang="en">Molecular</term> <term xml:lang="en">Female</term> <term xml:lang="en">Follow-Up Studies</term> <term xml:lang="en">Genetic Variation</term> <term xml:lang="en">Genome</term> <term xml:lang="en">Viral</term> <term xml:lang="en">Influenza</term> <term xml:lang="en">Human</term> <term xml:lang="en">Male</term> <term xml:lang="en">Middle Aged</term> <term xml:lang="en">Pandemics</term> <term xml:lang="en">Young Adult</term> </keywords> <classCode scheme="halDomain" n="sdv">Life Sciences [q-bio]</classCode> <classCode scheme="halTypology" n="ART">Journal articles</classCode> </textClass> <abstract xml:lang="en"> <p>BACKGROUND/OBJECTIVES: Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. METHODOLOGY: We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. PRINCIPAL FINDINGS: We found that i) Reunion pH1N1 sequences stemmed from global "clade 7" but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. CONCLUSIONS: Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.</p> </abstract> </profileDesc> </hal></record>Pour manipuler ce document sous Unix (Dilib)
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