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PLoS ONE. Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study
[Source: PLoS ONE, full text: (LINK). Abstract, edited.]
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Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study
Herv? Pascalis<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>#</SUP><SUP>?</SUP><SUP>*</SUP>, Sarah Temmam<SUP>1</SUP><SUP>,</SUP><SUP>3</SUP><SUP>#</SUP><SUP>?</SUP>, David A. Wilkinson<SUP>1</SUP><SUP>,</SUP><SUP>4</SUP><SUP>#</SUP><SUP>◊</SUP>, Najla Dsouli<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>#</SUP><SUP>◊</SUP>, Magali Turpin<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>, Xavier de Lamballerie<SUP>5</SUP>, Koussay Dellagi<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>
<SUP></SUP>
1 GIS CRVOI, Centre de Recherche et de Veille sur les maladies ?mergentes dans l?Oc?an Indien, Plateforme technologique CYROI, Saint-Denis, La R?union, France, 2 Institut de Recherche pour le D?veloppement (IRD), La R?union, France, 3 Ecologie microbienne (UMR 5557) CNRS-Universit? de Lyon, Lyon, France, 4 Universit? de La R?union, Saint-Denis, La R?union, France, 5 Unit? des Virus Emergents (UMR-S 190), IRD-Universit? de la M?diterran?e, Marseille, France
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.
Citation: Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, et al. (2012) Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study. PLoS ONE 7(8): e43742. doi:10.1371/journal.pone.0043742
Editor: Krzysztof Pyrc, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Poland
Received: May 25, 2012; Accepted: July 23, 2012; Published: August 27, 2012
Copyright: ? 2012 Pascalis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was supported by funds from CPER-ERDF (Contrat Programme Etat/Region and European Regional Development Fund), INSERM/IMMI and CRVOI. D.A. Wilkinson post-doctoral fellowships were funded by RUN-Emerge: European project funded by European Commission under FP7 program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: herve.pascalis@ird.fr
# These authors contributed equally to this work.
? These authors are joint first authors on this work.
◊ These authors are joint second authors.
-Herv? Pascalis<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>#</SUP><SUP>?</SUP><SUP>*</SUP>, Sarah Temmam<SUP>1</SUP><SUP>,</SUP><SUP>3</SUP><SUP>#</SUP><SUP>?</SUP>, David A. Wilkinson<SUP>1</SUP><SUP>,</SUP><SUP>4</SUP><SUP>#</SUP><SUP>◊</SUP>, Najla Dsouli<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>#</SUP><SUP>◊</SUP>, Magali Turpin<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>, Xavier de Lamballerie<SUP>5</SUP>, Koussay Dellagi<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>
<SUP></SUP>
1 GIS CRVOI, Centre de Recherche et de Veille sur les maladies ?mergentes dans l?Oc?an Indien, Plateforme technologique CYROI, Saint-Denis, La R?union, France, 2 Institut de Recherche pour le D?veloppement (IRD), La R?union, France, 3 Ecologie microbienne (UMR 5557) CNRS-Universit? de Lyon, Lyon, France, 4 Universit? de La R?union, Saint-Denis, La R?union, France, 5 Unit? des Virus Emergents (UMR-S 190), IRD-Universit? de la M?diterran?e, Marseille, France
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.
Citation: Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, et al. (2012) Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study. PLoS ONE 7(8): e43742. doi:10.1371/journal.pone.0043742
Editor: Krzysztof Pyrc, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Poland
Received: May 25, 2012; Accepted: July 23, 2012; Published: August 27, 2012
Copyright: ? 2012 Pascalis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was supported by funds from CPER-ERDF (Contrat Programme Etat/Region and European Regional Development Fund), INSERM/IMMI and CRVOI. D.A. Wilkinson post-doctoral fellowships were funded by RUN-Emerge: European project funded by European Commission under FP7 program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: herve.pascalis@ird.fr
# These authors contributed equally to this work.
? These authors are joint first authors on this work.
◊ These authors are joint second authors.
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