Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations
Identifieur interne : 001070 ( Main/Exploration ); précédent : 001069; suivant : 001071Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations
Auteurs : Natalia Go I [Uruguay] ; Alvaro Fajardo [Uruguay] ; Gonzalo Moratorio [Uruguay] ; Rodney Colina [Uruguay] ; Juan Cristina [Uruguay]Source :
- Virology Journal [ 1743-422X ] ; 2009.
Abstract
A sudden emergence of Influenza A Virus (IAV) infections with a new pandemic H1N1 IAV is taking place since April of 2009. In order to gain insight into the mode of evolution of these new H1N1 strains, we performed a Bayesian coalescent Markov chain Monte Carlo (MCMC) analysis of full-length neuraminidase (NA) gene sequences of 62 H1N1 IAV strains (isolated from March 30th to by July 28th, 2009).
The results of these studies revealed that the expansion population growth model was the best to fit the sequence data. A mean of evolutionary change of 7.84 × 10-3 nucleotide substitutions per site per year (s/s/y) was obtained for the NA gene. A significant contribution of first codon position to this mean rate was observed. Maximum clade credibility trees revealed a rapid diversification of NA genes in different genetic lineages, all of them containing Oseltamivir-resistant viruses of very recent emergence. Mapping of naturally occurring amino acid substitutions in the NA protein from 2009 H1N1 IAV circulating in 62 different patients revealed that substitutions are distributed all around the surface of the molecule, leaving the hydrophobic core and the catalytic site essentially untouched.
High evolutionary rates and fast population growth have contributed to the initial transmission dynamics of 2009 H1N1 IAV. Naturally occurring substitutions are preferentially located at the protein surface and do not interfere with the NA active site. Antigenic regions relevant for vaccine development can differ from previous vaccine strains and vary among patients.
Url:
DOI: 10.1186/1743-422X-6-215
PubMed: 19961611
PubMed Central: 2794274
Affiliations:
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sort="Fajardo, Alvaro" uniqKey="Fajardo A" first="Alvaro" last="Fajardo">Alvaro Fajardo</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay</nlm:aff><country xml:lang="fr">Uruguay</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo</wicri:regionArea><wicri:noRegion>11400 Montevideo</wicri:noRegion></affiliation></author><author><name sortKey="Moratorio, Gonzalo" sort="Moratorio, Gonzalo" uniqKey="Moratorio G" first="Gonzalo" last="Moratorio">Gonzalo Moratorio</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay</nlm:aff><country xml:lang="fr">Uruguay</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo</wicri:regionArea><wicri:noRegion>11400 Montevideo</wicri:noRegion></affiliation></author><author><name sortKey="Colina, Rodney" sort="Colina, Rodney" uniqKey="Colina R" first="Rodney" last="Colina">Rodney Colina</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay</nlm:aff><country xml:lang="fr">Uruguay</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo</wicri:regionArea><wicri:noRegion>11400 Montevideo</wicri:noRegion></affiliation></author><author><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo, Uruguay</nlm:aff><country xml:lang="fr">Uruguay</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Igua 4225, 11400 Montevideo</wicri:regionArea><wicri:noRegion>11400 Montevideo</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>A sudden emergence of Influenza A Virus (IAV) infections with a new pandemic H1N1 IAV is taking place since April of 2009. In order to gain insight into the mode of evolution of these new H1N1 strains, we performed a Bayesian coalescent Markov chain Monte Carlo (MCMC) analysis of full-length neuraminidase (NA) gene sequences of 62 H1N1 IAV strains (isolated from March 30<sup>th </sup>to by July 28<sup>th</sup>, 2009).</p></sec><sec><title>Results</title><p>The results of these studies revealed that the expansion population growth model was the best to fit the sequence data. A mean of evolutionary change of 7.84 × 10<sup>-3 </sup>nucleotide substitutions per site per year (s/s/y) was obtained for the NA gene. A significant contribution of first codon position to this mean rate was observed. Maximum clade credibility trees revealed a rapid diversification of NA genes in different genetic lineages, all of them containing Oseltamivir-resistant viruses of very recent emergence. Mapping of naturally occurring amino acid substitutions in the NA protein from 2009 H1N1 IAV circulating in 62 different patients revealed that substitutions are distributed all around the surface of the molecule, leaving the hydrophobic core and the catalytic site essentially untouched.</p></sec><sec><title>Conclusion</title><p>High evolutionary rates and fast population growth have contributed to the initial transmission dynamics of 2009 H1N1 IAV. Naturally occurring substitutions are preferentially located at the protein surface and do not interfere with the NA active site. Antigenic regions relevant for vaccine development can differ from previous vaccine strains and vary among patients.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Neumann, G" uniqKey="Neumann G">G Neumann</name></author><author><name sortKey="Brownlee, Gg" uniqKey="Brownlee G">GG Brownlee</name></author><author><name sortKey="Fodor, E" uniqKey="Fodor E">E Fodor</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nguyen Van Tam, Js" uniqKey="Nguyen Van Tam J">JS Nguyen-Van-Tam</name></author><author><name sortKey="Hampson, Aw" uniqKey="Hampson A">AW Hampson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wolf, Yi" uniqKey="Wolf Y">YI Wolf</name></author><author><name sortKey="Viboud, C" uniqKey="Viboud C">C Viboud</name></author><author><name sortKey="Holmes, Ec" uniqKey="Holmes 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sortKey="Waterman, S" uniqKey="Waterman S">S Waterman</name></author><author><name sortKey="Smole, S" uniqKey="Smole S">S Smole</name></author><author><name sortKey="Guevara, Hf" uniqKey="Guevara H">HF Guevara</name></author><author><name sortKey="Belongia, Ea" uniqKey="Belongia E">EA Belongia</name></author><author><name sortKey="Clark, Pa" uniqKey="Clark P">PA Clark</name></author><author><name sortKey="Beatrice, St" uniqKey="Beatrice S">ST Beatrice</name></author><author><name sortKey="Donis, R" uniqKey="Donis R">R Donis</name></author><author><name sortKey="Katz, J" uniqKey="Katz J">J Katz</name></author><author><name sortKey="Finelli, L" uniqKey="Finelli L">L Finelli</name></author><author><name sortKey="Bridges, Cb" uniqKey="Bridges C">CB Bridges</name></author><author><name sortKey="Shaw, M" uniqKey="Shaw M">M Shaw</name></author><author><name sortKey="Jernigan, Db" uniqKey="Jernigan D">DB Jernigan</name></author><author><name sortKey="Uyeki, Tm" uniqKey="Uyeki T">TM 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Miagostovich</name></author><author><name sortKey="Ferreira, Ms" uniqKey="Ferreira M">MS Ferreira</name></author><author><name sortKey="Vieira, Cb" uniqKey="Vieira C">CB Vieira</name></author><author><name sortKey="Fioretti, Jm" uniqKey="Fioretti J">JM Fioretti</name></author><author><name sortKey="Leite, Jp" uniqKey="Leite J">JP Leite</name></author><author><name sortKey="Colina, R" uniqKey="Colina R">R Colina</name></author><author><name sortKey="Cristina, J" uniqKey="Cristina J">J Cristina</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Collins, Pj" uniqKey="Collins P">PJ Collins</name></author><author><name sortKey="Haire, Lf" uniqKey="Haire L">LF Haire</name></author><author><name sortKey="Lin, Yp" uniqKey="Lin Y">YP Lin</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Russell, Rj" uniqKey="Russell R">RJ Russell</name></author><author><name sortKey="Walker, Pa" uniqKey="Walker P">PA Walker</name></author><author><name sortKey="Skehel, Jj" uniqKey="Skehel J">JJ Skehel</name></author><author><name sortKey="Martin, Sr" uniqKey="Martin S">SR Martin</name></author><author><name sortKey="Hay, Aj" uniqKey="Hay A">AJ Hay</name></author><author><name sortKey="Gamblin, Sj" uniqKey="Gamblin S">SJ Gamblin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Collins, Pj" uniqKey="Collins P">PJ Collins</name></author><author><name sortKey="Haire, Lf" uniqKey="Haire L">LF Haire</name></author><author><name sortKey="Lin, Yp" uniqKey="Lin Y">YP Lin</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Russell, Rj" uniqKey="Russell R">RJ Russell</name></author><author><name sortKey="Walker, Pa" uniqKey="Walker P">PA Walker</name></author><author><name sortKey="Martin, Sr" uniqKey="Martin S">SR Martin</name></author><author><name sortKey="Daniels, Rs" uniqKey="Daniels R">RS Daniels</name></author><author><name sortKey="Gregory, V" uniqKey="Gregory V">V Gregory</name></author><author><name sortKey="Skehel, Jj" uniqKey="Skehel J">JJ Skehel</name></author><author><name sortKey="Gamblin, Sj" uniqKey="Gamblin S">SJ Gamblin</name></author><author><name sortKey="Hay, Aj" uniqKey="Hay A">AJ Hay</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Uruguay</li></country></list><tree><country name="Uruguay"><noRegion><name sortKey="Go I, Natalia" sort="Go I, Natalia" uniqKey="Go I N" first="Natalia" last="Go I">Natalia Go I</name></noRegion><name sortKey="Colina, Rodney" sort="Colina, Rodney" uniqKey="Colina R" first="Rodney" last="Colina">Rodney Colina</name><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name><name sortKey="Fajardo, Alvaro" sort="Fajardo, Alvaro" uniqKey="Fajardo A" first="Alvaro" last="Fajardo">Alvaro Fajardo</name><name sortKey="Moratorio, Gonzalo" sort="Moratorio, Gonzalo" uniqKey="Moratorio G" first="Gonzalo" last="Moratorio">Gonzalo Moratorio</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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