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The evolutionary dynamics of influenza A virus adaptation to mammalian hosts

Identifieur interne : 001428 ( Main/Exploration ); précédent : 001427; suivant : 001429

The evolutionary dynamics of influenza A virus adaptation to mammalian hosts

Auteurs : S. Bhatt [Royaume-Uni] ; T. T. Lam [Royaume-Uni] ; S. J. Lycett [Royaume-Uni] ; A. J. Leigh Brown [Royaume-Uni] ; T. A. Bowden [Royaume-Uni] ; E. C. Holmes [États-Unis] ; Y. Guan [République populaire de Chine] ; J. L. N. Wood [Royaume-Uni] ; I. H. Brown [Royaume-Uni] ; P. Kellam [Royaume-Uni] ; O. G. Pybus [Royaume-Uni] ; Ian Brown ; Sharon Brookes ; Anna Germundsson ; Alex Cook ; Susanna Williamson ; Stephen Essen ; Fanny Garcon ; George Gunn ; Manuel Sanchez ; Diogo Marques ; James Wood ; Dan Tucker ; Ian Mccrone ; Julia Gog ; Roberto Saenz ; Meg Staff ; Pablo Murcia ; Wendy Barclay ; Christl Donnelly ; Ruth A. Elderfield ; Paul Kellam ; Greg Baillie ; Eve Coulter ; Barbara Wieland ; Alex Mastin ; John Mccauley ; Andy Leigh Brown ; Sam Lycett ; Mark Woolhouse ; Oliver Pybus ; Samir Bhatt ; Andrew Hayward ; David Ishola ; Alan Archibald ; Tom Freeman ; Bryan Charleston ; Eric Lefevre ; Mick Bailey ; Charlotte Inman ; Chris Stokes ; Kin Chow Chang ; Stephen Dunham ; Gavin White ; Jonathan Nguyen-Van-Tam ; Joanne Enstone

Source :

RBID : ISTEX:4290F759B211E07869BC69247BCC8E10B0558A4B

Abstract

Few questions on infectious disease are more important than understanding how and why avian influenza A viruses successfully emerge in mammalian populations, yet little is known about the rate and nature of the virus’ genetic adaptation in new hosts. Here, we measure, for the first time, the genomic rate of adaptive evolution of swine influenza viruses (SwIV) that originated in birds. By using a curated dataset of more than 24 000 human and swine influenza gene sequences, including 41 newly characterized genomes, we reconstructed the adaptive dynamics of three major SwIV lineages (Eurasian, EA; classical swine, CS; triple reassortant, TR). We found that, following the transfer of the EA lineage from birds to swine in the late 1970s, EA virus genes have undergone substantially faster adaptive evolution than those of the CS lineage, which had circulated among swine for decades. Further, the adaptation rates of the EA lineage antigenic haemagglutinin and neuraminidase genes were unexpectedly high and similar to those observed in human influenza A. We show that the successful establishment of avian influenza viruses in swine is associated with raised adaptive evolution across the entire genome for many years after zoonosis, reflecting the contribution of multiple mutations to the coordinated optimization of viral fitness in a new environment. This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts.

Url:
DOI: 10.1098/rstb.2012.0382


Affiliations:


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<name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name>
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<name sortKey="Baillie, Greg" sort="Baillie, Greg" uniqKey="Baillie G" first="Greg" last="Baillie">Greg Baillie</name>
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<name sortKey="Wieland, Barbara" sort="Wieland, Barbara" uniqKey="Wieland B" first="Barbara" last="Wieland">Barbara Wieland</name>
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<name sortKey="Mastin, Alex" sort="Mastin, Alex" uniqKey="Mastin A" first="Alex" last="Mastin">Alex Mastin</name>
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<name sortKey="Mccauley, John" sort="Mccauley, John" uniqKey="Mccauley J" first="John" last="Mccauley">John Mccauley</name>
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<name sortKey="Brown, Andy Leigh" sort="Brown, Andy Leigh" uniqKey="Brown A" first="Andy Leigh" last="Brown">Andy Leigh Brown</name>
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<name sortKey="Woolhouse, Mark" sort="Woolhouse, Mark" uniqKey="Woolhouse M" first="Mark" last="Woolhouse">Mark Woolhouse</name>
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<name sortKey="Pybus, Oliver" sort="Pybus, Oliver" uniqKey="Pybus O" first="Oliver" last="Pybus">Oliver Pybus</name>
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<name sortKey="Bhatt, Samir" sort="Bhatt, Samir" uniqKey="Bhatt S" first="Samir" last="Bhatt">Samir Bhatt</name>
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<name sortKey="Hayward, Andrew" sort="Hayward, Andrew" uniqKey="Hayward A" first="Andrew" last="Hayward">Andrew Hayward</name>
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<name sortKey="Ishola, David" sort="Ishola, David" uniqKey="Ishola D" first="David" last="Ishola">David Ishola</name>
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<name sortKey="Archibald, Alan" sort="Archibald, Alan" uniqKey="Archibald A" first="Alan" last="Archibald">Alan Archibald</name>
</author>
<author wicri:is="80%">
<name sortKey="Freeman, Tom" sort="Freeman, Tom" uniqKey="Freeman T" first="Tom" last="Freeman">Tom Freeman</name>
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<author wicri:is="80%">
<name sortKey="Charleston, Bryan" sort="Charleston, Bryan" uniqKey="Charleston B" first="Bryan" last="Charleston">Bryan Charleston</name>
</author>
<author wicri:is="80%">
<name sortKey="Lefevre, Eric" sort="Lefevre, Eric" uniqKey="Lefevre E" first="Eric" last="Lefevre">Eric Lefevre</name>
</author>
<author wicri:is="80%">
<name sortKey="Bailey, Mick" sort="Bailey, Mick" uniqKey="Bailey M" first="Mick" last="Bailey">Mick Bailey</name>
</author>
<author wicri:is="80%">
<name sortKey="Inman, Charlotte" sort="Inman, Charlotte" uniqKey="Inman C" first="Charlotte" last="Inman">Charlotte Inman</name>
</author>
<author wicri:is="80%">
<name sortKey="Stokes, Chris" sort="Stokes, Chris" uniqKey="Stokes C" first="Chris" last="Stokes">Chris Stokes</name>
</author>
<author wicri:is="80%">
<name sortKey="Chang, Kin Chow" sort="Chang, Kin Chow" uniqKey="Chang K" first="Kin Chow" last="Chang">Kin Chow Chang</name>
</author>
<author wicri:is="80%">
<name sortKey="Dunham, Stephen" sort="Dunham, Stephen" uniqKey="Dunham S" first="Stephen" last="Dunham">Stephen Dunham</name>
</author>
<author wicri:is="80%">
<name sortKey="White, Gavin" sort="White, Gavin" uniqKey="White G" first="Gavin" last="White">Gavin White</name>
</author>
<author wicri:is="80%">
<name sortKey="Nguyen Van Tam, Jonathan" sort="Nguyen Van Tam, Jonathan" uniqKey="Nguyen Van Tam J" first="Jonathan" last="Nguyen-Van-Tam">Jonathan Nguyen-Van-Tam</name>
</author>
<author wicri:is="80%">
<name sortKey="Enstone, Joanne" sort="Enstone, Joanne" uniqKey="Enstone J" first="Joanne" last="Enstone">Joanne Enstone</name>
</author>
</analytic>
<monogr></monogr>
<series>
<title level="j" type="main">Philosophical Transactions of the Royal Society B</title>
<title level="j" type="issue">Discussion Meeting Issue 'Next-generation molecular and evolutionary epidemiology of infectious disease' compiled and edited by O. G. Pybus, C. Fraser and A. Rambaut</title>
<title level="j" type="abbrev">Phil. Trans. R. Soc. B</title>
<idno type="ISSN">0962-8436</idno>
<idno type="eISSN">1471-2970</idno>
<imprint>
<publisher>The Royal Society</publisher>
<date type="published">2013</date>
<biblScope unit="vol">368</biblScope>
<biblScope unit="issue">1614</biblScope>
</imprint>
<idno type="ISSN">0962-8436</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt>
<idno type="ISSN">0962-8436</idno>
</seriesStmt>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract">Few questions on infectious disease are more important than understanding how and why avian influenza A viruses successfully emerge in mammalian populations, yet little is known about the rate and nature of the virus’ genetic adaptation in new hosts. Here, we measure, for the first time, the genomic rate of adaptive evolution of swine influenza viruses (SwIV) that originated in birds. By using a curated dataset of more than 24 000 human and swine influenza gene sequences, including 41 newly characterized genomes, we reconstructed the adaptive dynamics of three major SwIV lineages (Eurasian, EA; classical swine, CS; triple reassortant, TR). We found that, following the transfer of the EA lineage from birds to swine in the late 1970s, EA virus genes have undergone substantially faster adaptive evolution than those of the CS lineage, which had circulated among swine for decades. Further, the adaptation rates of the EA lineage antigenic haemagglutinin and neuraminidase genes were unexpectedly high and similar to those observed in human influenza A. We show that the successful establishment of avian influenza viruses in swine is associated with raised adaptive evolution across the entire genome for many years after zoonosis, reflecting the contribution of multiple mutations to the coordinated optimization of viral fitness in a new environment. This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts.</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Royaume-Uni</li>
<li>République populaire de Chine</li>
<li>États-Unis</li>
</country>
<region>
<li>Angleterre</li>
<li>Angleterre de l'Est</li>
<li>Maryland</li>
<li>Oxfordshire</li>
<li>Pennsylvanie</li>
<li>Écosse</li>
</region>
<settlement>
<li>Cambridge</li>
<li>Oxford</li>
<li>University Park (Pennsylvanie)</li>
<li>Édimbourg</li>
</settlement>
<orgName>
<li>Université d'Oxford</li>
<li>Université d'Édimbourg</li>
<li>Université d'État de Pennsylvanie</li>
<li>Université de Cambridge</li>
</orgName>
</list>
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<name sortKey="Baillie, Greg" sort="Baillie, Greg" uniqKey="Baillie G" first="Greg" last="Baillie">Greg Baillie</name>
<name sortKey="Barclay, Wendy" sort="Barclay, Wendy" uniqKey="Barclay W" first="Wendy" last="Barclay">Wendy Barclay</name>
<name sortKey="Bhatt, Samir" sort="Bhatt, Samir" uniqKey="Bhatt S" first="Samir" last="Bhatt">Samir Bhatt</name>
<name sortKey="Brookes, Sharon" sort="Brookes, Sharon" uniqKey="Brookes S" first="Sharon" last="Brookes">Sharon Brookes</name>
<name sortKey="Brown, Andy Leigh" sort="Brown, Andy Leigh" uniqKey="Brown A" first="Andy Leigh" last="Brown">Andy Leigh Brown</name>
<name sortKey="Brown, Ian" sort="Brown, Ian" uniqKey="Brown I" first="Ian" last="Brown">Ian Brown</name>
<name sortKey="Chang, Kin Chow" sort="Chang, Kin Chow" uniqKey="Chang K" first="Kin Chow" last="Chang">Kin Chow Chang</name>
<name sortKey="Charleston, Bryan" sort="Charleston, Bryan" uniqKey="Charleston B" first="Bryan" last="Charleston">Bryan Charleston</name>
<name sortKey="Cook, Alex" sort="Cook, Alex" uniqKey="Cook A" first="Alex" last="Cook">Alex Cook</name>
<name sortKey="Coulter, Eve" sort="Coulter, Eve" uniqKey="Coulter E" first="Eve" last="Coulter">Eve Coulter</name>
<name sortKey="Donnelly, Christl" sort="Donnelly, Christl" uniqKey="Donnelly C" first="Christl" last="Donnelly">Christl Donnelly</name>
<name sortKey="Dunham, Stephen" sort="Dunham, Stephen" uniqKey="Dunham S" first="Stephen" last="Dunham">Stephen Dunham</name>
<name sortKey="Elderfield, Ruth A" sort="Elderfield, Ruth A" uniqKey="Elderfield R" first="Ruth A." last="Elderfield">Ruth A. Elderfield</name>
<name sortKey="Enstone, Joanne" sort="Enstone, Joanne" uniqKey="Enstone J" first="Joanne" last="Enstone">Joanne Enstone</name>
<name sortKey="Essen, Stephen" sort="Essen, Stephen" uniqKey="Essen S" first="Stephen" last="Essen">Stephen Essen</name>
<name sortKey="Freeman, Tom" sort="Freeman, Tom" uniqKey="Freeman T" first="Tom" last="Freeman">Tom Freeman</name>
<name sortKey="Garcon, Fanny" sort="Garcon, Fanny" uniqKey="Garcon F" first="Fanny" last="Garcon">Fanny Garcon</name>
<name sortKey="Germundsson, Anna" sort="Germundsson, Anna" uniqKey="Germundsson A" first="Anna" last="Germundsson">Anna Germundsson</name>
<name sortKey="Gog, Julia" sort="Gog, Julia" uniqKey="Gog J" first="Julia" last="Gog">Julia Gog</name>
<name sortKey="Gunn, George" sort="Gunn, George" uniqKey="Gunn G" first="George" last="Gunn">George Gunn</name>
<name sortKey="Hayward, Andrew" sort="Hayward, Andrew" uniqKey="Hayward A" first="Andrew" last="Hayward">Andrew Hayward</name>
<name sortKey="Inman, Charlotte" sort="Inman, Charlotte" uniqKey="Inman C" first="Charlotte" last="Inman">Charlotte Inman</name>
<name sortKey="Ishola, David" sort="Ishola, David" uniqKey="Ishola D" first="David" last="Ishola">David Ishola</name>
<name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name>
<name sortKey="Lefevre, Eric" sort="Lefevre, Eric" uniqKey="Lefevre E" first="Eric" last="Lefevre">Eric Lefevre</name>
<name sortKey="Lycett, Sam" sort="Lycett, Sam" uniqKey="Lycett S" first="Sam" last="Lycett">Sam Lycett</name>
<name sortKey="Marques, Diogo" sort="Marques, Diogo" uniqKey="Marques D" first="Diogo" last="Marques">Diogo Marques</name>
<name sortKey="Mastin, Alex" sort="Mastin, Alex" uniqKey="Mastin A" first="Alex" last="Mastin">Alex Mastin</name>
<name sortKey="Mccauley, John" sort="Mccauley, John" uniqKey="Mccauley J" first="John" last="Mccauley">John Mccauley</name>
<name sortKey="Mccrone, Ian" sort="Mccrone, Ian" uniqKey="Mccrone I" first="Ian" last="Mccrone">Ian Mccrone</name>
<name sortKey="Murcia, Pablo" sort="Murcia, Pablo" uniqKey="Murcia P" first="Pablo" last="Murcia">Pablo Murcia</name>
<name sortKey="Nguyen Van Tam, Jonathan" sort="Nguyen Van Tam, Jonathan" uniqKey="Nguyen Van Tam J" first="Jonathan" last="Nguyen-Van-Tam">Jonathan Nguyen-Van-Tam</name>
<name sortKey="Pybus, Oliver" sort="Pybus, Oliver" uniqKey="Pybus O" first="Oliver" last="Pybus">Oliver Pybus</name>
<name sortKey="Saenz, Roberto" sort="Saenz, Roberto" uniqKey="Saenz R" first="Roberto" last="Saenz">Roberto Saenz</name>
<name sortKey="Sanchez, Manuel" sort="Sanchez, Manuel" uniqKey="Sanchez M" first="Manuel" last="Sanchez">Manuel Sanchez</name>
<name sortKey="Staff, Meg" sort="Staff, Meg" uniqKey="Staff M" first="Meg" last="Staff">Meg Staff</name>
<name sortKey="Stokes, Chris" sort="Stokes, Chris" uniqKey="Stokes C" first="Chris" last="Stokes">Chris Stokes</name>
<name sortKey="Tucker, Dan" sort="Tucker, Dan" uniqKey="Tucker D" first="Dan" last="Tucker">Dan Tucker</name>
<name sortKey="White, Gavin" sort="White, Gavin" uniqKey="White G" first="Gavin" last="White">Gavin White</name>
<name sortKey="Wieland, Barbara" sort="Wieland, Barbara" uniqKey="Wieland B" first="Barbara" last="Wieland">Barbara Wieland</name>
<name sortKey="Williamson, Susanna" sort="Williamson, Susanna" uniqKey="Williamson S" first="Susanna" last="Williamson">Susanna Williamson</name>
<name sortKey="Wood, James" sort="Wood, James" uniqKey="Wood J" first="James" last="Wood">James Wood</name>
<name sortKey="Woolhouse, Mark" sort="Woolhouse, Mark" uniqKey="Woolhouse M" first="Mark" last="Woolhouse">Mark Woolhouse</name>
</noCountry>
<country name="Royaume-Uni">
<region name="Angleterre">
<name sortKey="Bhatt, S" sort="Bhatt, S" uniqKey="Bhatt S" first="S." last="Bhatt">S. Bhatt</name>
</region>
<name sortKey="Bhatt, S" sort="Bhatt, S" uniqKey="Bhatt S" first="S." last="Bhatt">S. Bhatt</name>
<name sortKey="Bowden, T A" sort="Bowden, T A" uniqKey="Bowden T" first="T. A." last="Bowden">T. A. Bowden</name>
<name sortKey="Brown, I H" sort="Brown, I H" uniqKey="Brown I" first="I. H." last="Brown">I. H. Brown</name>
<name sortKey="Kellam, P" sort="Kellam, P" uniqKey="Kellam P" first="P." last="Kellam">P. Kellam</name>
<name sortKey="Lam, T T" sort="Lam, T T" uniqKey="Lam T" first="T. T." last="Lam">T. T. Lam</name>
<name sortKey="Leigh Brown, A J" sort="Leigh Brown, A J" uniqKey="Leigh Brown A" first="A. J." last="Leigh Brown">A. J. Leigh Brown</name>
<name sortKey="Lycett, S J" sort="Lycett, S J" uniqKey="Lycett S" first="S. J." last="Lycett">S. J. Lycett</name>
<name sortKey="Pybus, O G" sort="Pybus, O G" uniqKey="Pybus O" first="O. G." last="Pybus">O. G. Pybus</name>
<name sortKey="Pybus, O G" sort="Pybus, O G" uniqKey="Pybus O" first="O. G." last="Pybus">O. G. Pybus</name>
<name sortKey="Wood, J L N" sort="Wood, J L N" uniqKey="Wood J" first="J. L. N." last="Wood">J. L. N. Wood</name>
</country>
<country name="États-Unis">
<region name="Pennsylvanie">
<name sortKey="Holmes, E C" sort="Holmes, E C" uniqKey="Holmes E" first="E. C." last="Holmes">E. C. Holmes</name>
</region>
<name sortKey="Holmes, E C" sort="Holmes, E C" uniqKey="Holmes E" first="E. C." last="Holmes">E. C. Holmes</name>
</country>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Guan, Y" sort="Guan, Y" uniqKey="Guan Y" first="Y." last="Guan">Y. Guan</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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