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Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade

Identifieur interne : 000162 ( France/Analysis ); précédent : 000161; suivant : 000163

Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade

Auteurs : San Sorn [Cambodge] ; Touch Sok [Cambodge] ; Sovann Ly [Cambodge] ; Sareth Rith [Cambodge] ; Nguyen Tung [Viêt Nam] ; Alain Viari [France] ; Laurent Gavotte [France] ; Davun Holl [Cambodge] ; Heng Seng [Cambodge] ; Nima Asgari [Cambodge] ; Beat Richner [Cambodge] ; Denis Laurent [Cambodge] ; Nora Chea [Cambodge] ; Veasna Duong [Cambodge] ; Tetsuya Toyoda [République populaire de Chine] ; Chadwick Y. Yasuda [Cambodge] ; Paul Kitsutani [Cambodge] ; Paul Zhou [République populaire de Chine] ; Sun Bing [République populaire de Chine] ; V. Deubel [Cambodge] ; Ruben Donis [États-Unis] ; Roger Frutos [France] ; Philippe Buchy [Cambodge]

Source :

RBID : Hal:pasteur-00793265

Abstract

In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry.


Url:
DOI: 10.1016/j.meegid.2012.05.013


Affiliations:

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Hal:pasteur-00793265

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<country>Cambodge</country>
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<name sortKey="Donis, Ruben" sort="Donis, Ruben" uniqKey="Donis R" first="Ruben" last="Donis">Ruben Donis</name>
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<country>États-Unis</country>
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<name sortKey="Frutos, Roger" sort="Frutos, Roger" uniqKey="Frutos R" first="Roger" last="Frutos">Roger Frutos</name>
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<date type="start">2009-01-01</date>
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<addrLine>Campus International de Baillarguet TA A-17/G 34398 Montpellier cedex 5</addrLine>
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<date type="start">1984-06-01</date>
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<addrLine>Siège 42, rue Scheffer 75116 Paris</addrLine>
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<orgName>Université Claude Bernard Lyon 1</orgName>
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<addrLine>43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex</addrLine>
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<region type="region" nuts="2">Auvergne-Rhône-Alpes</region>
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<author>
<name sortKey="Buchy, Philippe" sort="Buchy, Philippe" uniqKey="Buchy P" first="Philippe" last="Buchy">Philippe Buchy</name>
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<orgName>Institut Pasteur du Cambodge</orgName>
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<addrLine>25, rue du Dr Roux 75724 Paris Cedex 15</addrLine>
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<ref type="url">https://research.pasteur.fr/ip-network</ref>
</desc>
</org>
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</hal:affiliation>
<country>Cambodge</country>
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</author>
</analytic>
<idno type="DOI">10.1016/j.meegid.2012.05.013</idno>
<series>
<title level="j">Infection, Genetics and Evolution</title>
<idno type="ISSN">1567-1348</idno>
<imprint>
<date type="datePub">2012</date>
</imprint>
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<keywords scheme="mix" xml:lang="es">
<term>Avian influenza</term>
<term>Cambodia</term>
<term>Emergence</term>
<term>H5N1</term>
<term>Polymorphism</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry.</p>
</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Cambodge</li>
<li>France</li>
<li>République populaire de Chine</li>
<li>Viêt Nam</li>
<li>États-Unis</li>
</country>
<region>
<li>Aquitaine</li>
<li>Auvergne-Rhône-Alpes</li>
<li>Nouvelle-Aquitaine</li>
<li>Rhône-Alpes</li>
</region>
<settlement>
<li>Bordeaux</li>
<li>Lyon</li>
</settlement>
<orgName>
<li>Université Claude Bernard Lyon 1</li>
<li>Université de Bordeaux</li>
<li>Université de Lyon</li>
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<name sortKey="Sorn, San" sort="Sorn, San" uniqKey="Sorn S" first="San" last="Sorn">San Sorn</name>
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<name sortKey="Asgari, Nima" sort="Asgari, Nima" uniqKey="Asgari N" first="Nima" last="Asgari">Nima Asgari</name>
<name sortKey="Buchy, Philippe" sort="Buchy, Philippe" uniqKey="Buchy P" first="Philippe" last="Buchy">Philippe Buchy</name>
<name sortKey="Chea, Nora" sort="Chea, Nora" uniqKey="Chea N" first="Nora" last="Chea">Nora Chea</name>
<name sortKey="Deubel, V" sort="Deubel, V" uniqKey="Deubel V" first="V." last="Deubel">V. Deubel</name>
<name sortKey="Duong, Veasna" sort="Duong, Veasna" uniqKey="Duong V" first="Veasna" last="Duong">Veasna Duong</name>
<name sortKey="Holl, Davun" sort="Holl, Davun" uniqKey="Holl D" first="Davun" last="Holl">Davun Holl</name>
<name sortKey="Kitsutani, Paul" sort="Kitsutani, Paul" uniqKey="Kitsutani P" first="Paul" last="Kitsutani">Paul Kitsutani</name>
<name sortKey="Laurent, Denis" sort="Laurent, Denis" uniqKey="Laurent D" first="Denis" last="Laurent">Denis Laurent</name>
<name sortKey="Ly, Sovann" sort="Ly, Sovann" uniqKey="Ly S" first="Sovann" last="Ly">Sovann Ly</name>
<name sortKey="Richner, Beat" sort="Richner, Beat" uniqKey="Richner B" first="Beat" last="Richner">Beat Richner</name>
<name sortKey="Rith, Sareth" sort="Rith, Sareth" uniqKey="Rith S" first="Sareth" last="Rith">Sareth Rith</name>
<name sortKey="Seng, Heng" sort="Seng, Heng" uniqKey="Seng H" first="Heng" last="Seng">Heng Seng</name>
<name sortKey="Sok, Touch" sort="Sok, Touch" uniqKey="Sok T" first="Touch" last="Sok">Touch Sok</name>
<name sortKey="Yasuda, Chadwick Y" sort="Yasuda, Chadwick Y" uniqKey="Yasuda C" first="Chadwick Y." last="Yasuda">Chadwick Y. Yasuda</name>
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<noRegion>
<name sortKey="Tung, Nguyen" sort="Tung, Nguyen" uniqKey="Tung N" first="Nguyen" last="Tung">Nguyen Tung</name>
</noRegion>
</country>
<country name="France">
<region name="Auvergne-Rhône-Alpes">
<name sortKey="Viari, Alain" sort="Viari, Alain" uniqKey="Viari A" first="Alain" last="Viari">Alain Viari</name>
</region>
<name sortKey="Frutos, Roger" sort="Frutos, Roger" uniqKey="Frutos R" first="Roger" last="Frutos">Roger Frutos</name>
<name sortKey="Gavotte, Laurent" sort="Gavotte, Laurent" uniqKey="Gavotte L" first="Laurent" last="Gavotte">Laurent Gavotte</name>
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<name sortKey="Toyoda, Tetsuya" sort="Toyoda, Tetsuya" uniqKey="Toyoda T" first="Tetsuya" last="Toyoda">Tetsuya Toyoda</name>
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<name sortKey="Bing, Sun" sort="Bing, Sun" uniqKey="Bing S" first="Sun" last="Bing">Sun Bing</name>
<name sortKey="Zhou, Paul" sort="Zhou, Paul" uniqKey="Zhou P" first="Paul" last="Zhou">Paul Zhou</name>
</country>
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<noRegion>
<name sortKey="Donis, Ruben" sort="Donis, Ruben" uniqKey="Donis R" first="Ruben" last="Donis">Ruben Donis</name>
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</record>

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