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

Sorn San, Sok Touch, Ly Sovann, Rith Sareth, Nguyen Tung, Viari Alain, Gavotte Laurent, Holl Davun, Seng Heng, Asgari Nima, Richner Beat, Laurent Denis, Chea Nora, Duong Veasna, Toyoda Tetsuya, Yasudai Chadwick Y., Kitsutani Paul, Zhoui Paul, Bing Sun, Deubel Vincent, Donis Ruben, Frutos Roger, Buchy Philippe. 2013. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infection, Genetics and Evolution, 15, spec. : pp. 87-94. International Giardia and Cryptosporidium Conference. 4, Wellington, Afrique du Sud, 30 January 2012/3 February 2012.

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Quartile : Q2, Sujet : INFECTIOUS DISEASES

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Anthropologie-Ethnologie

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. (Résumé d'auteur)

Mots-clés Agrovoc : Influenzavirus aviaire, Surveillance épidémiologique, Descendance, Polymorphisme génétique, Séquence nucléotidique, Bioinformatique, Lignée

Mots-clés géographiques Agrovoc : Viet Nam, Cambodge, Thaïlande

Mots-clés complémentaires : Émergence

Classification Agris : L73 - Animal diseases
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : Axe 4 (2005-2013) - Santé animale et maladies émergentes

Auteurs et affiliations

  • Sorn San, NAVRI (KHM)
  • Sok Touch, Ministère de la santé (Cambodge) (KHM)
  • Ly Sovann, Ministère de la santé (Cambodge) (KHM)
  • Rith Sareth, Institut Pasteur du Cambodge (KHM)
  • Nguyen Tung, NCVD (VNM)
  • Viari Alain, INRIA (FRA)
  • Gavotte Laurent, UM2 (FRA)
  • Holl Davun, NAVRI (KHM)
  • Seng Heng, Ministère de la santé (Cambodge) (KHM)
  • Asgari Nima, World Health Organization (KHM)
  • Richner Beat, Kantha Bopha Hospital (KHM)
  • Laurent Denis, Kantha Bopha Hospital (KHM)
  • Chea Nora, World Health Organization (KHM)
  • Duong Veasna, Institut Pasteur du Cambodge (KHM)
  • Toyoda Tetsuya, Institut Pasteur de Shanghai (CHN)
  • Yasudai Chadwick Y., Institut Pasteur de Shanghai (CHN)
  • Kitsutani Paul, Centers for Disease Control and Prevention (KHM)
  • Zhoui Paul, Institut Pasteur de Shanghai (CHN)
  • Bing Sun, Institut Pasteur de Shanghai (CHN)
  • Deubel Vincent, Institut Pasteur du Cambodge (KHM)
  • Donis Ruben, Institut Pasteur de Shanghai (CHN)
  • Buchy Philippe, Institut Pasteur du Cambodge (KHM)

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