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

San Sorn (1, 2) , Touch Sok (3) , Sovann Ly (3) , Sareth Rith (1) , Nguyen Tung (4) , Alain Viari (5) , Laurent Gavotte (6) , Davun Holl (2) , Heng Seng (3) , Nima Asgari (7) , Beat Richner (8) , Denis Laurent (8) , Nora Chea (7) , Veasna Duong (1) , Tetsuya Toyoda (9) , Chadwick Y. Yasuda (10) , Paul Kitsutani (11) , Paul Zhou (9) , Sun Bing (9) , V. Deubel (1) , Ruben Donis (12) , Roger Frutos (13) , Philippe Buchy (1)

1 Institut Pasteur du Cambodge
2 National Veterinary Research Institute [Phnom Penh]
3 CDC MOH - Communicable Disease Department [Phnom Penh]
4 National Centre for Veterinary Diagnostics [Hanoi]
5 BAMBOO - An algorithmic view on genomes, cells, and environments
6 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
7 WHO - World Health Organization [Phnom Penh]
8 Kantha Bopha Hospitals Foundation
9 IPS-CAS - Institut Pasteur de Shanghai, Académie des Sciences de Chine - Chinese Academy of Sciences
10 US Naval Medical Research Unit n°2
11 Centers for Disease Control and Prevention [Phnom Penh]
12 CDC - Centers for Disease Control and Prevention [Atlanta]
13 UMR INTERTRYP - Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides

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.

Mots clés: H5N1; Avian influenza; Emergence; Cambodia; Polymorphism

Domaines: Virologie

San Sorn, Touch Sok, Sovann Ly, Sareth Rith, Nguyen Tung, et al.. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infection, Genetics and Evolution, 2012, pp.N/A. ⟨10.1016/j.meegid.2012.05.013⟩. ⟨pasteur-00793265⟩