Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004–2007
Philippe Buchy , Mathieu Fourment, Sek Mardy, San Sorn, Davun Holl, Sowath Ly, Sirenda Vong, Vincent Enouf, J.S. Malik Peiris, and Silvie van der Werf
Author affiliations: Institut Pasteur, Phnom Penh, Cambodia (P. Buchy, M. Fourment, S. Mardy, S. Ly, S. Vong); Ministry of Agriculture, Fisheries and Forestry, Phnom Penh (S. Sorn, D. Holl); Institut Pasteur, Paris, France (V. Enouf, S. van der Werf); Hong Kong University, Hong Kong Special Administrative Region, People’s Republic of China (J.S.M. Peiris)
Figure 1. Phylogenetic relationships of the hemagluttinin (HA) (A) and neuraminidase (NA) (B) genes of 33 Cambodian strains and of representative influenza A viruses (H5N1). Trees were generated by Bayesian analysis using MrBayes v3.1 software (2). Numbers above and below branches indicate Bayesian posterior probability and maximum likelihood bootstrap values (PHYML v2.4 software, www.atgc-montpellier.fr/phyml), respectively. Analysis was based on nucleotides 28–1578 of the HA gene and 67 to 1248 of the NA gene. Both trees were rooted to A/goose/Guangdong/6/96. Scale bar indicates 0.3 and 0.2 substitutions per site for HA and NA genes, respectively. Dk, duck; Ck, chicken; Gs, goose; Bhg, bar headed goose; Pg, pigeon; Gh, gray heron; Ql, quail; Mall, Mallard duck; Tg, tiger; CAM, Cambodia, VNM, Vietnam, THA, Thailand, MAL, Malaysia, CHI, People’s Republic of China; TRK, Turkey; RUS, Russia, JPN, Japan. Cambodian subtype H5N1 viruses that are grouped in closely related phylogenetic sublineages and are denoted by sublineage number (arbitrarily numbered I–VII for purposes of molecular epidemiology) and these sublineages are also denoted in the map (Figure 2) to show where these viruses have found and the likely virus introduction routes. It is to be emphasized that all these viruses are within the World Health Organization (WHO) clade 1, and these sublineage numbers are not to be confused with the WHO clade/subclade nomenclature.
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