Influenza A(H5N1) Virus Surveillance at Live Poultry Markets, Cambodia, 2011
Figure 2. . Phylogenetic relationship of the hemagglutinin (HA) gene among various influenza A(H5N1) strains; HA sequences for 48 strains (36 from Cambodia, 11 from Vietnam and one from China) were included in the analysis. Black triangles indicate viruses detected during this study of environmental samples from live poultry markets in Cambodia. Phylogenetic trees were generated by using the distance method and applying the neighbor-joining algorithm with bootstrap analysis (1,000 replicates). Analysis was based on nt 1–1,661 of the HA gene. The trees were rooted to A/goose/China/Guangdong/1/96 (H5N1). Numbers above and below branch nodes indicate bootstrap value of >70%. Scale bar represents the number of nucleotide changes per site. Lineage numbers 1–6, clades, and subclades indicate strains that are grouped in closely related phylogenetic lineages, as described (14). All sequences included in the analysis are available in GenBank.