FIGURE 2-4 Phylogenetic relationships of the haemagglutinin (a) and matrix protein (b) genes of representative influenza A viruses isolated in southeastern Asia, including 2 of 6 from Indonesia, 5 of 8 from Thailand, and 4 of 12 from Vietnam. Trees were generated by using maximum parsimony in the PAUP* program (Swofford, 2001) (neighbor-joining analysis with the Tamura–Nei γ-model, implemented in the MEGA program [Kumar et al., 2001], revealed the same relationships). Numbers below branches indicate bootstrap values from 1,000 replicates. Only bootstrap values that define important groups have been included owing to space constraints. Analysis was based on nucleotides 1–1012 (1,012 bp) of the HA gene and 90–945 (856 bp) of the M gene. The HA tree was rooted to A/tern/South Africa/61 and the M tree to A/equine/Prague/1/56. Scale bar, 10 nucleotide changes. Green text indicates viruses isolated from wild birds in Hong Kong; pink text indicates viruses from smuggled birds in China; and other colours show the country of origin of isolates from the late 2003 to early 2004 H5N1 outbreak. Underlined viruses have the amantadine-resistance mutation (Ser31Asn) in the M2 ion channel. Ck, chicken; Dk, duck; Gd, Guangdong; Gf, Guinea fowl; Gs, goose; HK, Hong Kong; HN, Hunan; Qa, quail; SCk, silky chicken; ST, Shantou; WDk, wild duck; YN, Yunnan.

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