The HIV epidemic in men who have sex with men (MSM) continues to grow in most countries. However, the phylodynamic and virological differences among HIV-1 strains circulating in MSM and other populations are not well characterized.Nearly full-length genomes (NFLGs) of the HIV-1 CRF01_AE were obtained from the Los Alamos HIV database. Phylogenetic analyses were conducted using the NFLG, gag, pol and env genes, using the maximum likelihood method. Selection pressure analyses at the codon level were performed for each gene in the phylogenetic clusters using PAML.Sequences isolated from MSM in China clustered in Clusters 1 (92.5%) and 2 (85.71%). The major risk factor for Cluster 3 was heterosexual transmission (62.16%). The ratio of non-synonymous to synonymous substitutions in the env gene (0.7-0.75) was higher than the gag (0.26-0.34) or pol (0.21-0.26) genes. In env gene, Cluster 1 (4.56×10(-3) subs/site/year) and 2 (6.01×10(-3) subs/site/year) had higher evolutionary rates than Cluster 3 (1.14×10(-3) subs/site/year). Positive selection affected 4.2-6.58% of the amino acid sites in the env gene. Two sites (HXB2:136 and 316) evolved similarly in Clusters 1 and 2, but not Cluster 3.The HIV-1 CRF01_AE in MSM is evolving differently than in other populations
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