title: Heterogeneous Evolution of HIV-1 CRF01_AE in Men Who Have Sex with Men (MSM) and Other Populations in China.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  The HIV-1 CRF01_AE in MSM is evolving differently than in other populations.
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Peng
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors.forename: Haibo
authors.initials: H
authors.lastname: Wu
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors.forename: Xiuming
authors.initials: X
authors.lastname: Peng
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors.forename: Changzhong
authors.initials: C
authors.lastname: Jin
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors.forename: Nanping
authors.initials: N
authors.lastname: Wu
mesh_terms: D002681:China; D019143:Evolution, Molecular; D005814:Genes, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D018451:Homosexuality, Male; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D010802:Phylogeny