Objective: To analyze the genetic characteristics of HIV-1 CRF01_AE strains prevailing in Beijing.
Methods: Plasma samples were collected from the newly diagnosed HIV-1 individuals being reported during 2006 to 2008 in Beijing. Gag gene fragments were amplified from RNA template which were extracted from plasma by RT and nested PCR methods. 105 CRF01_AE sequences were analyzed by phylogcnetic methods and characterized through calculating the genetic distance and Entropy analysis.
Results: There were four main sub-clusters in the phylogenetic tree. We named them as sub-clusters Homo-Max (67 sequences), Hetero (6 sequences), Mix (8 sequences) and Homo-Min (18 sequences) respectively, based on the mode of transmission. It was found that no international reference strain was closely related to the sub-cluster Homo-Max, Hetero or Homo-Min, including 91 samples. The strains in sub-cluster Mix consisting 8 cases that were closely related to the strains identified in Thailand and Vietnam. Genetic distance analysis on gag genes showed that the diversity of sub-clusters Homo-Max and Homo-Min was obviously less than that of the sub-cluster Hetero or Mix. When compared with sub-cluster Mix, there were 37, 29 and 11 significantly different nucleotides polymorphism compositions sites in sub-clusers Homo-Max Homo-Min and Hetero.
Conclusion: This was the first report describing that four main epidemic sub-clusters were existed in CRF01_AE strains prevailing in Beijing. The virus with sub-cluster Homo-Max was the dominant strain in this region with shorter period of circulation and higher proportion seen in the HIV-infected persons. The virus in sub-cluster Mix was highly homologic with the CRF01_AE strains from Thailand and Vietnam.