Genetic Characterization of HIV-1 CRF01_AE Prevailing in Four Provinces, Southern China
|Course||Biochemistry and Molecular Biology|
|Keywords||CRF01_AE Epidemic Cluster Phylogenetic analysis|
Objective: To explore the genetic characteristics of HIV-1 CRF01AE circulating in the four provinces of southern China.Methods: HIV-1 gag and env gene fragments were amplified from plasma samples collected from newly reported infections in Guangdong, Guangxi, Jiangxi and Hunan in 2006 through reverse transcription PCR and Nested PCR. The neighbour-joining phylogenetic trees were constructed from the acquired sequences and the concatenated sequence named gagenv. After identification of the epidemic clusters, further analyses were carried on the different clusters with VESPA, Entropy, and Consensus Maker. BEAST （Bayesian Evolutionary Analysis by Sampling Trees） was used to calculate the origin of epidemic and evolutionary rate of the epidemic clusters.Results: There are 210 individuals with CRF01AE strains obtained from the four provinces, predominantly infected through heterosexual （130/210, 61.9%） and drug injection （61/210, 29.1%） approaches. Phylogenetic trees were separately constructed using different genes sequences, founding that the three trees all emerged two clusters. In cluster I, 53.8 % people were infected through heterosexual contact, 35.4 % through injecting drug usage. In cluster II, the proportions became 77.2% and 14.0%. The VESPA result showed that gag gene contains 3 Signature Pattern sites between the two clusters while there were 10 Signature Pattern sites in env gene. The Entropy revealed that 82 sites where the nucleotide diversity were significant different. Among those sites, 42 sites were in gag gene and 40 sites in env gene. And the sites with significant difference mainly existed in the third position of the codon （36/42） in gag gene while existed in the second and third positions of the codon in env gene(18/40;14/40. The phylogenetic analysis revealed that the strains in cluster I were independent, and there were no CRF01AE strains which were downloaded from Los Alamos HIV Databasebeing related to them. The time to the most recent common ancestor for of cluster I was 13.0 years, which was estimated by BEAST, the evolutionary rate for the cluster I was 6.72×10-3 substitutions per site per year. On the contrary, the strains in cluster II were mixed with many sequences of Vietnam sampled in different time, and the time to the most recent common ancestor was 13.3 years, and the evolutionary rate of cluster II was 12.25×10-3 substitutions per site per year. Conclusion: It is the first time to discover two clusters among the CRF01AE strains prevailing in four provinces of southern China. Significant differences were found in demography distribution and genetic characteristic between the two clusters. Cluster I was unique and there was not any other CRF01AE strains sampled in different country closely related to it. Cluster I strains infected more people than cluster II strains, and the time to the most recent common ancestor was a little later, cluster I is the predominant strains of CRF01AE in the four provinces. What is necessary to point out is that strains of cluster II and Vietnam were highly homologous. Several transmission events maybe have happened between cluster II and Vietnam strains.