OBJECTIVE: To characterize full length gag gene and partial pol gene of Chinese prevalent HIV-1 B/C recombinant strains, to explore the genetic difference between parent strains and B/C recombinant strains, and to investigate the mechanism of different biologic phenotype among them. METHODS: The peripheral blood samples were collected from 138 HIV-positive persons from 12 regions of China respectively. Samples of total DNA were extracted from the peripheral blood mononuclear cells to undergo nested PCR and sequencing. The 117 HIV-1 CRF07-BC strains and 21 HIV-1 CRF08-BC strains were screened with the resulted that 5 CRF07-BC samples from Xinjiang and 1 CRF08-BC sample from Chongqing were regarded as the most potential new type recombinant viruses. The sequences thus obtained underwent phylogenetic tree analysis and amino acid variation analysis. Simplot software was used to analyze the sequence recombination and identify the breakpoints of B/C recombinant strains. To confirm the breakpoints, separate phylogenetic analysis according to the breakpoints was performed with MEGA software. The genetic distances of different gene fragments were calculated by DISTANCE program in GCG software package. The gene dispersion in the gene fragment of a length of 2550 bp of the recombinant HIV-1-B/C and the potential influence of gene recombination on its function were further analyzed. RESULTS: No change of breakpoint was found in the 5 samples from Xinjiang. But a breakpoint shift of 160 nucleotides occurred in RT region of a sample from Congqing city. CONCLUSION: CRF07-BC and CRF08-BC remain the main prevalent HIV-1 B/C recombinant strains in China. No epidemic of new mosaic recombinant strain is found. The variation of amino acids at the sites 286 and 799 may be the reasons of the transmission dominance of the B/C recombinant strain.
OBJECTIVE: To characterize full length gag gene and partial pol gene of Chinese prevalent HIV-1 B/C recombinant strains, to explore the genetic difference between parent strains and B/C recombinant strains, and to investigate the mechanism of different biologic phenotype among them. METHODS: The peripheral blood samples were collected from 138 HIV-positive persons from 12 regions of China respectively. Samples of total DNA were extracted from the peripheral blood mononuclear cells to undergo nested PCR and sequencing. The 117 HIV-1 CRF07-BC strains and 21 HIV-1 CRF08-BC strains were screened with the resulted that 5 CRF07-BC samples from Xinjiang and 1 CRF08-BC sample from Chongqing were regarded as the most potential new type recombinant viruses. The sequences thus obtained underwent phylogenetic tree analysis and amino acid variation analysis. Simplot software was used to analyze the sequence recombination and identify the breakpoints of B/C recombinant strains. To confirm the breakpoints, separate phylogenetic analysis according to the breakpoints was performed with MEGA software. The genetic distances of different gene fragments were calculated by DISTANCE program in GCG software package. The gene dispersion in the gene fragment of a length of 2550 bp of the recombinant HIV-1-B/C and the potential influence of gene recombination on its function were further analyzed. RESULTS: No change of breakpoint was found in the 5 samples from Xinjiang. But a breakpoint shift of 160 nucleotides occurred in RT region of a sample from Congqing city. CONCLUSION: CRF07-BC and CRF08-BC remain the main prevalent HIV-1 B/C recombinant strains in China. No epidemic of new mosaic recombinant strain is found. The variation of amino acids at the sites 286 and 799 may be the reasons of the transmission dominance of the B/C recombinant strain.