Genetic Diversity Of HIV-1 CRF07_BC And Reconstruction Of Its Epidemic History In Sichuan And Xinjiang

HIV-1 CRF07_BC is one of major HIV strains prevailing in China, mainly distributed in intravenous drug users (IDUs). The HIV-1 CRF07_BC infection was first identified among IDUs in Sichuan and Xinjiang in 1996. It is very important to understand the genetic variation of CRF07_BC in Sichuan and Xinjiang within an individual or population, for the purpose of delineating the mechanisms of immune escape, fitness and molecular evolution. We analyzed the gpl20 and gag genes amplified from CRF07_BC infected cases in Sichuan and Xinjiang to explore the genetic diversity in an individual or at a population level, then to reconstruct its epidemic history.HIV-1 infected cases were recruited from Sichuan and Xinjiang, and the gp120 and gag genes were obtained using single genome amplification and sequencing to determine the subtype and explore the genetic characteristics in an individual. Another 195 cases were recruited among IDUs in Sichuan and Xinjiang in 2007 and 2008. The C2-V4 fragments of env gene obtained in Sichuan (n=108) and Xinjiang (n=216) covering 1996-2008, were used to reconstruct the CRF07_BC epidemic history and delineate genetic dynamics of CRF07_BC there, by Bayesian coalescent inference.In CRF07_BC-infected individuals, there was complex variation forms, including different models of numerous substitutions, insertion/deletions, and interlineage genetic recombination among quasispecies, et al, which caused the shift of amino acid (aa) constitutes, the numbers of putative N-linked glycosation sites, and the length polymorphisms in domains. All these factors brought comprehensive genetic diversity into the CRF07_BC strains, and sequences thereby formed complex structure in phylogeny trees. The gp120 gene accounted for the major variation of CRF07_BC, especially in the four variable loops (V1, V2, V4 and V5). Although the independent evolution with higher average pairwise distances (APD) in V1/V2 (0.012-0.117) than that those in V4/V5 (APD 0.024-0.178) were observed, the weak correlations were formed between the lengths of the V1/V2 and those of V4/V5 (r=0.359, P<0.001). V3 loop of gp120 gene exhibited high degree of conservation, with the constant length of amino acid residues, the unanimous coreceptor usage (CCR5 tropism) and the conservative GPGQ tetra-peptide in the critical crown of V3 loop. These phenomena may be the consequence of high functional selection and virus fitness. The pl7 and p2p6 regions likewise expressed high genetic diversity in CRF07_BC gag gene. In Sichuan and Xinjiang, 43.6% of the gag genes harbored 7-aa deletion in the p6 overlapping coding regions, while another 18% cases had three to twelve amino acids insertion in p6 region of the gag gene, which enhances the weight of proline and alamine. These indels may facilitate CRF07_BC immune escape and fitness.Phylogenetic analysis indicated that CRF07_BC circulating in Sichuan and Xinjiang shared high homology and were presumed to originate from a common ancestor. All the sequences were intermingled in phylogenetic trees, irrespectively of region, nationality, or sampling year differences. The overall variation of CRF07_BC was indistinctive, except that the amino acid constitutes in partial sites showed the correlation to regions and nationality.By Bayesian coalescent inference, we reconstructed the epidemic history of CRF07_BC in Sichuan and Xinjiang. CRF07_BC strains were first introduced into Sichuan in 1994.0 (95% confidence interval, 1991.9-1995.7), and Xinjiangin 1995.0, (95% confidence interval, 1993.7-1995.8). Combined with the other literatures, our observations supported the hypothesis that the CRF07_BC was transmitted from southwest China (Yunnan, in 1993.3) into Xinjiang via Sichuan along the heroin trafficking route. After the introduction of CRF07BC into Sichuan and Xinjiang, the CRF07_BC epidemic was established and experienced similar epidemic history of three successive phases, including the introduction and establishment of CRF07_BC epidemic (1994-1996), the fast transmission and spread (1997-2002), and high prevalence of CRF07_BC (2003-2008). During the early phase of CRF07_BC epidemic, the strains were transmitted among a small IDU population, with high genetic homogeneity and low diversity. With the progress of the epidemic, the CRF07_BC diversity was steadily increasing. The present data suggested that the transmission rate of CRF07_BC slowed down in Sichuan and Xinjiang nowadays, with effective population getting close to saturation. Correspondingly, the circulating strains showed greater genetic diversity (APD of gp120 gene, nearly 0.09) and faster evolutionary rate (7-8×10^-3 substitutions/site/year). A high prevalence of CRF07_BC infections was maintained, and more measures should be taken to control the HIV/AIDS epidemic in Sichuan and Xinjiang.