Sequence analysis of the gag-pol gene of human immunodeficiency virus type 1 of intersubtype (B'/C) recombinant strain in Beijing, China.

Little is known about the molecular and biological properties of HIV-1 intersubtype B'/C in Beijing. To fill the gap, we sequenced and analyzed the gag-pol genes from 39 HIV-1 B'/C recombinant infectors in Beijing, China during 2007. The results show that 36 CRF07_BC and 2 CRF08_BC isolates have a structural profile identical or nearly identical to CRF07_BC or CRF08_BC according to sequences in the gag-pol regions. The CRF07_BC circulating in injecting drug users (IDUs) and heterosexuals forms a diverse phylogenetic tree and most isolates from homosexuals cluster together. However, all the B'/C recombinant strains were remarkable for their low interpatient diversity in gag-pol genes (3.1, 3.0, and 2.2% for isolates from IDUs, heterosexuals, and homosexuals, respectively). We identified I7V, E91G, N242T, and K361R in the gag gene and R290I (HXB2 positions) in the pol gene as signature amino acid substitutions characteristic of HIV-1 CRF07_BC from the Beijing lineage. In addition, one new B'/C recombinant was detected. These results may contribute to an understanding of HIV-1 in Beijing.

[Genetic characteristics of HIV-1 CRF01_AE strains circulating in Beijing].

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.

[Subtype and sequence analysis of gag genes among HIV-1 strains circulating in Beijing during 2007].

To investigate the subtype distribution and sequence characteristics of HIV-1 strains prevalent in Beijing during 2007 and to analyze the relationship between distribution of HIV-1 subtypes and transmission routes, we collected the anti-conglutinated whole blood samples from HIV-1 newly infected individuals in Beijing during 2007 and separated plasma specimens from the aamples. RNAs were extracted and the gag genes from the various samples were amplified by RT-PCR and nest-PCR. The PCR products were sequenced directly and phylogenetic analyses of gag genes were performed using the MEGA2 software. Among 200 HIV-1 plasma samples,161 gag HIV-1 gene fragments were amplified and analyzed. Seven HIV-1 subtypes or circulating recombinant forms (CRFs) of HIV-1 including A1 (1 strains), B (35 strains), Thai B (19 strains), C (3 strains), CRF01_AE (49 strains), CRF07_BC (51 strains), CRF08_BC (3 strain) were identified circulating in Beijing. The gene divergences inside the subtypes were different, with 7.7%, 6.5%, 6.7%, 6.7%, 5.5%, 4.3%, 5.8%, in subtype A1, B, Thai B, C, CRF01_AE, CRF07_BC, CRF08_BC, respectively. Subtypes CRF07_BC and CRF01_AE were predominant in Beijing account for 31.7% and 30.4% among samples. Seven HIV-1 subtypes exist in Beijing and the surveillance of HIV-1 gene variation should be paid more attention.

[Association between sequence variation of Env, Gag genes from the same source and HIV-1 disease progression and host genetic polymorphism].

OBJECTIVE: To understand the relationship between the HIV-1 viral sequence variation and host factors associated with HIV-1 disease progression. METHODS: Env and gag fragments of HIV-1 were amplified with PCR, cloned and sequenced. Bioinformatics was employed to find the genetic variation, N-linked glycosylation, hypermutation etc. Host gene polymorphism was analysed by using restricted fragment length polymorphism (RFLP). RESULTS: Significant difference was found in genetic divergence between Env PCR dominant and clonal sequences (0.1 and 0.06, respectively) in non-treated group, but no significant difference was found in the HAART treated group. V3 GPGQ accounted for the most part in both treated and nontreated groups, rare V3 loop such as GPGH, GQGR and GLGR was found in treated group, V3 substitutions of I/V (position 12) and Y/H (position 21) was associated with the relatively rapid progression (RRP). Glycosylation was significantly higher in RRP than in TP for Env region, GA substitution in RRP was also significantly higher than that in TP group. SDF1-3primeA and CCR2 V64I gene frequency was higher in TP than in RRP, but the difference was not significant. CONCLUSION: Disease progression was associated with V3 AA change, glycosylation and GA substitution in env gene. SDF1-3primeA, CCR2 V64I and CX3CR1 V249I/M280T was not associated with disease progression significantly.