HIV-1 genetic diversity and genotypic drug susceptibility in the Republic of Georgia

The genetic diversity and genotypic drug susceptibility of HIV-1 strains circulating in the Republic of Georgia, formerly part of the Soviet Union, were investigated for first time. Forty-eight HIV-positive drug-naive Georgian individuals contributed PBMC DNA between 1998 and 2003. On the basis of phylogenetic analyses of partial pol sequences, the predominant HIV-1 genetic forms were subtype A (70%), followed by subtype B (26%); both genetic forms were carried by injecting drug users and heterosexuals. There was also one subtype C (2%) and one CRF18_cpx (2%). The Georgian subtype A strains clustered with subtype A from Russia, designated A(FSU). Twelve of the subtype A strains (25%) contained the secondary protease inhibitor mutation V77I and 9 also had two other silent mutations. This "V77I haplotype" marks one particular genetic lineage of the epidemic in the former Soviet Union. Two strains (4%) carried antiretroviral (ARV) drug resistance mutations. Nearly full-length genome sequences of five Georgian strains were also completed. Two, 98GEMZ011 (subtype A) and 98GEMZ003 (subtype B), closely resembled the parental strains that recombined to create CRF03_AB. The use of these parental strains in the analysis revealed an additional segment of subtype A in CRF03_AB. Thus, the HIV-1 epidemic in Georgia was composed of a mixture of subtype A(FSU) and subtype B.     

Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979)

HIV-1 envelope sequence variants were RT-PCR amplified from serum samples cryopreserved in San Francisco in 1978-1979. The HIV-1 subtype B env V3-V5 sequences from four homosexual men clustered phylogenetically, with a median nucleotide distance of 2.8%, reflecting a recent common origin. These early U.S. HIV-1 env variants mapped close to the phylogenetic root of the subtype B tree while env variants collected in the United States throughout the 1980s and 1990s showed, on average, increasing genetic diversity and divergence from the subtype B consensus sequence. These results indicate that the majority of HIV-1 currently circulating in the United States may be descended from an initial introduction and rapid spread during the mid- to late 1970s of subtype B viruses with limited variability (i.e., a founder effect). As expected from the starburst-shaped phylogeny of HIV-1 subtype B, contemporary U.S. strains were, on average, more closely related at the nucleic acid and amino acid levels to the earlier 1978-1979 env variants than to each other. The growing levels of HIV-1 genetic diversity, one of multiple obstacles in designing a protective vaccine, may therefore be mitigated by using epidemic founding variants as antigenic strains for protection against contemporary strains.     

HIV type 1 pol gene diversity and antiretroviral drug resistance mutations in the Democratic Republic of Congo (DRC)

To study recombination and the natural polymorphism in pol of HIV-1 strains in the Democratic Republic of Congo (DRC) we sequenced the protease and RT genes for 70 HIV-1 strains previously characterized in the env V3-V5 region from a sentinel surveillance study in 2002. For 41 of the 70 (58.6%) strains, the same subtype/ CRF designations were observed in pol and env. Twenty-three (32.9%) of 70 pol sequences were complex recombinants involving two to five subtypes as well as fragments that could not be classified into any of the known subtypes. All subtypes were involved in recombination events. Unclassified (U) and env subtype H strains were very likely to be recombinant strains. Overall, many minor mutations were identified in the protease sequences. Although at the time of our study ARV use was not yet widespread in DRC, three strains were identified with one major mutation associated with drug resistance: L90M and M46L in protease and K103N in RT.     

上海市新诊断114例人类免疫缺陷病毒Ⅰ型感染者的分子生物学研究

目的对上海市2004至2005年新诊断的114例人类免疫缺陷病毒Ⅰ型（H1V-1）感染者进行分子流行病学调查，为确定上海市流行的HIV-1的分子生物学特征提供监测依据。方法应用逆转录聚合酶链反应扩增HIV-1多聚酶基因，DNA测序后进行进化系统树分析确定基因亚型并与国际耐药数据库比对辨别耐药性突变位点。结果1．114例中除1例不详外，本市户口33例，占28．95％，外来人口80例，占70．18％；经性传播感染51例，占44．74％，经静脉注射吸毒感染43例，占37．72％，经采供血和输血感染3例，占2．63％，感染途径不详17例，占14．91％；2．基因亚型分别为B亚型9例，占7．89％，B’亚型15例，占13．16％，C亚型1例，占0．88％，G亚型1例，占0．88％，CRF01_AE38例，占33．33％，CRF07_BC46例，占40．35％和CRF08BC4例，占3．51％；3．耐药分析结果表明本次研究人群的耐药性主突变率为18．42％。与蛋白酶抑制剂（PRIs）和逆转录酶抑制剂（RTIs）耐药相关的基因主突变率分别为2．63％（3／114）和17．54％（20／114）。蛋白酶基因主突变位点突变频率为M46I，占66．67％，M46L，占33．33％。逆转录酶基因主突变位点突变频率分别为M41L，占7．69％、A62V，占7．69％、T69S，占7．69％、V75I／L，占15．38％、K103R，占25．00％、V118I,占23．08％、V179D／E／T，占33．33％、G190R，占8．33％、L210K／M／X，占38．46％、F227L／I，占16．67％、M230R，占8．33％和P236R，占8．33％。结论上海市新诊断的HIV-1感染者依然以静脉吸毒和性传播为主，感染者以外省市流动人口为主。HIV-1基因亚型流行呈多样性，主要以CRF01_AE、CRF07_BC和B／B’为主。在114例新诊断、尚未经抗病毒治疗的HIV-1感染者中，已存在与PRIs和RTIs耐药相关的基因主突变。     

Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon,Portugal

We have evaluated the genetic diversity of HIV-1 strains infecting injecting drug users (IDUs) in Lisbon, Portugal. Heteroduplex mobility assay and/or phylogenetic analysis revealed that env (C2V3C3 or gp41) subtype B is present in 63.7% of the 135 viral samples studied, followed by subtypes G (23.7%), A (6.7%), F (5.2%), and D (0.7%). Similar analysis of gag (p24/p7) performed on 91 of the specimens demonstrated that 49.5% of the infections were caused by subtype G viruses; other gag subtypes identified were B (39.5%), F (3.3%), A and D (1.1.% each), and the recombinant circulating form CRF02_AG (5.5%). Discordant env/gag sub-types were detected in 34.1% of the strains and may reflect the presence of dual infections and/or recombinant viruses. The presumptive B/G recombinant form was highly predominant (21 of 31). The genetic pattern of HIV-1 subtype B and G strains is suggestive of multiple introductions and recombination episodes and of a longstanding presence of both subtypes in the country. C2V3C3 amino acid sequences from IDU-derived subtype G viruses presented highly significant signatures, which distinguish the variants from this transmission group. The unusually high prevalence of subtype G sequences (34.1%), independent of the geographic origin of the infected individuals, makes this IDU HIV-1 epidemic unique.