Detection and characterization of HIV type 2 in Calcutta, India

Genetic Characterization of Full-Length HIV-2 Long Terminal Repeat Sequences: Identification of Rare Promoter Variants

In this study, we sequenced the full-length HIV type 2 (HIV-2) long terminal repeat region from the proviral DNA of 23 HIV-2-infected individuals from the southern parts of India. We identified two different promoter variant strains circulating in this region along with the globally circulating common promoter variant. Seven sequences had an additional nuclear factor kappa-light chain enhancer of activated B cells (NF-κB) binding motif and the sequence from another subject showed one NF-κB and one RBE-III binding site. Phylogenetic and subtyping analyses revealed that the circulating strains comprised HIV-2 subtype A. The occurrence of two NF-κB binding sites in ∼30% of the sequences analyzed in our study prompts us to hypothesize that as in the case of HIV-1 subtype C viruses that possess additional κB sites, the two NF-κB HIV-2 variants might possess superior replication fitness because of the increased magnitude of transcription, thus leading to the expansion of these variants in the country.

Molecular epidemiology of HIV type 2 infections in South India

A small but significant number of HIV-2 cases have been reported from India. Although all HIV-2 viruses identified belong to subtype A, there are no studies on the diversity of the HIV-2 envelope and other genomic regions from India. Furthermore, HIV-2 envelope quasispecies in infected individuals has not been studied in detail. This study was designed to address these gaps existing in the epidemiology of HIV-2 in the country. Amongst the 4685 HIV-positive samples, 27 (0.57%) were positive for antibodies to HIV-2 by Western blot. Amplification of HIV-2 genomic regions was possible in 10 of these 27 samples. Sequences of the envelope C2V3C3 region (n = 8), partial stretches of LTR (n = 9), and gag-pol (n = 2) were analyzed. Sequences belonged to HIV-2 subtype A clustered together in the phylogenetic tree and were closely related to sequences reported from the neighboring states of Karnataka. The mean quasispecies diversity in a sample was found to be 3.5%.

Molecular phylogenetics of nearly full-length HIV type 2 envelope gene sequences from West India

Abstract While infection with HIV-1 has become a pandemic, the presence of HIV-2 is also of concern in certain regions of the world. We have characterized the gp105 region of the envelope gene of HIV-2 isolates from Western India. Phylogenetic analysis of all 18 sequences revealed that these sequences were closely related to each other as well as to published African and European HIV-2 group A sequences, with an overall genetic divergence of 10.9% (range 2-14%). Our study sequences showed close relatedness with West African HIV-2 group A (CAM group) sequences from Guinea Bissau with 89% homology. This was further confirmed by SimPlot as well as RIP analysis. Accordingly, the sequences presented here demonstrate the predominance of HIV-2 group A infection and show no evidence of HIV-2 recombination in Western India.

Full-length genome characterization of an HIV type 2 isolate from India

An infectious Indian human immunodeficiency virus-2 (HIV-2) subtype A isolate was completely sequenced and analyzed and its phylogenetic relatedness was investigated. The unusual limited size of the long terminal repeat (LTR) from the isolate was caused due to a truncation within the nef open reading frame (ORF) located at the U3 region of the LTR. The genetic relatedness and lineage of this HIV-2 strain were investigated. The close relatedness of this isolate to West African HIV-2 isolates confirms a geographical entry route of HIV-2 to this part of the Indian subcontinent. This is the first report of an HIV-2 full genome analysis from the Indian subcontinent as well as from Asia.

Characterization of a long terminal repeat region from an infectious Indian HIV type 2 isolate

An infectious Indian human immunodeficiency virus type 2 isolate from Mumbai, propagated in this laboratory, was found to bear an unusually short long terminal repeat (LTR) region. Complete sequencing of the 601 bp LTR indicated a loss of around 250 nucleotide pairs from the unique 3' (U3) region as compared to other well-characterized HIV-2 isolates. Phylogenetic analysis of this LTR shows closest relatedness to the Guinea-Bissau subtype A isolates HIV-2(CAM2) and HIV-2(ALI). The LTR from the biologically active infectious clone with the observed deletion contained all functionally relevant promoter and polyadenylation sequences.

Indian primary HIV-2 isolates and relationship between V3 genotype, biological phenotype and coreceptor usage

The chemokine coreceptors play a significant role in HIV entry and pathogenesis. The V3 region of HIV envelope glycoprotein is considered as a principal determinant for viral phenotype and tropism. The present study describes lack of association between the V3 genotype and viral phenotype of 18 Indian HIV-2 isolates. The viruses were isolated, confirmed by PCR and the HIV subtypes were determined by sequencing V3 region of the env gene. The coreceptor usage and syncytium inducing (SI) capacity of isolates was determined. Our study indicated that CCR5 coreceptor usage and NSI phenotype is predominant among Indian HIV-2 isolates obtained from patients in the early stage of infection. Two of the four HIV-2 isolates obtained from the late stage patients were SI and dual tropic. Phylogenetic analysis of these isolates revealed close relatedness to the isolates from western and southern India.