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-2 LTR 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 NF-kB binding motif and the sequence from another subject showed one NF-kB and one RBE-III binding site. Phylogenetic and subtyping analyses revealed that the circulating strains comprised HIV-2 subtype-A. The occurrence of 2- NF-kB binding sites in about 30% of the sequences analysed in our study prompts us to hypothesize that as in the case of HIV-1 subtype C viruses that possess additional kB sites, the 2- NF-kB HIV-2 variants might possess superior replication fitness due to the increased magnitude of transcription, thus leading to the expansion of these variants in the country.