ABSTRACT
Surveillance of the different HIV-1 subtypes has important implications for developing candidate vaccines and understanding the dynamics of HIV transmission in various populations. In this study, HIV-1 viral subtypes were determined for homologies in the V3-V5 region by heteroduplex mobility assay (HMA) in 46 patients with sexually transmitted diseases (STD) in Pune, India. Proviral DNA from peripheral blood mononuclear cells (PBMCs) from 20 recent sero-coverters and 26 HIV seropositive individuals were analyzed. Of the 46 samples analyzed, 44 (96%) were HIV-1 subtype C and one each of subtypes A and B. Further analyses revealed that 29 (66%) of the C subtype samples had maximum homology to the C3-Indian reference strain, while 15 (34%) were most homologous to the C2-Zambian strain. The C3 genotype prevailed in the majority (80%) of the seropositive individuals. Most of the C3 (Indian) strains were closely homologous to each other, while more nucleotide sequence divergence was seen in C2 samples. A higher quasispecies complexity was observed in the samples collected from seropositive individuals. These findings may have important implications for the design and testing of effective candidate HIV-1 vaccines for India.