Increased promoter diversity reveals a complex phylogeny of human immunodeficiency virus type 1 subtype C in India

Objective: To evaluate human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) sequence diversity among distinct populations within India and to determine the prevalent subtype. Study Design/Methods: Analysis of the 3'LTR was conducted from 28 HIV-l-positive samples: 1992-1993 (Pune, New Delhi) and 1995-1996 (Pune, Mumbai and Vellore). Genomic DNA was extracted from cocultivated peripheral blood mononuclear cells (PBMCs) and used for polymerase chain reaction (PCR) amplification and sequencing using dye terminator chemistry. Sequences were edited, aligned, and analyzed phylogenetically utilizing gap-stripped and bootstrapping parameters. Mobility shift assays were used to confirm binding activity. Results: AU nucleotide sequences were HIV-1 subtype C based on phylogenetic analysis. The isolates from Pune/Delhi formed subclusters when analyzed separately, irrespective of time or sample source. However, no significant subclustering was observed with isolates from Mumbai or Vellore or with the entire sample set when analyzed collectively. Subtype specific enhancer analysis revealed an expected third NF-kappa B site but also revealed six isolates with insertions and deletions not previously described, one of which resembles an AP-1 binding site. Conclusions: The results confirm the prevalence of HIV-1C and suggest increasingly complex phylogeny of HIV-IC within India, such that the previously observed subclustering may no longer adequately reflect the diversity of isolates currently circulating throughout India.