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 ter minal repeat (LTR) sequence diversity among distinct populations within Ind ia and to determine the prevalent subtype. Study Design/Methods: Analysis of the 3'LTR was conducted from 28 HIV-l-pos itive samples: 1992-1993 (Pune, New Delhi) and 1995-1996 (Pune, Mumbai and Vellore). Genomic DNA was extracted from cocultivated peripheral blood mono nuclear cells (PBMCs) and used for polymerase chain reaction (PCR) amplific ation and sequencing using dye terminator chemistry. Sequences were edited, aligned, and analyzed phylogenetically utilizing gap-stripped and bootstra pping parameters. Mobility shift assays were used to confirm binding activi ty. Results: AU nucleotide sequences were HIV-1 subtype C based on phylogenetic analysis. The isolates from Pune/Delhi formed subclusters when analyzed se parately, irrespective of time or sample source. However, no significant su bclustering was observed with isolates from Mumbai or Vellore or with the e ntire sample set when analyzed collectively. Subtype specific enhancer anal ysis revealed an expected third NF-kappa B site but also revealed six isola tes with insertions and deletions not previously described, one of which re sembles an AP-1 binding site. Conclusions: The results confirm the prevalence of HIV-1C and suggest incre asingly complex phylogeny of HIV-IC within India, such that the previously observed subclustering may no longer adequately reflect the diversity of is olates currently circulating throughout India.