A GENETIC-ANALYSIS OF HIV-1 FROM PUNJAB, INDIA REVEALS THE PRESENCE OF MULTIPLE VARIANTS

Objective: To determine the extent of HIV-1 genetic variation in India n patients. Design: To avoid any bias in selecting viral variants, HIV -1 DNA was amplified directly from the peripheral blood mononuclear ce lls of patients and sequenced. Genetic similarity between Indian seque nces and other geographic isolates was analysed by phylogenetic analys is algorithms. Methods: A fragment encompassing the C2/V3-V5 regions o f HIV-1 gp120 was amplified from the lymphocyte DNA of 12 Indian patie nts. Multiple clones from each patient were sequenced. Nucleotide sequ ences encompassing about 650 base pairs were aligned for the Indian an d other geographically distinct isolates. Inter-isolate relationships were analysed by means of distance, parsimony and neighbour-joining al gorithms. Results: Nucleotide sequence comparisons showed low interpat ient variation. Amino-acid comparisons revealed a high degree of homol ogy between Indian sequences in this study and those studied earlier. On distance and parsimony trees, most of the Indian sequences clustere d together as subtype C. However, sequences from three patients also s howed significant homologies and phylogenetic clustering outside of su btype C. Conclusions: The predominant strain of HIV-1 in India belongs to subtype C and little interpatient nucleotide sequence divergence i n the majority of cases suggests recent spread of HIV-1 in this region . This study also presents the first evidence for non-C subtypes in th e Indian population with two epidemiologically linked samples remainin g unclassified for any existing env subtype. The presence of variant s ubtypes in Indian patients sheds light on the transmission routes of H IV-1 to India and emphasizes the need to include these sequences in va ccine development strategies.