Drug resistance-associated genotypic alterations in the pol gene of HIV type 1 isolates in ART-naive individuals in North India

We genotyped the RT and PI regions of the pol gene of HIV-1 from treatment-naive infected individuals in North India and evaluated their possible physiological relevance and association with drug resistance. Plasma samples from 52 newly diagnosed HIV-1-infected drug-naive individuals were subjected to CD4(+) cell count and plasma viral load. For genotyping, the protease and RT regions of the pol gene were amplified from cDNA reverse transcribed from plasma viral RNA by single or nested polymerase chain reaction (PCR). Sequences of amplified products were analyzed for mutations using the Stanford DR and REGA database. Two out of 49 amplicons showed mutations at known "major" subtype B drug resistance positions (one each in protease and RT). In the protease region it showed a major drug resistance mutation at M46I as well as "minor" positions F53L and T74P. In the RT gene, one patient showed a mutation at major NNRTI position G190V. Forty-nine percent had mutations in the hinge (M36I, R41K, H69K) and alpha-helix (L89M) regions of the C-virus protease, which has been linked to increased catalytic activity. Our study indicates that a number of major mutations associated with resistance to PIs, NNRTIs, and NRTIs do exist, though at a low frequency, among HIV-1 isolates from treatment-naive individuals in North India. Many minor or accessory mutations related to resistance to PIs and NRTIs are also present as the variants. These results point to the greater biochemical fitness of subtype C protease and faster decrease in drug sensitivity.