Analysis of HIV type 1 protease and reverse transcriptase in antiretroviral drug-naive Ugandan adults

We analyzed plasma HTV-1 from 27 antiretroviral drug-naive Ugandan adults. Previous subtype analysis of env and gag sequences from these samples ident ified subtypes A, C, D, and recombinant HIV-1. Sequences of HIV-1 protease and reverse transcriptase (RT) were obtained with a commercial HIV-1 genoty ping system. Subtypes based on protease sequences differed from gag subtype s for 5 of 27 samples, demonstrating a high fate of recombination between t he gag and pol regions. Protease and RT sequences were analyzed for the pre sence of amino acid polymorphisms at positions that are sites of previously characterized drug resistance mutations. At those sites, frequent polymorp hisms were detected at positions 36 and 69 in protease and positions 179, 2 11, and 214 in RT, Subtype-specific amino acid motifs were identified in pr otease, Most of the subtype A sequences had the amino acids DKKM at positio ns 35, 57, 69, and 89, whereas most subtype D sequences had the amino acids ERHL at those positions. Detection of those polymorphisms may provide a us eful approach for rapid identification of subtype A and D isolates in Ugand a, This analysis significantly increases the number of Ugandan protease and RT sequences characterized to date and demonstrates successful use of a co mmercial HTV-1 genotyping system for analysis of diverse non-B HIV-1 subtyp es.