Sequence Note: Analysis of HIV Type 1 Protease and Reverse Transcriptase in Antiretroviral Drug-Naive Ugandan Adults

Abstract

We analyzed plasma HIV-1 from 27 antiretroviral drug-naive Ugandan adults. Previous subtype analysis of env and gag sequences from these samples identified subtypes A, C, D, and recombinant HIV-1. Sequences of HIV-1 protease and reverse transcriptase (RT) were obtained with a commercial HIV-1 genotyping system. Subtypes based on protease sequences differed from gag subtypes for 5 of 27 samples, demonstrating a high rate of recombination between the gag and pol regions. Protease and RT sequences were analyzed for the presence of amino acid polymorphisms at positions that are sites of previously characterized drug resistance mutations. At those sites, frequent polymorphisms were detected at positions 36 and 69 in protease and positions 179, 211, and 214 in RT. Subtype-specific amino acid motifs were identified in protease. Most of the subtype A sequences had the amino acids DKKM at positions 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 useful approach for rapid identification of subtype A and D isolates in Uganda. This analysis significantly increases the number of Ugandan protease and RT sequences characterized to date and demonstrates successful use of a commercial HIV-1 genotyping system for analysis of diverse non-B HIV-1 subtypes.

Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes

“…An analysis of the HIV-1 sequences in GenBank indicates that relative to the B subtype, the reverse transcriptase enzyme exhibits 7-9% amino acid polymorphisms, the integrase between 7% and 9%, gp120 between 18% and 23%, gp41 between 22% and 27% and the matrix protein p17 between 22% and 27%. Even though systematic long-term clinical studies of the efficacy of existing protease inhibitors on non-B HIV-1 subtypes are not yet available, recent studies have pointed out to the existence of polymorphisms associated with drug resistance (8,26). At the protease level the studies presented here support those observations.…”

“…1B). For the subtype A protease our sequence was derived from the consensus sequence of subtype A protease from 14 antiretroviral naïve Ugandan adults (7,8). This sequence differs from the subtype B consensus sequence (6) at seven positions I13V͞ E35D͞M36I͞R41K͞R57K͞H69K͞L89M ( Fig.…”

“…1 A Left) and is identical to the sequences of two Ugandan isolates (nos. 225.706 and 230.706) (8). A second recombinant protease was generated based on a consensus sequence of subtype C proteases [92RW026 (Rwanda, GenBank no.…”

“…1). A significant number of amino acid polymorphisms exist among subtype A, B, and C sequences (7,8). Many of these are located in the hinge regions, residues 35, 36, 41, and 57.…”

“…It is noteworthy that some of these differences in sequence occur at sites that are known to be associated with inhibitor resistance in the B subtype (8). Position 36 is occupied by isoleucine in the A and C subtype proteases of drug-naïve patients.…”