POL GENE DIVERSITY OF 5 HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 SUBTYPES - EVIDENCE FOR NATURALLY-OCCURRING MUTATIONS THAT CONTRIBUTE TO DRUG-RESISTANCE, LIMITED RECOMBINATION PATTERNS, AND COMMON ANCESTRY FOR SUBTYPE-B AND SUBTYPE-D

Naturally occurring mutations in the polymerase gene of human immunode ficiency virus type 1 (HIV-1) have important implications for therapy and the outcome of clinical studies, Using 42 virus isolates obtained from the UNAIDS sample collection, we analyzed the protease (99 amino acids [aa]) and the first 297 aa of reverse transcriptase (RT) coding regions, Based on the V3 sequence analysis, the collection includes su btype A (n = 5), subtype B (n = 12), subtype C (n = 1), subtype D (n = 11), and subtype E (n = 13) viruses, Of the 42 protease genes, 37 con tained naturally occurring mutations at positions in the gene that con tribute to resistance to protease inhibitors (indinavir, saquinavir, r itonavir, and nelfinavir) in clade B isolates, The phenotypic effect o f these substitutions in non-B isolates is unclear, The 5'half RT codi ng region of the 42 isolates was found to be less variable, although 1 9 of the 42 RT sequences contained amino acid substitutions known to c ontribute to nucleoside and/or nonnucleoside drug resistance, Since th e virus isolates were obtained in 1992, it is unlikely that the infect ed subjects received protease inhibitors, but we found evidence that o ne subject acquired a zidovudine (AZT)-resistant HIV-1 strain from a c ontact who had received AZT. Phylogenetic analysis identified five sub type pol clusters: A, B, C, D, and A', Comparison of env and pol seque nces of the same viruses showed no more recombination events than were already identified on the basis of gag/env comparison (M, Cornelissen , G, Kampinga, F, Zorgdrager, J, Goudsmit, and the UNAIDS Network for HIV Isolation and Characterization, J, Virol, 70:8209-8212, 1996), In one of the known recombinants, a crossover site between subtypes A and C could be identified, and in another, a crossover site could not be identified due to lack of a reference subtype F pol sequence, We analy zed the ds/da ratio of gag, pol, and rnv sequences of 35 isolates, exc luding the recombinants, Our analysis showed that gag and pol are subj ected to purifying selection with an average ds/da ratio above 1, inde pendent of the subtype and in contrast with V3 (ds/da approximate to 1 ), Based on the low ds/da ratio of the intergroup analysis of A/E and B/D gag and pol sequences, we analyzed the evolutionary relation betwe en subtypes B and D in more detail by constructing separate phylogenet ic trees for synonymous and nonsynonymous substitutions, Our analysis suggests a common ancestry for subtypes B and D that is distinct from that of subtypes A and E.