Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: Classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population

Phylogenetic analysis of the reverse transcriptase (RT) and protease of 117 published complete human immunodeficiency virus (HIV) type 1 genome sequen ces demonstrated that these genes cluster into distinct subtypes. There was a slightly higher proportion of informative sites in the RT (40.4%) than i n the protease (34.8%; P = .03). Although most variation between subtypes w as due to synonymous nucleotide substitutions, several subtype-specific ami no acid patterns were observed. In the protease, the subtype-specific varia nts included 7 positions associated with drug resistance. Variants at posit ions 10, 20, 36, and 82 were more common in non-B isolates, whereas variant s at positions 63, 77, and 93 were more common in subtype B isolates. In th e RT, the subtype-specific mutations did not include positions associated w ith anti-retroviral drug resistance. RT and protease sequences from 2246 HI V-infected persons in northern California were also examined: 99.4% of the sequences clustered with subtype B, whereas 0.6% clustered with subtype A, C, or D.