title: Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population.
abstract: Phylogenetic analysis of the reverse transcriptase (RT) and protease of 117 published complete human immunodeficiency virus (HIV) type 1 genome sequences demonstrated that these genes cluster into distinct subtypes. There was a slightly higher proportion of informative sites in the RT (40.4%) than in the protease (34.8%; P= .03). Although most variation between subtypes was due to synonymous nucleotide substitutions, several subtype-specific amino acid patterns were observed. In the protease, the subtype-specific variants included 7 positions associated with drug resistance. Variants at positions 10, 20, 36, and 82 were more common in non-B isolates, whereas variants at positions 63, 77, and 93 were more common in subtype B isolates. In the RT, the subtype-specific mutations did not include positions associated with anti-retroviral drug resistance. RT and protease sequences from 2246 HIV-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.
authors.affiliation: Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA.
authors.forename: M J
authors.initials: MJ
authors.lastname: Gonzales
authors.forename: R N
authors.initials: RN
authors.lastname: Machekano
authors.forename: R W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D000595:Amino Acid Sequence; D016679:Genome, Viral; D016333:HIV Protease / Q000235:genetics*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D009154:Mutation; D009657:North Carolina; D010802:Phylogeny; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D054303:HIV Reverse Transcriptase; D016333:HIV Protease