Identification of Non‐B Human Immunodeficiency Virus Type 1 Subtypes in Rural Georgia

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Abstract
As part of an ongoing molecular epidemiological investigation of human immunodeficiency virus type 1 (HIV-1) in rural Georgia, the 5′ half of reverse transcriptase (RT) genotypes from 30 patients was sequenced and phylogenetically analyzed. Two patients, GA132 and GA169, were infected with pol sequences of non—B subtype origin that were found to cluster phylogenetically with subtype A-E of Thai origin. Sliding window bootstrap analysis of GA169 showed clear evidence of A/B recombination within the pol gene segment, whereas in the other patient, GA132, no break point within RT could be identified. Interestingly, pairwise comparisons between these 2 patients' C2-V3 env region revealed a 13.5% divergence. However, similar comparisons within the non-B pol segments yielded a 1.23% nucleotide divergence, which suggests a complex phylogenetic and epidemiological history of the subtype A pol genotype in this region. These data demonstrate an increasing diversity of HIV-1 subtypes and the potential emergence of previously unidentified HIV-1 A-E/B recombinants in the rural United States.

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