HIV-1 subtyping using phylogenetic analysis of pol gene sequences

HIV-1 pol gene sequencing is now used routinely in France to identify mutat ions associated with resistance to reverse transcriptase (RT) or protease ( PR) inhibitors. These sequences may also provide other information, such as the HIV-1 subtype. HIV-I subtyping was compared using the RT and PR gene s equences to heteroduplex mobility assay (HMA) of the envelope gene. The RT and PR genes of 51 samples that had been subtyped earlier by HMA were seque nced. Sequences were aligned and subtypes were determined by phylogenetic a nalysis with reference HIV sequences. HMA gave the following subtypes: A (2 0), B (19), C (I), D (3), F (1), Ci (3) and CRF01-AE (4). Phylogenetic anal ysis of the RT gene gave: A (5), B (19), C (2), D (3), F (1), G (6), J (2), CRF01_AE (4), CFR02_AG (7) and undetermined (2). PR gene analysis did not infer subtypes with sufficient confidence. HMA and RT subtyping was not in agreement in nine cases. RT subtyping can identify CFR02_AG and CRF01_AE va riants from A subtype RT. It was shown that phylogenetic analysis of the RT gene could provide a useful method for HIV-I subtyping. The length of the amplicon and the relative performance of each primer pair used in this stud y favoured RT sequences as a subtyping tool. One potential advantage over e nv subtyping HMA is the ability to identify some circulating recombinant fo rms (CRFs). (C) 2001 Elsevier Science B.V. All rights reserved.