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The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of theenv andgag genes. Information on thevpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of thevpu genes were analyzed, and the genetic subtypes determined by analysis of thevpu gene were compared with those previously determined by analysis of thegag andenv genes. Thevpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR products. HIV-1 subtypes were determined by sequence alignment and phylogenetic analysis with reference strains. The strains in all except one of the samples analyzed could be classified as subtype A, B, C, E, or G. Thevpu subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of theenv orgag gene. The genetic subtypes determined byvpu gene analysis were, in general, consistent with those determined bygag and/orenv gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in thevpu phylogenetic analyses were subtype E byenv gene analysis and subtype A bygag gene analysis. In summary, our genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan. While subtype E strains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission. Genetic analysis ofvpu may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.

Determination of Human Immunodeficiency Virus Type 1 Subtypes in Taiwan by vpu Gene Analysis