Determination of human immunodeficiency virus type 1 subtypes in Taiwan byvpu gene analysis

The genetic diversity of human immunodeficiency virus (HIV) type I (HIV-1) has been characterized mainly by analysis of the env and gag genes. Informa tion on the vpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpu genes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. The vpu genes were amplified by nested PCR of proviral DNA extracted front 363 HIV-1-infected individuals and were sequenced directly by use of the PCR pr oducts. HIV-1 subtypes mere determined by sequence alignment and phylogenet ic analysis with reference strains. The strains in all except one of the sa mples analyzed could be classified as subtype A, B, C, E, or C, The vpu sub type of one strain could not be determined. Of the strains analyzed, geneti c subtypes of 247 (68.0%) were also determined by analysis of the env or ga g gene. The genetic subtypes determined by vpu gene analysis were, In gener al, consistent with those determined by gag and/or env gene analysis except for those for two AG recombinant strains. All the strains that clustered w ith a Thailand subtype E strain in the Ipn phylogenetic analyses were subty pe E by env gene analysis and subtype A by gag gene analysis. In summary, o ur genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan, While subtype E str ains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission, Gene tic analysis of vpu may provide an alternate method for determination of HI V-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.