title: Determination of human immunodeficiency virus type 1 subtypes in Taiwan by vpu gene analysis.
abstract: The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of the env and gag genes. Information 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 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. The vpu subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of the env or gag gene. The genetic subtypes determined by vpu gene analysis were, in general, consistent with those determined by gag and/or env gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in the vpu phylogenetic analyses were subtype E by env gene analysis and subtype A by gag 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 of vpu may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.
authors.affiliation: School and Graduate Institute of Medical Technology, Taipei, Taiwan.
authors.forename: C N
authors.initials: CN
authors.lastname: Lee
authors.forename: W K
authors.initials: WK
authors.lastname: Wang
authors.forename: W S
authors.initials: WS
authors.lastname: Fan
authors.forename: S J
authors.initials: SJ
authors.lastname: Twu
authors.forename: S C
authors.initials: SC
authors.lastname: Chen
authors.forename: M C
authors.initials: MC
authors.lastname: Sheng
authors.forename: M Y
authors.initials: MY
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D005260:Female; D015752:Genes, env; D015750:Genes, gag; D016338:Genes, vpu; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D013624:Taiwan; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins