title: Genetic characterization of HIV before widespread testing of HIV vaccine candidates at a clinical trial site in Pretoria, South Africa.
abstract: We studied 123 samples from adult chronic HIV patients initiating HAART from various centers around a newly established clinical trial site in Pretoria. Each sample was sequenced in at least one structural gene (pol, gag, and env) or functional gene (vif, vpr, and vpu). A subset of 25 samples was subjected to near full-genome analysis. All samples were HIV-1 subtype C. Highly conserved regions within the gene sequences were observed. Overall, the gag and vif sequences showed closer similarity followed by the env, vpr, pol, and vpu. The env gene was the most difficult to sequence, resulting in only 31 sequences from 40 samples; of these, 25 were predicted to be R5 coreceptor tropic, while 6 were X4 tropic. The study asserted the predominance of HIV-1 subtype C within the catchment population.
authors: HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa.
authors: Andrew
authors: A
authors: Musyoki
authors: Khutso
authors: K
authors: Mothapo
authors: Johnny
authors: J
authors: Rakgole
authors: Azwidowi
authors: A
authors: Lukhwareni
authors: Pascal
authors: P
authors: Bessong
authors: Gloria
authors: G
authors: Selabe
authors: Helba
authors: H
authors: Bredell
authors: Carolyn
authors: C
authors: Williamson
authors: M Jeffrey
authors: MJ
authors: Mphahlele
mesh_terms: D016915:AIDS Vaccines; D000163:Acquired Immunodeficiency Syndrome / Q000188:drug therapy / Q000453:epidemiology* / Q000517:prevention & control; D000595:Amino Acid Sequence; D023241:Antiretroviral Therapy, Highly Active; D005260:Female; D005784:Gene Amplification; D015752:Genes, env / Q000235:genetics*; D015750:Genes, gag / Q000235:genetics*; D015751:Genes, pol / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D054298:Human Immunodeficiency Virus Proteins / Q000235:genetics; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013019:South Africa / Q000453:epidemiology; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics; D054320:vif Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054325:vpr Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D000086082:Viroporin Proteins
chemical_list: D016915:AIDS Vaccines; D054298:Human Immunodeficiency Virus Proteins; D054334:Viral Regulatory and Accessory Proteins; D054320:vif Gene Products, Human Immunodeficiency Virus; D054325:vpr Gene Products, Human Immunodeficiency Virus; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins