title: Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa.
abstract: HIV was first diagnosed within South Africa in 1982. Homosexual transmission of HIV-1 dominated the epidemic within the country in the early stages of the 1980s. Currently heterosexual transmission of HIV-1 is responsible for the majority of HIV cases in South Africa with subtype C HIV-1 being responsible for an estimated 95% of infections. Only a few papers have been published on non-subtype C HIV-1 detection within South Africa. This study characterized subgenomic and near full-length sequences of non-subtype C HIV-1 viruses from the Cape Town area. Amplification and direct sequencing characterized partial gene fragments of 11 samples. Phylogenetic analysis of the sequenced data, with online subtyping tools (REGA and jpHMM) and the drawing of NJ-trees revealed the presence of subtypes A1, B, and F1 as well as recombinant viral forms such as AD, AG and AC. Near full-length genome characterization of 4 of the 11 samples was performed. Analysis of sequenced data with the use of subtyping, recombination identification, and tree drawing tools revealed one subtype B and one A1 isolate. The other two isolates were identified as AC and AD recombinants. The data that was gathered will greatly improve our knowledge of non-subtype C isolates circulating within South Africa.
authors.affiliation: Division of Medical Virology, National Health Laboratory Services and University of Stellenbosch, Tygerberg 7505, South Africa.
authors.forename: Eduan
authors.initials: E
authors.lastname: Wilkinson
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
mesh_terms: D000328:Adult; D000368:Aged; D015331:Cohort Studies; D015684:Gene Products, pol / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013019:South Africa / Q000453:epidemiology; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D015684:Gene Products, pol; D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus