title: HIV type 1 subtype C gag and nef diversity in Southern Africa.
abstract: Several HIV-1 subtype C-specific gag- and/or nef-based vaccines are currently intended for clinical trial in southern Africa. Here we provide sequences of 64 gag and 45 nef genes sampled in Malawi, Zambia, Zimbabwe, and South Africa and assess the degree of southern African HIV-1 diversity that will confront these vaccines. Whereas reasonable phylogenetic evidence exists for geographical clustering of subtype C gag and nef sequences from various other parts of the world, there is little evidence of similar population founder effects in the southern African epidemic. The entire breadth of subtype C diversity is represented in the southern African genes suggesting there may be no advantage in producing region- or country-specific subtype C vaccines. We do not, however, find much evidence of intersubtype recombination in the Southern African genes, implying that the likelihood of vaccine failure due to the emergence of intersubtype recombinants is probably low.
authors.affiliation: Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa. hbredell@curie.uct.ac.za
authors.forename: Helba
authors.initials: H
authors.lastname: Bredell
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.forename: Joanne
authors.initials: J
authors.lastname: Van Harmelen
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
authors.forename: Haynes W
authors.initials: HW
authors.lastname: Sheppard
authors.forename: Richard
authors.initials: R
authors.lastname: Donovan
authors.forename: Clive M
authors.initials: CM
authors.lastname: Gray
authors.forename: Carolyn
authors.initials: C
authors.lastname: Williamson
mesh_terms: D000353:Africa, Southern / Q000453:epidemiology; D015750:Genes, gag / Q000235:genetics*; D015754:Genes, nef / Q000235:genetics*; D014644:Genetic Variation; D015658:HIV Infections / Q000453:epidemiology / Q000235:genetics*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny