title: Conserved domains of subtype C nef from South African HIV type 1-infected individuals include cytotoxic T lymphocyte epitope-rich regions.
abstract: We have characterized 43 nef sequences from subtype C HIV-1-infected South Africans and compared deduced amino acid sequences with other subtypes to identify areas of conservation. Our Nef amino acid sequences were aligned with a consensus subtype B, HXB2 reference strain and a consensus subtype C sequence. All were found to be highly homologous to subtype B in the central region of Nef, but more variable at the N and C termini of the molecule. Alignment of a consensus amino acid sequence generated from South African subtype C Nef with subtypes A, B, and D underscores cross-clade conservation in the central domain of the molecule. This domain is also rich in previously described cytotoxic T lymphocyte (CTL) epitopes that are restricted by commonly found HLA molecules in the South African population.
authors.affiliation: AIDS Research Unit, National Institute for Virology, 2 Modderfontein Road, Sandringham 2131, Johannesburg, South Africa.
authors.forename: T
authors.initials: T
authors.lastname: Mashishi
authors.forename: S
authors.initials: S
authors.lastname: Loubser
authors.forename: W
authors.initials: W
authors.lastname: Hide
authors.forename: G
authors.initials: G
authors.lastname: Hunt
authors.forename: L
authors.initials: L
authors.lastname: Morris
authors.forename: G
authors.initials: G
authors.lastname: Ramjee
authors.forename: S
authors.initials: S
authors.lastname: Abdool-Karim
authors.forename: C
authors.initials: C
authors.lastname: Williamson
authors.forename: C M
authors.initials: CM
authors.lastname: Gray
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology; D015693:Gene Products, nef / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013019:South Africa; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D018984:Epitopes, T-Lymphocyte; D015693:Gene Products, nef; D054311:nef Gene Products, Human Immunodeficiency Virus