Conserved domains of subtype C nef from South African HIV type 1-infected individuals include cytotoxic T lymphocyte epitope-rich regions

AIDS Res Hum Retroviruses. 2001 Nov 20;17(17):1681-7. doi: 10.1089/088922201753342103.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Conserved Sequence*
  • Epitopes, T-Lymphocyte / genetics*
  • Epitopes, T-Lymphocyte / immunology
  • Gene Products, nef / chemistry
  • Gene Products, nef / genetics*
  • Gene Products, nef / immunology
  • HIV Infections / virology
  • HIV-1 / classification*
  • HIV-1 / genetics
  • Molecular Sequence Data
  • Sequence Alignment
  • Sequence Analysis, DNA
  • South Africa
  • T-Lymphocytes, Cytotoxic / immunology*
  • nef Gene Products, Human Immunodeficiency Virus

Substances

  • Epitopes, T-Lymphocyte
  • Gene Products, nef
  • nef Gene Products, Human Immunodeficiency Virus