title: CTL epitope distribution patterns in the Gag and Nef proteins of HIV-1 from subtype A infected subjects in Kenya: use of multiple peptide sets increases the detectable breadth of the CTL response.
abstract: BACKGROUND
  Subtype A is a major strain in the HIV-1 pandemic in eastern Europe, central Asia and in certain regions of east Africa, notably in rural Kenya. While considerable effort has been focused upon mapping and defining immunodominant CTL epitopes in HIV-1 subtype B and subtype C infections, few epitope mapping studies have focused upon subtype A.
  
  
  RESULTS
  We have used the IFN-gamma ELIspot assay and overlapping peptide pools to show that the pattern of CTL recognition of the Gag and Nef proteins in subtype A infection is similar to that seen in subtypes B and C. The p17 and p24 proteins of Gag and the central conserved region of Nef were targeted by CTL from HIV-1-infected Kenyans. Several epitope/HLA associations commonly seen in subtype B and C infection were also observed in subtype A infections. Notably, an immunodominant HLA-C restricted epitope (Gag 296-304; YL9) was observed, with 8/9 HLA-CW0304 subjects responding to this epitope. Screening the cohort with peptide sets representing subtypes A, C and D (the three most prevalent HIV-1 subtypes in east Africa), revealed that peptide sets based upon an homologous subtype (either isolate or consensus) only marginally improved the capacity to detect CTL responses. While the different peptide sets detected a similar number of responses (particularly in the Gag protein), each set was capable of detecting unique responses not identified with the other peptide sets.
  
  
  CONCLUSIONS
  Hence, screening with multiple peptide sets representing different sequences, and by extension different epitope variants, can increase the detectable breadth of the HIV-1-specific CTL response. Interpreting the true extent of cross-reactivity may be hampered by the use of 15-mer peptides at a single concentration and a lack of knowledge of the sequence that primed any given CTL response. Therefore, reagent choice and knowledge of the exact sequences that prime CTL responses will be important factors in experimentally defining cross-reactive CTL responses and their role in HIV-1 disease pathogenesis and validating vaccines aimed at generating broadly cross-reactive CTL responses.
authors.affiliation: The US Military HIV Research Program, Rockville, MD 20850, USA. jcurrier@hivresearch.org
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Currier
authors.forename: Unchalee
authors.initials: U
authors.lastname: Visawapoka
authors.forename: Sodsai
authors.initials: S
authors.lastname: Tovanabutra
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Mason
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Birx
authors.forename: Francine E
authors.initials: FE
authors.lastname: McCutchan
authors.forename: Josephine H
authors.initials: JH
authors.lastname: Cox
mesh_terms: D001483:Base Sequence; D004797:Enzyme-Linked Immunosorbent Assay / Q000379:methods; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry / Q000276:immunology*; D015683:Gene Products, gag / Q000737:chemistry / Q000235:genetics / Q000276:immunology*; D015693:Gene Products, nef / Q000737:chemistry / Q000235:genetics / Q000276:immunology*; D015658:HIV Infections / Q000276:immunology*; D015497:HIV-1 / Q000145:classification / Q000276:immunology* / Q000302:isolation & purification; D015236:HLA-C Antigens / Q000378:metabolism; D006650:Histocompatibility Testing; D006801:Humans; D016056:Immunodominant Epitopes / Q000737:chemistry / Q000276:immunology; D007371:Interferon-gamma / Q000032:analysis; D007630:Kenya; D008969:Molecular Sequence Data; D010455:Peptides / Q000276:immunology; D017422:Sequence Analysis, DNA; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D018984:Epitopes, T-Lymphocyte; D015683:Gene Products, gag; D015693:Gene Products, nef; D015236:HLA-C Antigens; C106548:HLA-C*03:04 antigen; D016056:Immunodominant Epitopes; D010455:Peptides; D054311:nef Gene Products, Human Immunodeficiency Virus; D007371:Interferon-gamma