title: High degree of inter-clade cross-reactivity of HIV-1-specific T cell responses at the single peptide level.
abstract: OBJECTIVE
  To determine HIV-1-specific T cell responses in clade B infected individuals recognizing the clade A, B and C consensus sequences in order to assess the degree of inter-clade cross-reactivity of these immune responses at the single epitope level.
  
  
  METHODS
  HIV-1-specific T cell responses were assessed cross-sectionally in 27 chronically HIV-1-infected individuals from a population infected mainly with clade B viral strains, using an interferon-gamma Elispot assay with a total of 1230 overlapping peptides spanning the entire amino acid sequence of the clade A, B and C 2001 consensus sequences.
  
  
  RESULTS
  No significant difference was observed between the total magnitude or breadth of T cell responses recognizing either the clade A, B or C consensus sequences. However, at the single peptide level, 194 T cell responses were identified that recognized only one of the three different clade-specific peptide variants (A: B: C, 34: 105: 55), 125 T cell responses recognized two of the three peptide variants (AB: AC: BC, 71: 15: 39) and 166 T cell responses (34%) were cross-reactive with all three different peptide variants. Peptides recognized in all three consensus sequence variants had a significantly lower entropy (P < 0.0001) and a significantly higher inter-clade homology (P < 0.0001).
  
  
  CONCLUSIONS
  Viral epitopes within regions of low HIV-1 clade B diversity and high inter-clade homology can be recognized in the clade A, B and C variants and indicate a wide degree of cross-isolate and cross-clade recognition by HIV-1-specific T cells. These regions may therefore be of particular relevance for the design of HIV-1 vaccines.
authors.affiliation: Partners AIDS Research Center and Infectious Disease Division, Massachusetts General Hospital, 149 13th Street, Boston, MA 02129, USA. xyu@partners.org
authors.forename: Xu G
authors.initials: XG
authors.lastname: Yu
authors.forename: Mathias
authors.initials: M
authors.lastname: Lichterfeld
authors.forename: Beth
authors.initials: B
authors.lastname: Perkins
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kalife
authors.forename: Stanley
authors.initials: S
authors.lastname: Mui
authors.forename: Jianping
authors.initials: J
authors.lastname: Chen
authors.forename: Michael
authors.initials: M
authors.lastname: Cheng
authors.forename: Wenzhen
authors.initials: W
authors.lastname: Kang
authors.forename: Galit
authors.initials: G
authors.lastname: Alter
authors.forename: Christian
authors.initials: C
authors.lastname: Brander
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Walker
authors.forename: Marcus
authors.initials: M
authors.lastname: Altfeld
mesh_terms: D000328:Adult; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology*; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D016384:Consensus Sequence / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000276:immunology; D015658:HIV Infections / Q000276:immunology*; D015497:HIV-1 / Q000276:immunology*; D006801:Humans; D007111:Immunity, Cellular; D008875:Middle Aged
chemical_list: D018984:Epitopes, T-Lymphocyte