title: Detection of HIV-1-specific CTL responses in Clade B infection with Clade C Peptides and not Clade B consensus peptides.
abstract: The variability of HIV-1 sequences within and between persons in vivo complicates immunologic screening with a fixed sequence, and using peptides based on consensus sequences therefore has become a common practice for pathogenesis and vaccine studies. Here, we screen a cohort of HIV-1-infected persons in the United States for CD8+ T lymphocyte (CTL) responses using Gag peptides based on the Clade C primary isolate DU422 and the consensus sequence for Clade B. Surprisingly, the DU422 and Clade B consensus peptides are similar in sensitivity, but many responses are detected only by one set or the other. About equal numbers of discordantly detected responses are specific to consensus Clade B peptides as DU422 peptides. A minority of discordant detection is due to the varying frames of the peptide sets and therefore a technical artifact; the majority is due to sequence differences. This lack of superiority of the Clade B consensus peptides to detect CD8+ T lymphocyte responses is an unexpected finding that suggests that detection of HIV-1-specific cellular immunity with these peptides may be significantly insensitive and raises questions as to whether screening with a single sequence adequately reflects responses to the viral swarm in vivo.
authors.affiliation: Department of Medicine, Geffen School of Medicine, UCLA Medical Center, University of California, Los Angeles 90095, USA.
authors.forename: Rachel Lubong
authors.initials: RL
authors.lastname: Sabado
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kilpatrick
authors.forename: Ayub
authors.initials: A
authors.lastname: Ali
authors.forename: Mirabelle
authors.initials: M
authors.lastname: Dagarag
authors.forename: Hwee L
authors.initials: HL
authors.lastname: Ng
authors.forename: Huyen
authors.initials: H
authors.lastname: Cao
authors.forename: Otto O
authors.initials: OO
authors.lastname: Yang
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D015331:Cohort Studies; D016384:Consensus Sequence; D005260:Female; D015683:Gene Products, gag / Q000276:immunology*; D015658:HIV Infections / Q000276:immunology*; D015497:HIV-1 / Q000276:immunology*; D006801:Humans; D016056:Immunodominant Epitopes / Q000276:immunology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010455:Peptides / Q000276:immunology*; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*
chemical_list: D015683:Gene Products, gag; D016056:Immunodominant Epitopes; D010455:Peptides