Multiple T-cell epitopes overlap positively-selected residues in the pi spacer protein of HIV-1 gag

Objectives: The p1 region of HIV-1 gag contains the frameshift stem-loop, gag-pol transframe and a protease cleavage site that are crucial for viral assembly, replication and infectivity. Identifying and characterizing CD8+ epitopes that are under host immune selection in this region will help in designing effective vaccines for HIV-1. Design: An approach combining bioinformatical analysis and interferon gamma enzyme-linked immunosorbent spot (ELISPOT) assays is used to identify and characterize the epitopes. Potential human leukocyte antigen (HLA)-restricted epitopes were identified by correlating the positively-selected mutations with host HLA alleles. Methods: ELISPOT analysis with overlapping peptides was used to confirm and characterize the epitopes. Results: Four positively-selected residues were significantly associated with HLA class I alleles, including HLA B*1302 (K4R, P = 0.0008 and I5L, P = 0.0108), A*7401 (S9N, P = 0.0002) and A*30 genotypes (P7S, P = 0.009), suggesting epitopes restricted by these alleles are present in this region. ELISPOT analysis with patient peripheral blood mononuclear cells (PBMCs) identified seven novel epitopes restricted by the 3 alleles. Two types of epitopes were observed in this region based on the ELISPOT responses, Type I: the positively-selected variation does not affect CD8+ T-cell responses;and Type II: the CD8+ T-cell responses are determined by the epitope variants. Conclusion: We identified and characterized seven novel CD8+ epitopes in the p1 spacer protein region. Classifying the effects of positively-selected variants on CD8+ T-cell responses will help in designing effective vaccines for HIV-1. © 2009 Wolters Kluwer Health | Lippincott Williams & Wilkins.