title: Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil.
abstract: Genetic analysis of HIV-1 is essential to improve treatment strategies and select epitopes for vaccine programs. The objective of this study was to determine whether known CD4+ and CD8+ epitopes were present in Brazilian HIV-1 strains. We used previously described CD8+ and CD4+ epitopes from the Los Alamos laboratory to search for these epitopes in the Brazilian sequences using the HIVbase program and we compared the frequency results with the analyses using physical-chemical profile tools from Network Protein Sequence Analysis (NPSA), and the SYFPEITHI program. Furthermore, this analysis was carried out with the Prosite tool using the GeneDoc program and ds/dn analyses using the Synonymous Nonsynonymous Analysis Program (SNAP). The HIVbase epitope mapping demonstrated that 30 CD8+ and 6 CD4+ epitopes were present in the Brazilian sequences at a high frequency. Only two of these epitopes were heavily glycosylated. Interestingly, ds/dn analyses showed evidence of purifying selective pressure. These types of analyses could be useful for the assessment of possible vaccine efficiency in populations.
authors.affiliation: Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil.
authors.forename: Artur Trancoso Lopo de
authors.initials: AT
authors.lastname: Queiroz
authors.forename: Luciane Amorim
authors.initials: LA
authors.lastname: Santos
authors.forename: Domingos Ramon
authors.initials: DR
authors.lastname: Moreau
authors.forename: Tulio de
authors.initials: Td
authors.lastname: Oliveira
authors.forename: David I
authors.initials: DI
authors.lastname: Watkins
authors.forename: Bernardo
authors.initials: B
authors.lastname: Galvão-Castro
authors.forename: Luiz Carlos Junior
authors.initials: LC
authors.lastname: Alcantara
mesh_terms: D001938:Brazil; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology*; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D000939:Epitopes / Q000235:genetics*; D015686:Gene Products, env / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000276:immunology; D006801:Humans
chemical_list: D000939:Epitopes; D015686:Gene Products, env