Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil.
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.
Queiroz
Artur Trancoso Lopo de
AT
Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil.
Santos
Luciane Amorim
LA
Moreau
Domingos Ramon
DR
Oliveira
Tulio de
Td
Watkins
David I
DI
Galvão-Castro
Bernardo
B
Alcantara
Luiz Carlos Junior
LC
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
D000939:Epitopes; D015686:Gene Products, env