Mapping the molecular characteristics of Brazilian human T-cell lymphotropic virus type 1 Env (gp46) and Pol amino acid sequences for vaccine design

this study was carried out to evaluate the molecular pattern of all available brazilian human t-cell lymphotropic virus type 1 env (n = 15) and pol (n = 43) nucleotide sequences via epitope prediction, physico-chemical analysis, and protein potential sites identification, giving support to the brazilian aids vaccine program. in 12 previously described peptides of the env sequences we found 12 epitopes, while in 4 peptides of the pol sequences we found 4 epitopes. the total variation on the amino acid composition was 9 and 17% for human leukocyte antigen (hla) class i and class ii env epitopes, respectively. after analyzing the pol sequences, results revealed a total amino acid variation of 0.75% for hla-i and hla-ii epitopes. in 5 of the 12 env epitopes the physico-chemical analysis demonstrated that the mutations magnified the antigenicity profile. the potential protein domain analysis of env sequences showed the loss of a ck-2 phosphorylation site caused by d197n mutation in one epitope, and a n-glycosylation site caused by s246y and v247i mutations in another epitope. besides, the analysis of selection pressure have found 8 positive selected sites (w = 9.59) using the codon-based substitution models and maximum-likelihood methods. these studies underscore the importance of this env region for the virus fitness, for the host immune response and, therefore, for the development of vaccine candidates.