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

• Main Authors: Aline Cristina Mota-Miranda, Tulio de-Oliveira, Domingos Ramon Moreau, Catarina Bomfim, Bernardo Galvão-Castro, Luiz Carlos Junior Alcantara
• Format: Article
• Language: English
• Published: Instituto Oswaldo Cruz, Ministério da Saúde 2007-09-01
• Series: Memórias do Instituto Oswaldo Cruz.
• Subjects: human T-cell lymphotropic virus type 1; Env; Pol; epitope
• Online Access: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762007000600014
• ISSN: 0074-0276; 1678-8060

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.