title: Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies.
abstract: The analysis of genetic data for human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1) is essential to improve treatment and public health strategies as well as to select strains for vaccine programs. However, the analysis of large quantities of genetic data requires collaborative efforts in bioinformatics, computer biology, molecular biology, evolution, and medical science. The objective of this study was to review and improve the molecular epidemiology of HIV-1 and HTLV-1 viruses isolated in Brazil using bioinformatic tools available in the Laboratório Avançado de Sáude Pública (Lasp) bioinformatics unit. The analysis of HIV-1 isolates confirmed a heterogeneous distribution of the viral genotypes circulating in the country. The Brazilian HIV-1 epidemic is characterized by the presence of multiple subtypes (B, F1, C) and B/F1 recombinant virus while, on the other hand, most of the HTLV-1 sequences were classified as Transcontinental subgroup of the Cosmopolitan subtype. Despite the high variation among HIV-1 subtypes, protein glycosylation and phosphorylation domains were conserved in the pol, gag, and env genes of the Brazilian HIV-1 strains suggesting constraints in the HIV-1 evolution process. As expected, the functional protein sites were highly conservative in the HTLV-1 env gene sequences. Furthermore, the presence of these functional sites in HIV-1 and HTLV-1 strains could help in the development of vaccines that pre-empt the viral escape process.
authors.affiliation: Laboratório Avançado de Saúde Pública, Centro de Pesquisa Gonçalo Moniz-Fiocruz, Salvador, BA, Brasil.
authors.forename: Artur Trancoso Lopo
authors.initials: AT
authors.lastname: de Queiroz
authors.forename: Aline Cristina Andrade
authors.initials: AC
authors.lastname: Mota-Miranda
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
authors.forename: Domingos Ramon
authors.initials: DR
authors.lastname: Moreau
authors.forename: Caroline de Carvalho
authors.initials: Cde C
authors.lastname: Urpia
authors.forename: Chandra Mara
authors.initials: CM
authors.lastname: Carvalho
authors.forename: Bernardo
authors.initials: B
authors.lastname: Galvão-Castro
authors.forename: Luiz Carlos Junior
authors.initials: LC
authors.lastname: Alcantara
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001938:Brazil; D019295:Computational Biology; D005838:Genotype; D006031:Glycosylation; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D015368:Human T-lymphotropic virus 1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010766:Phosphorylation