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 toRecent advances have led to an unprecedented increase in sequence data for human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1). For example, the number of HIV-1 sequences in GenBank had increased from approximately 42,000 in September 2000 (Gaschen et al. 2001) to nearly 115,000 sequences on September 2004. These sequences are also a valuable source of data for genetic analyses, such as the HIV-1 drug resistance study in which mutations into protease and reverse transcriptase genes can be used to better manage antiretroviral treatment (Shafer et al. 2000). Vaccine initiatives use sequences from the immunodominant regions of the viruses to design artificial peptides that stimulate the immune system and control the viral replication (Addo et al. 2001). Other research projects are evaluating whether the HTLV-1 envelope protein immunodominant region could elicit neutralizing antibody responses against HTLV-1. Such information could be used in the development of vaccines and to improve diagnostic methods (Sundaram et al. 2004).The post-translational modifications in the virus proteins are essential for HIV-1 and HTLV-1 fitness, assembly, and immune escape. The most frequent modifications are N-glycosilation, N-myristylation, and phosphorylation by protein kinases (Adachi et al. 1992, Reitter et al. 1998, Ono et al. 2000, Bouamir et al. 2003, Grassmann et al. 2005 The HIV-1 epidemic in Brazil was initially dominated by HIV-1 subtype B ) and the virus spread to all the states in the country through different transmission routes. HIV-1 subtype F1 was first identified in Salvador and recombinants of subtypes B and F1 were identified in Rio de Janeiro . A more recent heterosexual epidemic, characterized by the presence of subtype C viruses, was identified in South Brazil , Soares et al. 2003. Other reports have also demonstrated that distinct HIV-1 subtypes (A, B, C, D, F1) and recombinant forms (B/C, B/ F1) are actively participating in the Brazilian Aids epidemic (Morgado et al. 1998, Caride et al. 2001, Soares et al. 2005, Couto-Fernandez et al. 2005, Barreto et al. 2006, De Sa Filho et al. 2006).Financial support: Fapesp, PN-DST/AIDS +Corresponding author: lalcan@cpqgm.fiocruz.br ATLQ and ACAM-M contribute equally to this paper.

Phylogenetic and molecular analysis of HTLV‐1 isolates from a medium sized town in Northern of Brazil: Tracing a common origin of the virus from the most endemic city in the country

“…The average inter-sequence diversity into LTR sequences from Cruz das Almas was of the 0.8% while among these sequences and the Salvador sequences it was 1%. In addition, as previously demonstrated, the average inter-sequence diversity within LTR sequences from Salvador was 1.1% [de Queiroz et al, 2007]. The bootstrap values (>50% and using 1000 bootstrap samples) on the branches represent the percentage of trees for which the sequences located at the right end of the branch form a monophyletic group.…”

Prevalência de subtipos do HIV-1 em amostra de pacientes de um centro urbano no sul do Brasil

“…18 No Brasil, estudos indicam que o subtipo B é o mais prevalente na maioria das regiões geográfi cas, seguido pelos subtipos F e C, com poucos casos identifi cados dos subtipos D e A. 4,6 Entretanto, a região Sul do País tem se caracterizado pela maior freqüência do subtipo C, principalmente no estado do Rio Grande do Sul (RS). …”

HTLV‐1 infection in blood donors from the Western Brazilian Amazon region: Seroprevalence and molecular study of viral isolates

“…Otherwise, two different posttranslational modifications were identified into the gp21 protein: one N-myristylation site at 7-18aa and one PKC phosphorylation site at 22-24a. The potential protein sites described for these three new env sequences are the same sites that have been described previously [Queiroz et al, 2007] for all Brazilian env gene sequences submitted previously to GenBank. These confirm the conservative pattern of these proteins and their importance to the virus.…”