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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology

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Author(s):
Pessoa, Rodrigo [1] ; Watanabe, Jaqueline Tomoko [1] ; Nukui, Youko [2] ; Pereira, Juliana [2] ; Kasseb, Jorge [3] ; Penalva de Oliveira, Augusto Cesar [3] ; Segurado, Aluisio Cotrim [4] ; Sanabani, Sabri Saeed [5]
Total Authors: 8
Affiliation:
[1] Sao Paulo Inst Trop Med, Dept Virol, Sao Paulo - Brazil
[2] Univ Sao Paulo, Fac Med, Dept Hematol, Sao Paulo - Brazil
[3] Inst Infectol Emilio Ribas, Dept Neurol, Sao Paulo - Brazil
[4] Univ Sao Paulo, Fac Med, Dept Infect Dis, Sao Paulo - Brazil
[5] Univ Sao Paulo, Sch Med, Hosp Clin, Clin Lab, Dept Pathol, Sao Paulo - Brazil
Total Affiliations: 5
Document type: Journal article
Source: PLoS One; v. 9, n. 3 MAR 31 2014.
Web of Science Citations: 25
Abstract

Background: Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Methods: Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. Results: A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210-and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. Conclusions: This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the evolutionary history of this medically important virus. (AU)

FAPESP's process: 11/12297-2 - Profiling the human T-cells miRNA, REX and tax transcriptomes in the course of HTLV-1 infection using a deep sequencing approach
Grantee:Sabri Saeed Mohamed Ahmed Al-Sanabani
Support type: Regular Research Grants