title: Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.
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.
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, São Paulo, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Pessôa
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, São Paulo, Brazil.
authors.forename: Jaqueline Tomoko
authors.initials: JT
authors.lastname: Watanabe
authors.affiliation: Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Youko
authors.initials: Y
authors.lastname: Nukui
authors.affiliation: Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Juliana
authors.initials: J
authors.lastname: Pereira
authors.forename: Jorge
authors.initials: J
authors.lastname: Casseb
authors.affiliation: Department of Neurology, Institute of Infectology Emilio Ribas, São Paulo, Brazil.
authors.forename: Jorge
authors.initials: J
authors.lastname: Kasseb
authors.affiliation: Department of Neurology, Institute of Infectology Emilio Ribas, São Paulo, Brazil.
authors.forename: Augusto César Penalva
authors.initials: AC
authors.lastname: de Oliveira
authors.affiliation: Department of Infectious Diseases, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Aluisio Cotrim
authors.initials: AC
authors.lastname: Segurado
authors.affiliation: Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Sabri Saeed
authors.initials: SS
authors.lastname: Sanabani
mesh_terms: D001483:Base Sequence / Q000235:genetics*; D002353:Carrier State / Q000821:virology; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D000091344:Filaggrin Proteins; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D015490:HTLV-I Infections / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D015368:Human T-lymphotropic virus 1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D015493:Paraparesis, Tropical Spastic / Q000821:virology; D010802:Phylogeny
chemical_list: D004279:DNA, Viral; C000717249:FLG protein, human; D000091344:Filaggrin Proteins