title: Enhanced detection of viral diversity using partial and near full-length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil.
abstract: BACKGROUND
  Here, we report application of high-throughput near full-length genome (NFLG) and partial human immunodeficiency virus Type 1 (HIV-1) proviral genome deep sequencing to characterize HIV in recently infected blood donors at four major blood centers in Brazil.
  
  
  METHODS
  From 2007 to 2011, a total of 341 HIV+ blood donors from four blood centers were recruited to participate in a case-control study to identify HIV risk factors and motivations to donate. Forty-seven (17 from São Paulo, eight from Minas Gerais, 11 from Pernambuco, and 11 from Rio de Janeiro) were classified as recently infected based on testing by less-sensitive enzyme immunoassays. Five overlapping amplicons spanning the HIV genome were polymerase chain reaction amplified from peripheral blood mononuclear cells. The amplicons were molecularly barcoded, pooled, and sequenced by a paired-end protocol (Illumina).
  
  
  RESULTS
  Of the 47 recently infected donor samples studied, 39 (82.9%) NFLGs and six (12.7%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Subtype B was the only nonrecombinant virus identified in this study and accounted for 62.2% (28/45) of samples. The remaining 37.8% (17/45) of samples showed various patterns of subtype discordance in different regions of HIV-1 genomes, indicating two to four circulating recombinant subtypes derived from Clades B, F, and C. Fourteen samples (31.1%) from this study harbored drug resistance mutations, indicating higher rate of drug resistance among Brazilian blood donors.
  
  
  CONCLUSIONS
  Our findings revealed a high proportion of HIV-1 recombinants among recently infected blood donors in Brazil, which has implications for future blood screening, diagnosis, therapy, and vaccine development.
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Pessôa
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Jaqueline Tomoko
authors.initials: JT
authors.lastname: Watanabe
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Paula
authors.initials: P
authors.lastname: Calabria
authors.affiliation: Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Cecilia Salete
authors.initials: CS
authors.lastname: Alencar
authors.affiliation: Pernambuco State Center of Hematology and Hemotherapy-HEMOPE, Recife, Pernambuco, Brazil.
authors.forename: Paula
authors.initials: P
authors.lastname: Loureiro
authors.affiliation: Hemorio, Rio de Janeiro, Brazil.
authors.forename: Maria Esther
authors.initials: ME
authors.lastname: Lopes
authors.affiliation: Minas Gerais State Center of Hematology and Hemotherapy-HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Anna Barbara
authors.initials: AB
authors.lastname: Proetti
authors.affiliation: Department of Virology, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Alvina Clara
authors.initials: AC
authors.lastname: Félix
authors.affiliation: Department of Infectious Disease/Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Ester C
authors.initials: EC
authors.lastname: Sabino
authors.affiliation: Blood Systems Research Institute, San Francisco, California.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Busch
authors.affiliation: Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Sabri S
authors.initials: SS
authors.lastname: Sanabani
mesh_terms: D001782:Blood Donors / Q000706:statistics & numerical data; D001938:Brazil; D016679:Genome, Viral / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007124:Immunoenzyme Techniques; D008969:Molecular Sequence Data