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Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes from recently infected blood donors at four blood centers in Brazil


Monitoring the genetic diversity of HIV-1 during the early stage of infection offers the best opportunity for understanding viral transmission dynamics and evolution of transmitted/founder viruses. Previous studies of HIV-infected donors in Brazil employing pol region sequencing have shown a predominance of subtype B (~80%) followed by F and C, with rare recombinant viruses. Here, we report application of high-throughput near-full-length (NFLG) and partial HIV-1 proviral genome deep sequencing to characterize HIV in recently infected blood donors at four major blood centers in Brazil.


From 2007-2011, 341 HIV+ blood donors from 4 blood centers were recruited to participate in a case control study to identify risk exposure and motivation to donate. Forty-seven (17 from São Paulo [SP], 8 from Minas Gerais [MG], 11 from Pernambuco [PE] and 11 from Rio de Janeiro [RJ]) were classified as recently infected based on testing by less-sensitive (LS) or "detuned" enzyme immunoassay (Vironostika HIV-1 MicroElisa; bioMérieux, Durham, NC) or an LS chemiluminescent immunoassay (Vitros HIV-1/2 Assay; Ortho Diagnostics, Rochester, NY). Five overlapping amplicons spanning the HIV genome were PCR amplified from peripheral blood mononuclear cells (PBMCs). The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol.


Of the 47 recently infected donor samples studied, 39 (82.9%) NFLGs and 6 (12.7%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Subtype B was the only non-recombinant virus characterized in this study and accounted for 60% (27/45) of samples. The remaining 40% (18/45) specimens showed various patterns of subtype discordance in different regions of HIV-1 genomes indicating 2-4 circulating recombinant subtypes derived from clades B, F and C. Over 50% of infection in MG and RJ harbor unique inter-subtype recombinant forms.


Our findings revealed a high proportion of HIV-1 recombinants among recently infected blood donors in Brazil which has implications for future diagnosis, therapy and efficient vaccine development.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

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Pessôa, R., Watanabe, J.T., Loureiro, P. et al. Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes from recently infected blood donors at four blood centers in Brazil. BMC Infect Dis 14 (Suppl 2), P58 (2014).

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