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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.)

Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors

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Author(s):
Pessoa, Rodrigo [1] ; Loureiro, Paula [2] ; Lopes, Maria Esther [3] ; Carneiro-Proietti, Anna B. F. [4] ; Sabino, Ester C. [5] ; Busch, Michael P. [6] ; Sanabani, Sabri S. [1]
Total Authors: 7
Affiliation:
[1] Univ Sao Paulo, Sch Med, Clin Lab, Dept Pathol, LIM 03, HC, Sao Paulo - Brazil
[2] Pernambuco State Ctr Hematol & Hemotherapy HEMOPE, Recife, PE - Brazil
[3] Hemorio, Rio De Janeiro - Brazil
[4] Minas Gerais State Ctr Hematol & Hemotherapy HEMO, Belo Horizonte, MG - Brazil
[5] Univ Sao Paulo, Inst Trop Med, Dept Infect Dis, Sao Paulo - Brazil
[6] Blood Syst Res Inst, San Francisco, CA - USA
Total Affiliations: 6
Document type: Journal article
Source: PLoS One; v. 11, n. 3 MAR 31 2016.
Web of Science Citations: 13
Abstract

Background Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (Sao Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70). Materials and Methods A total of 259 blood samples were obtained from 195 donors with long-standing infections and 64 donors with a lack of stage information. DNA was extracted from the peripheral blood mononuclear cells (PBMCs) to amplify the HIV-1 NFLGs from five overlapping fragments. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. Results Of the 259 samples studied, 208 (80%) NFLGs and 49 (18.8%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Of these 257 samples, 183 (71.2%) were pure subtypes consisting of clade B (n = 167, 65%), C (n = 10, 3.9%), F1 (n = 4, 1.5%), and D (n = 2, 0.7%). Recombinant viruses were detected in 74 (28.8%) samples and consist of unique BF1 (n = 41, 15.9%), BC (n = 7, 2.7%), BCF1 (n = 4, 1.5%), CF1 and CDK (n = 1, 0.4%, each), CRF70\_BF1 (n = 4, 1.5%), CRF71\_BF1 (n = 12, 4.7%), and CRF72\_BF1 (n = 4, 1.5%). Evidence of dual infection was detected in four patients coinfected with the same subtype (n = 3) and distinct subtype (n = 1). Conclusion Based on this work, subtype B appears to be the prevalent subtype followed by a high proportion of intersubtype recombinants that appeared to be arising continually in this country. Our study represents the largest analysis of the viral NFLG ever undertaken worldwide and provides insights into the understanding the genesis of the HIV-1 epidemic in this particular area of South America and informs vaccine design and clinical trials. (AU)

FAPESP's process: 14/24596-2 - HIV massively parallel sequencing data in plasma and peripheral blood mononuclear cells from untreated blood donors: comparison of the near full-length genome subtypes, drug resistance mutations and co-receptor usage
Grantee:Rodrigo Pessoa de Farias
Support type: Scholarships in Brazil - Doctorate
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
FAPESP's process: 11/11090-5 - Complete genomes for HIV: viral genetic diversity among seropositive first-time blood donors in four blood centres in Brazil
Grantee:Sabri Saeed Mohamed Ahmed Al-Sanabani
Support type: Regular Research Grants