HIV-1 massively parallel sequencing data in plasma and peripheral blood mononuclea...
| Full text | |
| Author(s): |
Total Authors: 2
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| Affiliation: | [1] Univ Sao Paulo, Sch Med, Hosp Clin, Dept Pathol, Sao Paulo - Brazil
Total Affiliations: 1
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| Document type: | Journal article |
| Source: | DATA IN BRIEF; v. 6, p. 267-274, MAR 2016. |
| Web of Science Citations: | 0 |
| Abstract | |
The determination of viral tropism is critically important and highly recommended to guide therapy with the CCR5 antagonist, which does not inhibit the effect of X4-tropic viruses. Here, we report the prevalence of HIV-1 x 4 HIV strains in 84 proviral DNA massively parallel sequencing ``MPS{''} data from well-defined non-recently infected first-time Brazilian blood donors. The MPS data covering the entire V3 region of the env gene was extracted from our recently generated HIV-1 genomes sequenced by a paired-end protocol (Illumina). Of the 84 MPS data samples, 63 (75%) were derived from donors with long-standing infection and 21 (25%) were lacking stage information. HIV-1 tropism was inferred using Geno2pheno (g2p) ({[}454]) algorithm (FPR = 1%, 2.5%, and 3.75%). Among the 84 data samples for which tropism was defined by g2p(2.5%), 13 (15.5%) participants had detectable CXCR4-using viruses in their MPS reads. Mixed infections with R5 and X4 were observed in 11.9% of the study subjects and minority X4 viruses were detected in 7 (8.3%) of participants. Nine of the 63 (14.3%) subjects with LS infection were predicted by g2p (2.5%) to harbor proviral CXCR4-using viruses. Our findings of a high proportion of blood donors (15.5%) harboring CXCR4-using viruses in PBMCs may indicate that this phenomenon is common. These findings may have implications for clinical and therapeutic aspects and may benefit individuals who plan to receive CCR5 antagonists. (C) 2015 The Authors. Published by Elsevier Inc. (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 |