Unknown,Transcriptomics,Genomics,Proteomics

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DNA-seq or genomic RNA region of HIV-1 reverse transcriptase, protease and integrase gene

ABSTRACT: To assess compatibility in sequence analysis we compared results from Sanger sequencing (with sequencing threshold >15%) and Next Generation Sequencing (with sequencing treshold >5%). Totally, there were 60 patients included in this part of the study. Here we demonstrate how reliable tool for fast and accurate identification of low-level viral quasispecies is deep-sequencing.

INSTRUMENT(S): Illumina MiniSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Ana Planinić

PROVIDER: E-MTAB-13563 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We assessed correlates of protection from disease progression in a rare subset of HIV-infected individuals, viremic non-progressors (VNPs). These individuals have high viral load for several years, but in contrast to the majority of infected individuals, they do not progress to AIDS. Here we found this lack of progression was associated with selective preservation of two essential subsets of memory CD4+ T cells, central memory (TCM) and stem-cell memory (TSCM) cells. Compared to HIV-infected putative progressors, VNPs had higher proliferation of these indispensable subsets of memory cells, which was associated with the number of TCM. In addition, the long-lived CD4+ TCM and TSCM cells in VNPs had decreased HIV infection compared to the less critical effector memory CD4+ T cells, which indicates a possible mechanism by which VNPs maintain their CD4+ T cell pool after several years of infection, and remain free from AIDS progression. 6 HIV-infected patients fitting the clinical criteria of Viremic Non-Progressors were identified. VNPs were defined as having confirmed HIV-1 infection for at least 9 years with sustained plasma HIV RNA levels >10,000 copies/ml and maintenance of peripheral blood CD4+ T cell counts >500 cells/mm3 and a CD4% (of all lymphocytes) >15%. As controls, 7 HIV-infected Putative Progressors were identified. PPs were defined as having plasma HIV RNA levels >10,000 copies/mL, CD4+ T cell counts >400 cells/mm3 and having been initially infected with HIV 2-24 months prior to the index visit. The estimated date of initial HIV infection was calculated according to published algorithms that incorporate âde-tunedâ anti-HIV-1 antibody ELISA results or by a documented sero-conversion window of <6 months. All participants were required to be antiretroviral therapy (ART)-naÃ¯ve. RNA from 6 VNP and 7 PPs was purified from PAXgene whole blood tubes and hybridized to Affymetrix U133 Plus 2.0 arrays. During data analysis, one VNP patient (PID 4015) was determined to be an outlier and removed from further analysis. Thus, 5 VNPs and 7 PPs are represented in this Series.

Dataset Information

DNA-seq or genomic RNA region of HIV-1 reverse transcriptase, protease and integrase gene

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