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

Abstract

HIV-1 virus is known to exhibit tremendous genetic variation. Even within a single subject, the virus exists as a swarm of highly related but genetically diverse variants. Although much of these variations are derived from mutations introduced by the error prone reverse transcriptase, viral recombination contributes significantly to genetic evolution as well. In clinical practice, the viral genotypic and tropism features are commonly defined on plasma RNA as representative of the viral population by standard bulk-sequencing but this assay may not detect minority variants. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. It is obvious that retrieving HIV drug resistance mutations (DRMs) and defining coreceptor usage in sequences from cell-associated viruses may be easier and less expensive than in plasma RNA viruses, but their clinical significance in proviral DNA is still not clear. As a result, comparative studies of plasma and PBMC viral population are needed to address this potential shift in sample type selection. In our last study, we were able to generate the MPS of HIV-1 proviral near-full length genomes (NFLG) from 270 blood donors' samples. In the current project, we aimed to further explore our last findings by generating HIV-1 NFLG MPS data from 70 plasma samples of the last group and compare the plasma viral population against the PBMC population in terms of viral genetic diversities, drug resistance mutations and coreceptor usage. To this end, viral RNA will be extracted and converted to double stranded DNA. Consequently, the dsDNA will directly be fragmented, molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol (detailed information and pilot results are enclosed in the project). Results from this study are expected to enhance our standing of the HIV-1 evolution within hosts and address whether PBMC and plasma hosted drastically different viral variants and what the implications of these variants in predict treatment outcomes and coreceptor usage. (AU)