Molecular Characterisation and HIV Drug Resistance Patterns of HIV-1 Variants in Plasma and Peripheral Blood Mononuclear Cells Sample Pairs

Abstract

Objective: Plasma is currently the specimen of choice for routine HIV drug resistance (HIVDR) testing. However, HIV compartmentalization has been well documented in different reservoirs, including peripheral blood mononuclear cells (PBMCs). We molecularly characterized paired plasma and PBMC sample pairs and compared their HIVDR mutation patterns. Methods: To compare HIVDR mutation patterns in plasma and PBMC sample pairs, whole blood was collected for plasma and PBMC isolation from 43 treatment-naive and 10 treatment-experienced individuals, and HIVDR profiles determined by sequencing the pol gene. Treatment-naive individuals were initiated on Efavirenz/Emtricitabine/ Tenofovir fixed dose combination therapy and follow up HIV-1 viral loads were performed after at least 6 months of treatment. Results: HIVDR mutation prevalence in the treatment-naive group was 5.1% in plasma samples compared to 10.3% when both plasma and PBMC sequences were considered. Variable amino acid positions were detected in 21% and 12% of the protease and reverse transcriptase genes, respectively. These were generally not in HIVDR positions and did not form signature patterns. The subset of patients with additional resistance associated sequence variations detected in PBMCs had undetectable HIV-1 viral loads after at least 6 months of anti-retroviral therapy. Conclusions: The sequencing of paired plasma and PBMC specimens provided additional HIVDR data which were not detected when only plasma samples were tested. However the resistant variants detected in the PBMCs did not seem to negatively affect treatment outcome at 6 months as viral suppression was achieved. These data highlight proviral HIVDR mutations in HIV infected individuals and longer follow up on patients on treatment may be needed to determine their clinical impact.