Sensitive HIV-1 DNA Pol Next-Generation Sequencing for the Characterisation of Archived Antiretroviral Drug Resistance

Abstract

Modern HIV-1 treatment effectively suppresses viral amplification in people living with HIV. However, the persistence of HIV-1 DNA as proviruses integrated into the human genome remains the main barrier to achieving a cure. Next-generation sequencing (NGS) offers increased sensitivity for characterising archived drug resistance mutations (DRMs) in HIV-1 DNA for improved treatment options. In this study, we present an ultra-sensitive targeted PCR assay coupled with NGS and a robust pipeline to characterise HIV-1 DNA DRMs from buffy coat samples. Our evaluation supports the use of this assay for Pan-HIV-1 analyses with reliable detection of DRMs across the HIV-1 Pol region. We propose this assay as a new valuable tool for monitoring archived HIV-1 drug resistance in virologically suppressed individuals, especially in clinical trials investigating novel therapeutic approaches.

Trial registration: ClinicalTrials.gov NCT04337450.

Keywords: HIV-1; HIV-1 DNA; NGS; drug resistance; provirus; sanger.

Figure 1

Correlation plots for each major/minor variant mixture, between observed mutation frequencies (x-axis) and expected mutation (y-axis) frequencies (5% cut-off applied). The expected frequency is calculated.

Figure 2

Mean sequence coverage graph of PrRT and INT MiSeq NGS vs. HXB2 (Genbank: K03455.1). The coloured vertical lines represent primer binding locations.