Speaker
Description
Introduction
Widespread drug resistance to NNRTI-based therapies prompted a shift to INSTI-based combination antiretroviral therapy (cART), essential for the health of individuals living with HIV and global HIV elimination efforts. Our study focuses on low-frequency mutations (LFMs) to understand drug resistance dynamics, utilizing our novel AMPHEUS system with the veSEQ pipeline for whole-genome sequencing and viral load testing, highlighting the role of LFMs in drug resistance evolution within the African PANGEA consortium.
Methods
We refined the veSEQ protocol for low-volume samples to screen for HIV and detect drug resistance mutations via the HIVdb Stanford algorithm. Our approach calculates linkage disequilibrium (LD) among LFMs from Illumina reads, distinguishing minor variant lineages from random mutations to study drug-resistant HIV strain evolution and transmission in PANGEA cohorts. Population-level correlations between major and minor mutations used a linear regression model (‘lm’ model in R).
Results
AMPHEUS detects viral loads and generates whole genomes from 200 µl of plasma with viral loads above 1000 RNA copies/ml. It aligns drug resistance predictions with clinical assays at higher mutation frequencies and captures lower frequency mutations, indicative of HIV's mutation rate. Clusters of LFMs in LD near critical resistance sites, including K65 and K103, were identified. Although no significant individual-level association was found between consensus-level NRTI resistance and minor mutations near K65 (χ² = 1.86, p = 0.173), a significant community-prevalence correlation emerged (p < 0.01; R² = 0.59), linking higher prevalence of NRTI resistance with increased minor mutations, suggesting transmitted NRTI resistance in areas with high treatment failure rates.
Conclusion
Our results indicate that high rates of LFMs may represent reversions from less-fit, multi-drug resistant viruses, suggesting that transmitted NRTI resistance is underestimated by conventional sequencing. We emphasize the need for vigilant INSTI-cART outcome surveillance, especially in populations with potential transmitted NRTI resistance.
