HIV-1 APOBEC-context Mutations Detected by Next-Generation Sequencing in Plasma: Implications for Drug Resistance Interpretation.

BACKGROUND

APOBEC3-mediated cytidine deamination produces G→A substitutions in HIV genomes, described in proviral DNA but detectable in plasma HIV-1 RNA using NGS. APOBEC-signature mutations reflect G→A enrichment substitutions, whereas APOBEC-context mutations are substitutions at drug resistance-associated positions compatible with APOBEC editing. We evaluated theirprevalence and impact on resistance interpretation.

METHODS

We retrospectively analysed plasma HIV-1 NGS-sequences from antiretroviral-naive individuals in 2022-2023. Sequencing was performed in participating laboratories, and FASTQ centrally reanalyzed using DeepChek. APOBEC-signature mutations, APOBEC-context drug resistance mutations (DRMs), and stop codons were assessed in protease, reverse transcriptase, and integrase at 1%, 3%, and 5% thesholds.

RESULTS

Among 290 individuals, 268 had complete NGS. At 1%, APOBEC-signature mutations were detected in 159 individuals and APOBEC-context DRMs in 64 (22%). Both patterns coexisted in 52 (18%), decreasing to 17 (6%) and 8 (3%) at 3% and 5% thresholds. Certain mutations, including M184I, G190E, G140S, and R263K, remained detectable at higher thresholds. R263K co-occurred with multiple APOBEC-signature mutations and stop codons indicating extensive APOBEC-mediated editing.

CONCLUSIONS

APOBEC-associated mutations are detectable in plasma HIV-1 RNA and may affect resistance interpretation. Conservative frequency thresholds (5%) APOBEC-signatures evaluation may reduce misclassification of APOBEC-induced variants as clinically relevant resistance.