Journal Article

P97 Next generation sequencing (NGS) of proviral HIV DNA and analysis of APOBEC-induced mutations to assess suitability for long-acting cabotegravir/rilpivirine therapy

Bruzzone, B, Giurco, M, Stefanelli, F, Massobrio, G, Nofri, M, A Di Biagio, Taramasso, L, Cardaci, S, Limongelli, A, Randazzo, N, Bassetti, M

2025

Overview

BackgroundGenotyping Resistance Test (GRT) of HIV DNA in NGS is a useful tool for clinical treatment optimization, especially when GRT on RNA is unavailable and/or unfeasible and treatment history unreliable, and is particularly relevant when considering the prescription of long-acting (LA) therapies based on cabotegravir (CAB) and rilpivirine (RPV). However, NGS data interpretation, along with APOBEC-related mutations discrimination, remains complex and its clinical implications are still under investigation. This study evaluates NGS-GRT on DNA in individuals not eligible to standard enrolment criteria for CAB-RPV LA treatment, highlighting its potential in the challenges in HIV care.Materials and MethodsA retrospective observational study was conducted at a single tertiary hospital, in individuals who underwent NGS-GRT on DNA and later started LA therapy. Library for NGS was prepared using the commercial kit AD4SEQ HIV-1 Solution v2 (Arrow Diagnostics). Consensus sequences were analyzed on HIV Drug Resisting Database (Stanford University). Mutations were considered APOBEC-induced if they appeared at low frequency and especially if associated with unusual mutations and/or stop codons. Data were described using the mean and standard deviation (SD) for normally distributed continuous variables and the median and interquartile range (IQR) for non-normally distributed continuous variables. Virological failure (VF) was defined as the occurrence of two consecutive viral load measurements >50 copies/mL.ResultsOur study included a cohort of 82 people living with HIV (PLWH) receiving LA therapy. Of these, 51 had NGS-GRT on DNA, 22 had mutations or stop codons, 10 had APOBEC-related mutations at sites that could potentially confer drug resistance (4 NRTI, 2 PI, 4 NNRTI, 6 INSTI).Among the nine individuals with APOBEC-associated INSTI or NNRTI mutations, none experienced VF. Only one study participant was switched to an oral INSTI-containing regimen due to the historical detection of E138Q in GRT on RNA, a low-level resistance mutation for RPV. Comparing individuals with (n=22) and without (n=29) APOBEC-associated mutations, the mean time from diagnosis to virological suppression was 10.2 (±7.9) vs. 3.2 (±5.3) years (p=0.002) and the mean duration of infection was 25.4 (±10.1) vs. 2.1 (±5.6) years (p=0.001). This suggests that a longer duration of unsuppressed viral replication may be associated with a higher likelihood of APOBEC- related mutation emergence.ConclusionAs the presence of mutations attributed to APOBEC activity is associated to defective virus, it does not preclude the efficacy of LA therapy with CAB/RPV; in fact, their correct identification in the INSTI and NNRTI drug classes should rather encourage clinicians in the use of LA therapy, in a setting of reduced viral fitness and growing capability. An accurate interpretation of NGS-GRT on DNA is therefore crucial to avoid unnecessary exclusion of individuals from LA therapy with CAB/RPV.

• Publisher: BMJ Publishing Group LTD
• Subject: Drug resistance / HIV / Human immunodeficiency virus / Mutation