Role of low-frequency INSTI resistance mutations on virological outcomes in ART-Naïve individuals initiating second-generation integrase inhibitors

Objectives: This study investigated the role of low-frequency INSTI resistance mutations, detectable by next-generation sequencing (NGS), in predicting virological rebound (VR) among people with HIV (PWH) starting second-generation INSTI-based first-line regimens. Methods: This case-control study compared PWH (retrieved from the Icona cohort; www.icona.org) who experienced VR (cases) with those maintained virological control (controls) under first-line regimens based on dolutegravir or bictegravir. NGS data obtained through the Illumina platform were interpreted with HIVdb algorithm v9.7. Major (MRM), accessory (ARM) and other (ORM) INSTI resistance mutations were analysed at 5%, 10%, 20% NGS cut-offs. Conditional logistic regression (CLR) was used to evaluate association between INSTI resistance and risk of VR. Results: Among 266 PWH (90 cases, 176 controls), cases experienced VR with a median (IQR) viremia of 317 (93-6,060) copies/mL after 15 (8-28) months from ART start. The prevalence of MRM was low (NGS cut-off 5%, 10%, 20%: 1.9%, 0.8%, 0.4%), while it was moderate for ARM (7.5%, 7.1%, 6.4%) and high for ORM (50.0%, 44.7%, and 42.1%). There was no evidence for a difference in prevalence of ≥1 MRM, ARM or ORM between cases and controls. At 5% NGS cut-off, the prevalence of ≥2 ORM was higher in cases compared to controls. After adjusting for confounders, including HIV-1 subtype, ≥2 ORM detected as minority variants remained associated with VR risk. Conclusion: Our findings suggest that combinations of low-frequency ORM may increase the risk of VR in individuals starting dolutegravir or bictegravir-based regimens. Further studies are needed to better understand these findings.