Role of low-frequency integrase strand transfer inhibitor resistance mutations on virological outcomes in antiretroviral therapy-naïve individuals initiating second-generation integrase inhibitors

Objectives: This study investigated the role of low-frequency integrase strand transfer inhibitor (INSTI) resistance mutations, detectable by next-generation sequencing (NGS), at 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 who maintained virological control (controls) under first-line regimens based on dolutegravir or bictegravir. NGS data obtained through the Illumina platform were interpreted using the HIVdb algorithm version 9.7. Major (MRM), accessory (ARM), and other (ORM) INSTI resistance mutations were analysed at 5%, 10%, and 20% NGS cut-offs, respectively. Conditional logistic regression was used to evaluate the association between INSTI resistance and risk of VR. Results: Among 266 PWH (90 cases, 176 controls), cases experienced VR with a median (interquartile range) viremia of 317 (93–6060) copies/mL after 15 (8–28) months from antiretroviral therapy start. The prevalence of MRM was low (NGS cut-off 5%, 10%, 20%: 1.9%, 0.8%, 0.4%, respectively), while it was moderate for ARM (7.5%, 7.1%, 6.4%) and high for ORM (50.0%, 44.7%, 42.1%). There was no evidence of 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 with 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.