Longitudinal profiling of blood-tissue HIV-1 reservoirs reveals the mechanism of failure to long-acting cabotegravir/rilpivirine: a case report

We report a case of confirmed virological failure on long-acting cabotegravir/rilpivirine (LA-CAB/RPV) in a patient with HIV-1 subtype B who met all eligibility criteria, maintained long-term viral suppression, and received all injections on schedule, with retrospective liquid chromatography-tandem mass spectrometry showing adequate plasma drug levels. Retrospective next-generation sequencing of proviral DNA revealed the non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance-associated mutation 188L in peripheral blood mononuclear cells 41 months prior to LA-CAB/RPV initiation, despite its absence in baseline plasma genotyping. This finding suggests that resistant variants may have been transmitted and archived from the start or selected during a brief NNRTI-based regimen. Mutational profiles differed across compartments, and the use of provirus-aware bioinformatic filters helped to down-weight resistance calls supported mainly by reads harboring frameshifts, stop codons or hypermutation-related APOBEC signatures within the sequenced regions, thus enhancing interpretability in a real-world clinical setting. This case illustrates how NGS, assisted by recent proviral sequence filtering tools, can be used to better select or offer individualized follow-up to individual undergoing injectable treatment. Trial registration PBMCs and gut-associated lymphoid tissue biopsies were prospectively collected from people living with HIV enrolled in two clinical studies conducted at the University Hospital of Liège, Belgium: the EDIT study (ClinicalTrials.gov identifier: NCT05351684) and the IDOLTIB study (ClinicalTrials.gov identifier NCT04034862)