Background: Lenacapavir (LEN), the first-in-class HIV-1 capsid (CA) inhibitor, was recently approved for highly treatment-experienced (HTE) people with HIV and multidrug resistance (MDR). Resistance-associated mutations in HIV-1 have been reported for LEN. We evaluated the resistance profile and the genetic evolution of the CA region in HTE individuals with MDR treated with LEN in the Italian PRESTIGIO Registry.

Materials and Methods: Plasma and PBMC samples from nine HTE with MDR were collected before LEN switch (T0, when available) and during LEN treatment (T1) from the PRESTIGIO biobank. Next-generation sequencing (NGS) of CA, PR/RT and IN regions was performed using MiSeq Illumina platform. Resistance to LEN, PIs, RTIs, and INSTIs was evaluated using the HIVDB Program v.9.8. Intra-patient p-distance, estimated by MEGA11, was used to assess the HIV-1 DNA genetic variability over time and the genetic differences between HIV-1 DNA and RNA.

Results: Participants were treated with LEN for a median of 20 months [IQR 19-24] (Table 1). At T0, no major LEN resistance mutations were detected in plasma or PBMCs. One participant harboured the accessory mutation T107A as a minority variant (5.9%) in PBMCs, with a minimal genetic variability compared to plasma compartment in the CA region (p-distance 0.005 [SE: 0.002]). In two participants, starting treatment with plasma HIV-1 RNA <50 cps/mL and maintaining virological control, any intra-patient evolution in PBMCs over time (after about 20 months) was found (p-distance 0.000). Seven participants started LEN during virological failure (median HIV-1 RNA 2,010 [IQR 763-24,400] cps/mL). Among them, six achieved virological suppression without genetic evolution in PBMCs over time (p-distance 0.000 in both CA and IN regions). Conversely, PR/RT showed genetic variability (mean p-distance 0.038 [SE: 0.005]). One of them showed a viral blip (52 cps/mL) and developed Q67K (5.7%) at T1 in plasma only (Table 2), with a CA p-distance of 0.040 (SE:0.008) and a PR/RT p-distance of 0.050 (SE:0.006) between plasma and PBMCs at T1. The only participant with persistent viremia (HIV-1 RNA 39,400 cps/mL) at 28 months under LEN harboured the primary mutations K70H (97.8% in plasma, 75.6% in PBMCs) and Q67K (98.5% in plasma, 75.7% in PBMCs) (Table 2); however, no evolutionary divergence was found in the CA region (p-distance =0.000 between plasma and PBMCs) at T1, while a genetic variability was found in PR/RT (p-distance: 0.057 [SE:0.007]).

Conclusions: In this small cohort of HTE people with MDR, LEN was associated with maintenance or achievement of virological suppression, with one participant remaining viraemic and harbouring LEN-resistant variants, however without evolutionary diversity in the CA region between plasma and PBMCs. A genetic stability of CA and IN regions was found over time. By contrast, PR/RT regions showed a continuous ongoing evolutionary pressure over time and between plasma and PBMCs.