Next-generation sequencing and drug resistance mutations of HIV-1 subtypes in people living with HIV in Sicily, Italy, 2021-2023

Abstract

Objectives: HIV-1 infection continues to be a significant public health concern, notwithstanding the expanded utilization of antiretroviral treatment (ART), due to the emergence of drug resistance. The prevalence of transmitted drug resistance remains uncertain, particularly concerning integrase inhibitors. This study aimed to assess the extent of HIV resistance in both ART-naïve and experienced individuals living with HIV (PLHIV) at the University Hospital in Palermo, Italy.

Methods: Genotyping and mutation analysis were performed on ART naïve and experienced PLHIV admitted from June 2021 to October 2023 by the NGS method. Mutations were detected by testing different NGS frequency cut-offs: ≥5 %, ≥10 %, and ≥20 %. Demographic, clinical, virological, and immunological data were retrospectively collected.

Results: Of the PLHIV, 85 (70 %) were ART-naïve, while 36 (30 %) were ART-experienced with virological failure. The main HIV-1 subtype was B (54 %), which was significantly associated with Italy-born (P < 0.001) and experienced PLHIV (P = 0.024). In the remaining cases, A1 (6 %), C (3 %), F1 (7 %), G (2 %), and Circulating Recombinant Forms (28 %) were reported. At least one mutation for a drug class was detected in 39.7 %, 45.4 %, and 53.7 % of cases at HIV-1 NGS thresholds of 20 %, 10 %, and 5 %, respectively. Drug resistance was found in 18.2 %, 25.6 %, and 33.0 %, by NGS cut-off of 20 %, 10 %, and 5 % respectively. The lowering of NGS cut-offs mainly increased the rates of integrase strand transfer inhibitor resistance. For overall resistance, no difference was observed between B and non-B subtypes for any NGS cut-offs.

Keywords: Drug resistance mutations; Genotypic resistance testing; HIV drug resistance testing; HIV subtypes; Next-generation sequencing; Virological failure.