Next-Generation Sequencing Analysis for HIV-1 Genotyping and Drug Resistance Mutations Mapping in Sicily, Italy

Background: The advent and continuous improvement in antiretroviral therapy (ART) have profoundly altered the clinical course of HIV infection, shifting the focus from AIDS-related complications to the management of age-related comorbidities and non-AIDS-related hospitalizations. In this evolving context, optimizing ART is essential, with genotypic resistance testing (GRT), particularly through next-generation sequencing (NGS), playing a pivotal role. Methods: This multicenter, retrospective cross-sectional study investigated HIV-1 subtypes, resistance mutations, and drug resistance profiles among 367 people living with HIV (PLWH) in Sicily, based on 384 GRTs performed at the Microbiology Laboratory of the University Hospital of Palermo. Results: Subtype B was the most prevalent (50%), followed by circulating recombinant forms (30%). Among treatment-naïve individuals, resistance-associated mutations were infrequent, with prevalence rates of 0.4% for NRTIs, 5.5% for NNRTIs, 1.3% for PIs, and 0.8% for INIs. Conversely, treatment-experienced individuals showed significantly higher resistance rates, especially to NRTIs (16.3%), NNRTIs (10.6%), and INIs (9.6%). No significant differences in resistance patterns were observed between B and non-B subtypes. Conclusions: This study provides the first regional overview of HIV drug resistance across Sicily. Despite the detection of resistance-associated mutations, the overall prevalence of clinically relevant resistance, particularly to currently recommended therapies, remains low, especially among treatment-naïve individuals.