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

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.