Background Monitoring HIV-1 subtype circulation and transmitted drug resistance (TDR) remains a key priority, particularly since the rollout of high-sensitivity next-generation sequencing (NGS). Methods Routine plasma HIV-1 RNA NGS genotyping data were collected from newly diagnosed individuals in Italy over 2022-24. HIV-1 TDR and genotypic susceptibility were evaluated through HIVdb with NGS set at 10% and 20%. Subtype and transmission clusters (TC) were determined through the maximum likelihood phylogeny based on the GTR + F + R9 model. Results Seven hundred and forty-two individuals were included, 51.9% harbouring non-B strains [CRF02_AG (18.1%); CRF BF (6.1%); A1/A3/A6 (7.1%); others (20.5%)]. TDR prevalence to any class was 11.7% at Sanger-like NGS-setting (>20%), slightly increased (15.0%) at 10% NGS-setting, and significantly varied across subtypes, with the highest prevalence observed in B subtype. Most antiretrovirals showed full genotypic activity in nearly 99% of individuals, except for efavirenz and rilpivirine (proportion of individuals with full activity <92%). A total of 57 TC were detected: 40 pairs, 17 clusters (>2 sequences). Thirteen TC (22.8%, 8 pairs, 5 clusters) involved individuals harbouring TDR. TDR was detected as minority mutations in five TC. Conclusions A high proportion of HIV-1 non-B subtypes circulate in Italy. TDR prevalence is around 12% using NGS at Sanger-like threshold and moderately increases to 15% when NGS is set at 10%. However, the impact of the detected TDR on the susceptibility to currently used antiretrovirals in clinical practice is negligible.
Evaluation of HIV-1 transmitted drug-resistance among subtypes circulating from 2022 to 2024 in Italy: A refined analysis through next-generation sequencing / Armenia, D.; Alteri, C.; Micheli, V.; Allice, T.; Bonura, C.; Bruzzone, B.; Bon, I.; Corsini, R.; Zerbini, A.; Morelli, L.; Cerutti, F.; Giammanco, G.; Randazzo, N.; Bertoldi, A.; Novazzi, F.; Ibba, G.; Bertoli, A.; Bezenchek, A.; Ceccherini-Silberstein, F.; Zazzi, M.; Santoro, M. M.; Stefanelli, F.; Zanussi, S.; Mancini, N.; Carone, C.; Giovanelli, I.; Galli, V.; Gennari, W.; Tagliazucchi, S.; Clerici, P.; De Paschale, M.; Franzetti, M.; Andriolo, M.; Malandrin, S.; Tallarita, M.; Arosio, M. E. G.; Guarneri, D.; Lai, A.; Bracchitta, F.; Borghi, E.; Clementi, N.; Callegaro, A. P.; Rossetti, B.; Colao, M. G.; Pace, P.; Tekle, S.; Capria, A.; Filippini, F.; Saladini, F.; Vicenti, I.; Berno, G.; Fabeni, L.; Forbici, F.; Maggi, F.; Rueca, M.; Lombardi, F.; Santangelo, M. R.; Antonelli, G.; Turriziani, O.; Colagrossi, L.; Perno, C. F.; Scutari, R.; Yagai, B.; Bellocchi, M. C.; Carioti, L.; Moghadam Hossein, E.; El Khalili, O.; Marchegiani, G.; Santoro, M.; Spalletta, D.; Bernardini, S.; Grelli, S.; Petrone, V.; Piermatteo, L.; Torre, G.; Cuomo, N.; Raddi, A.; Bonifacio, M. A.; Mariggi, M. A.; Volpe, A.; Lipsi, M. R.; Angioj, F.; Pollicino, T.; Uzzau, S.; Cannella, S.; Giammanco, G. M.; Mascarella, C.; Ceccarelli, M.. - In: JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. - ISSN 0305-7453. - 81:4(2026). [10.1093/jac/dkag084]
Evaluation of HIV-1 transmitted drug-resistance among subtypes circulating from 2022 to 2024 in Italy: A refined analysis through next-generation sequencing
Mancini N.;Guarneri D.;Clementi N.;Filippini F.;Lombardi F.;Volpe A.;
2026-01-01
Abstract
Background Monitoring HIV-1 subtype circulation and transmitted drug resistance (TDR) remains a key priority, particularly since the rollout of high-sensitivity next-generation sequencing (NGS). Methods Routine plasma HIV-1 RNA NGS genotyping data were collected from newly diagnosed individuals in Italy over 2022-24. HIV-1 TDR and genotypic susceptibility were evaluated through HIVdb with NGS set at 10% and 20%. Subtype and transmission clusters (TC) were determined through the maximum likelihood phylogeny based on the GTR + F + R9 model. Results Seven hundred and forty-two individuals were included, 51.9% harbouring non-B strains [CRF02_AG (18.1%); CRF BF (6.1%); A1/A3/A6 (7.1%); others (20.5%)]. TDR prevalence to any class was 11.7% at Sanger-like NGS-setting (>20%), slightly increased (15.0%) at 10% NGS-setting, and significantly varied across subtypes, with the highest prevalence observed in B subtype. Most antiretrovirals showed full genotypic activity in nearly 99% of individuals, except for efavirenz and rilpivirine (proportion of individuals with full activity <92%). A total of 57 TC were detected: 40 pairs, 17 clusters (>2 sequences). Thirteen TC (22.8%, 8 pairs, 5 clusters) involved individuals harbouring TDR. TDR was detected as minority mutations in five TC. Conclusions A high proportion of HIV-1 non-B subtypes circulate in Italy. TDR prevalence is around 12% using NGS at Sanger-like threshold and moderately increases to 15% when NGS is set at 10%. However, the impact of the detected TDR on the susceptibility to currently used antiretrovirals in clinical practice is negligible.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
