Non-B subtypes account for a large proportion of clustered primary HIV-1 infections in Italy.

Objectives and Design: Using pol sequences obtained for routine resistance testing, we characterised the molecular patterns of HIV-1 transmission and factors associated with being part of a transmission cluster among individuals who in 2008-2014 presented with primary HIV-1 infection (PHI) at 11 urban centres across Italy.
Methods: Pol sequences were obtained by Sanger sequencing. Transmission clusters were identified by phylogenetic analysis (maximum likelihood method, confirmed by Bayesian analysis). Multivariable logistic regression explored factors associated with a participant being part of a transmission cluster.
Results: The PHI cohort comprised 186 participants (159/186, 85.5% males) with median age 44 years, median CD4 count 464 cells/mm ³ and median plasma HIV-1 RNA 5.6 log ₁₀ copies/mL. Drug resistance associated mutations were found in 16/186 (8.6%). A diversity of non-B subtypes accounted for 60/186 (32.3%) of all infections. A total of 17 transmission clusters were identified, including 44/186 (23.7%) participants. Each cluster comprised 2-6 sequences. Non-B subtypes accounted for seven clusters and 22/44 (50%) of clustered sequences. In multivariable logistic regression analysis, factors associated with being part of a transmission cluster comprised harbouring a non-B subtype (adjusted OR (adjOR) 2.28; 95% CI 1.03 to 5.05; p=0.04) and showing a lower plasma HIV-1 RNA (adjOR 0.80, 95% CI 0.64 to 0.99; p=0.04).
Conclusions: There was a large contribution of diverse non-B subtypes to transmission clusters among people presenting with acute or recent HIV-1 infection in this cohort, illustrating the evolving dynamics of the HIV-1 epidemic in Italy, where subtype B previously dominated.
Competing Interests: Competing interests: LT reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Gilead Sciences, Janssen, Viiv Healthcare and no other conflict of interest. MF reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Gilead Sciences, Janssen, Viiv Healthcare, BMS, MSD and no other conflict of interest. SR reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Gilead Sciences, Janssen, Viiv Healthcare and no other conflict of interest. AG reports past (within 36 months) financial relationships (educational support) with Mylan and no other conflict of interest. EF reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Gilead Sciences, Janssen, Viiv Healthcare, MSD and no other conflict of interest. CP reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Janssen. GM reports past (within 36 months) financial relationships (advisory board membership or consultancy fees, speakers’ honoraria or travel support) with Gilead Sciences, Janssen, Viiv Healthcare, MSD and no other conflict of interest. AG reports past (within 36 months) grant/research supports, honoraria or consultation fees, speaker’s bureau compensation and/or travel support from Abbvie, Astellas, BMS, Boeringher, Gilead, Janssen, MSD, Novartis, Pfizer, Roche, ViiV and no other conflict of interest.
(© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)