HIV transmission links between past and newly diagnosed infections: a molecular epidemiology study

Abstract Background Understanding the driving forces of HIV infection is crucial for developing intervention strategies. We aimed to infer these forces from genetic linkages between past and newly diagnosed cases by a molecular approach. Methods We recruited newly diagnosed HIV patients from all three HIV specialist clinics in Hong Kong, China, between 2016 and 2018 to collect their HIV sequences with corresponding behavioural and clinical data. We retrieved archived HIV sequences from 1994 to 2012 separately. We pooled and analysed sequences by constructing a network with 1·5% TN93 distance threshold and measured node degree centrality. We did univariate analyses to identify factors associated with genetic links with archived sequences among newly diagnosed patients, and used a generalised linear model to differentiate archived sequences having links with new cases adjusting for diagnosis year. Findings 2778 partial pol sequences were amalgamated for network construction, of which 426 were newly diagnosed. The network contained 1908 (69%) nodes and 23 305 edges. Some 703 (3%) edges linked 192 archived samples with 135 new cases. Of 239 newly diagnosed patients with genetic connections, those linked with past infections were more likely to be subtype B (odds ratio 3·31; p Interpretation HIV transmission chains linking new with past infections in Hong Kong were driven by younger MSM. Chemsex, emergence in recent years, only clustered in and contributed to some new infections. Formation of transmission linkages over time signified the importance of targeting new and established infections in developing prevention strategies. Funding Research Grants Council of Hong Kong (14103315) and AIDS Trust Fund (MSS 229 R and 243 R).