Speaker
Description
Background - British Columbia (BC), Canada, is rare in maintaining daily HIV phylogenetic monitoring for over a decade. Long-term monitoring enables evaluation of the impact large-scale prevention strategies have on HIV transmission suppression.
Methods - We analyzed HIV-1 pol sequences derived from 11,000+ individuals collected between 1996 and 2024, representing >80% of the estimated prevalence. Transmission clusters were inferred from a distribution of 100 phylogenetic trees using a patristic distance threshold of 0.02 substitutions/site. We quantified trends in changes in the viral population size (effective population size, Nₑτ), cluster birth rates, proportion of new diagnoses linked to clusters, and transmission intensity (lineage-level diversification rates). Changes were evaluated relative to implementation of province wide treatment as prevention (TasP; 2009) and pre-exposure prophylaxis (PrEP; 2018).
Findings – Phylodynamic estimates of Nₑτ revealed no decline during the ART era, a significant decline after introduction of TasP (slope change β=-0.051/yr,p<0.001) and further acceleration in decline after introduction of PrEP (slope change β=-0.052/yr,p<0.001). Declines in transmission were further evidenced by reductions in cluster births and declining proportions of new diagnoses linked to clusters. Reduction in clustering probability followed introduction of PrEP (odds ratio 0.24, 95%,CI:0.20-0.28). Cluster level diversification rates, reflecting transmission intensity, differed significantly across prevention eras (Kruskal-Wallis=26.85,p<0.001), with substantially lower rates after implementation of TasP compared with the pre-TasP period. Annual analyses demonstrated declines in log-transformed diversification rates subsequent to both generalized TasP and focused PrEP, despite persistence of a few established clusters. Residual transmission persisted within specific subpopulations.
Interpretation - This study provides empirical evidence that combined implementation of TasP and PrEP progressively fragments HIV transmission networks. Increasing fractions of non-clustered cases suggests contribution of multijurisdictional transmission. Sustained phylogenetic monitoring revealed durability of prevention gains, and persistence of residual transmission. Phylogenetic monitoring aided adaptation and focus of public health responses without exacerbating stigma.
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