Vasylyeva, Tetyana I.Plessis, Louis duPineda-Peña, Andrea C.Kühnert, DeniseLemey, PhilippeVandamme, Anne-MiekeGomes, PerpétuaCamacho, Ricardo J.Pybus, Oliver G.Abecasis, Ana B.Faria, Nuno R.2025-07-172025-07-172019-07Tetyana I Vasylyeva, Louis du Plessis, Andrea C Pineda-Peña, Denise Kühnert, Philippe Lemey, Anne-Mieke Vandamme, Perpétua Gomes, Ricardo J Camacho, Oliver G Pybus, Ana B Abecasis, Nuno R Faria, Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology, The Journal of Infectious Diseases, Volume 220, Issue 2, 15 July 2019, Pages 233–243, https://doi.org/10.1093/infdis/jiz0851537-6613http://hdl.handle.net/10400.26/58099Background Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. Methods Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. Results We identified 5 subtype B Portuguese clades (26–79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998–2000) and 2000 (95% BCI, 1998–2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73–2.09) to 0.62 (95% BCI,.52–.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39–1.59) to 0.72 (95% BCI, .63–.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. Conclusions The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.engHIVPortugalphylodynamicsepidemiologyreproductive numbertransmission groupsharm reductioncontribution to journal10.1093/infdis/jiz085