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BACKGROUND:Estimation of temporal changes in HIV transmission patterns can help to elucidate the impact of preventative strategies and public health policies. METHODS:Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference datasets 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 five subtype B Portuguese clades (n=26-79 sequences) and a large monophyletic subtype G Portuguese clade (n=236). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval 1998-2000) and 2000 (1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (1.73-2.09) to 0.62 (0.52-0.72). For subtype G, Re decreased from 1.49 (1.39-1.59) to 0.72 (0.63-0.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were at 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.

Original publication




Journal article


The Journal of infectious diseases

Publication Date



Department of Zoology, University of Oxford, Oxford, UK.