Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology.
Vasylyeva TI., du Plessis L., Pineda-Peña AC., Kühnert D., Lemey P., Vandamme A-M., Gomes P., Camacho RJ., Pybus OG., Abecasis AB., Faria NR.
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.