TY - JOUR
T1 - Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology
AU - Vasylyeva, Tetyana I.
AU - Du Plessis, Louis
AU - Pineda-Peña, AC
AU - Kühnert, Denise
AU - Lemey, Philippe
AU - Vandamme, AM
AU - Gomes, Perpétua
AU - Camacho, Ricardo Jorge
AU - Pybus, Oliver George
AU - Abecasis, AB
AU - Faria, Nuno Rodrigues
N1 - Funding Information:
Financial support. This work was supported by the New College of the University of Oxford (Juliana Cuyler Matthews Junior Research Fellowship to T. I. V.); the Royal Society and Wellcome Trust (Sir Henry Dale Fellowship [grant 204311/Z/16/Z] to N. R. F.); the European Research Council, under the European Commission Seventh Framework Programme (FP7/2007–2013)/European Research Council (grant agreement 614725-PATHPHYLODYN; to O.G. P and L. d. P.); the Max Planck Society (to D. K.); European Funds (grant ‘Bio-Molecular and Epidemiological Surveillance of HIV Transmitted Drug Resistance, Hepatitis Co-Infections and Ongoing Transmission Patterns in Europe—BEST HOPE—[project funded through HIVERA: Harmonizing Integrating Vitalizing European Research on HIV/AIDS; grant 249697]); L’Oréal Portugal Medals of Honor for Women in Science 2012 (financed through L’Oréal Portugal, Comissão Nacional da Unesco and Fundação para a Ciência e Tecnologia [ FCT]); by FCT for funds to GHTM-UID/Multi/04413/2013; by the MigrantHIV project (financed by FCT; PTDC/DTP-EPI/7066/2014); by Gilead Génese HIVLatePresenters; the Research Foundation Flanders (FWO G.0692.14); and the VIROGENESIS project, which receives funding from the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement 634650).
Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.
PY - 2019/6/19
Y1 - 2019/6/19
N2 - BACKGROUND: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.
AB - BACKGROUND: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.
KW - HIV
KW - Phylodynamics
KW - Epidemiology
KW - Reproductive number
KW - Transmission groups
KW - Harm reduction
KW - Portugal
UR - https://academic.oup.com/jid/article/220/2/233/5364937
U2 - 10.1093/infdis/jiz085
DO - 10.1093/infdis/jiz085
M3 - Article
C2 - 30805610
SN - 0022-1899
VL - 220
SP - 233
EP - 243
JO - Journal of Infectious Diseases
JF - Journal of Infectious Diseases
IS - 2
M1 - jiz085
ER -