Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology.

The Journal of Infectious Diseases
Tetyana I VasylyevaNuno R Faria

Abstract

Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. 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. 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. The estimated declines in Re coincide with the introduction of highly active ...Continue Reading

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Citations

May 30, 2019·Viruses·Francesca Di GiallonardoAnthony D Kelleher
Aug 21, 2019·Frontiers in Public Health·Kristof TheysGuy Baele
Apr 25, 2020·Viruses·Tetyana I VasylyevaSamuel R Friedman
Jan 22, 2021·Journal of the International AIDS Society·Francesca Di GiallonardoUNKNOWN NSW HIV Prevention Partnership Project
May 20, 2021·Molecular Biology and Evolution·Stilianos LoucaMatthew W Pennell

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Methods Mentioned

BETA
BaTS

Software Mentioned

Tempest
SpreaD3
R
Clustal Omega
TreeSlicer
BEASTv2
HyPhy
BEAST
BEAST2
RAxML

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