Drivers of HIV-1 transmission: The Portuguese case

Authors: Pineda-Peña AC, Pingarilho M, Li G, Vrancken B, Libin P, Gomes P, Camacho RJ, Theys K, Abecasis AB, Portuguese Hiv-1 Resistance Study Group
Publication Year: 2019
Journal: PLoS One
Link: https://www.ncbi.nlm.nih.gov/pubmed/31568476

BACKGROUND: Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines. METHODS: Demographic, clinical and genomic data were […]
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The impact of HIV-1 within-host evolution on transmission dynamics

Authors: Theys K, Libin P, Pieneda-Peña AC, Nowé A, Vandamme AM, Abecasis AB
Publication Year: 2018
Journal: Current Opinion in Virology
Link: https://www.sciencedirect.com/science/article/pii/S1879625717301372?via%3Dihub%20

The adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. This trade-off is visible in the disparity in […]
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PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Authors: Baele G, Bezenchek A, EucoHIV Study Group, Incardona F, Libin P, Nowé A, Sönnerborg A, Theys K, Vandamme AM, Vanden Eynden E
Publication Year: 2017
Journal: Bioinformatics
Link: https://www.ncbi.nlm.nih.gov/pubmed/28961923

MOTIVATION: Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially […]
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Zika genomics urgently need standardized and curated reference sequences

Authors: Abecasis AB, Cuypers L, Dallmeier K, Libin P, Pineda-Peña AC, Theys K, Vandamme AM
Publication Year: 2017
Journal: PLoS Pathogens
Link: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006528

Authors: Ceccherini-Silberstein F, Cento V, Cuypers L, Di Maio VC, Libin P, Lunar MM, Nevens F, Nowé A, Poljak M, Schrooten Y, Theys K, Van Laethem K, Vandamme AM
Publication Year: 2017
Journal: Infection Genetics and Evolution
Link: https://www.sciencedirect.com/science/article/pii/S1567134817301582?via%3Dihub

Resistance-associated variants (RAVs) have been shown to influence treatment response to direct-acting antivirals (DAAs) and first generation NS3/4A protease inhibitors (PIs) in particular. Interpretation of hepatitis C virus (HCV) genotypic drug resistance remains a challenge, especially in patients who previously failed DAA therapy and need to be retreated with a second DAA based regimen. Bayesian […]
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Drivers of HIV-1 transmission: The Portuguese case

The impact of HIV-1 within-host evolution on transmission dynamics

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Zika genomics urgently need standardized and curated reference sequences

Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning

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