Predictors of non adherence to antiretroviral therapy at an urban HIV care and treatment center in Tanzania

Authors: Aboud S, Chalamilla G, Kamuhabwa A, Lyamuya EF, Mosha F, Sangeda RZ, Van Wijngaerden E, Vandamme AM, Vercauteren J
Publication Year: 2018
Journal: Drug Healthcare and Patient Safety
Link: https://www.ncbi.nlm.nih.gov/pubmed/30174460

BACKGROUND: Measurement of adherence to antiretroviral therapy (ART) can serve as a proxy for virologic failure in resource-limited settings. The aim of this study was to determine the factors underlying nonadherence measured by three methods. PATIENTS AND METHODS: This is a prospective longitudinal cohort of 220 patients on ART at Amana Hospital in Dar es […]
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Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus–infected donors in the Netherlands and Flanders

Authors: Bezemer D, Claas EC, Compernolle V, de Smet A, van de Laar TJ, Van Laethem K, van Sighem AI, Van Wijngaerden E, Vandamme AM, Vandewalle G, Zaaijer HL
Publication Year: 2017
Journal: Transfusion
Link: https://onlinelibrary.wiley.com/doi/abs/10.1111/trf.14097

Separate transmission networks for human immunodeficiency virus (HIV) coexist. Molecular typing of viral genomes can provide insight in HIV transmission routes in donors for whom risk behavior-based donor selection failed. This study includes all HIV-infected Dutch and Flemish donors in the period 2005 to 2014 (n = 55). Part of the HIV polymerase (pol) gene was amplified, […]
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Quantifying next generation sequencing sample pre-processing bias in HIV-1 complete genome sequencing

Authors: Baele G, Lemey P, Trovão NS, Van Laethem K, Van Wijngaerden E, Vandamme AM, Vrancken B
Publication Year: 2016
Journal: Viruses
Link: http://www.mdpi.com/1999-4915/8/1/12%20

Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome […]
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HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

Authors: Beheydt G, Bruzzone B, Camacho RJ, De Luca A, Deforche K, Grossman Z, Imbrechts S, Incardona F, Libin P, Pironti A, Rhee SY, Ruiz L, Sangeda RZ, Shafer RW, Sönnerborg A, Theys K, Torti C, Van de Vijver DA, Van Laethem K, Van Wijngaerden E, Vandamme AM, Vercauteren J, Zazzi M
Journal: Infection Genetics and Evolution
Link: http://www.ncbi.nlm.nih.gov/pubmed/23523594

We previously modeled the in vivo evolution of human immunodeficiency virus-1 (HIV-1) under drug selective pressure from cross-sectional viral sequences. These fitness landscapes (FLs) were made by using first a Bayesian network (BN) to map epistatic substitutions, followed by scaling the fitness landscape based on an HIV evolution simulator trying to evolve the sequences from treatment naïve patients into sequences from patients failing treatment.
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RegaDB: Community-driven data management and analysis for infectious diseases

Authors: Alcantara LC, Assel M, Ayouba A, Beheydt G, Boucher C, Camacho RJ, Carvalho AP, Cavaco-Silva J, De Bel A, De Munter P, De Oliveira T, Deforche K, Ferreira F, Grossman Z, Imbrechts S, Kaiser R, Lacor P, Lapadula G, Libin P, Otelea D, Paraschiv S, Peeters M, Ruelle J, Sloot P, Snoeck J, Theys K, Torti C, Van Laethem K, Van Wijngaerden E, Vandamme AM, Wesner S, Zazzi M
Journal: Bioinformatics
Link: http://www.ncbi.nlm.nih.gov/pubmed/23645815

RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.
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Predictors of non adherence to antiretroviral therapy at an urban HIV care and treatment center in Tanzania

Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus–infected donors in the Netherlands and Flanders

Quantifying next generation sequencing sample pre-processing bias in HIV-1 complete genome sequencing

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

RegaDB: Community-driven data management and analysis for infectious diseases

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