Van Wijngaerden E

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

Autores: 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
Ano de Publicação: 2013
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

Autores: Alcantara LCJ, 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
Ano de Publicação: 2013
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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Clinical Evaluation of Rega 8: An Updated Genotypic Interpretation System That Significantly Predicts HIV-Therapy Response

Autores: Beheydt G, Camacho R, Clotet B, De Luca A, Geretti AM, Grossman Z, Imbrechts S, Kaiser R, Libin P, Prosperi M, Schmit JC, Sönnerborg A, Torti C, Van Laethem K, Van Wijngaerden E, Vandamme AM, Vercauteren J, Zazzi M
Ano de Publicação: 2013
Journal: PLoS One
Link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061436

Clinically evaluating genotypic interpretation systems is essential to provide optimal guidance in designing potent individualized HIV-regimens. This study aimed at investigating the ability of the latest Rega algorithm to predict virological response on a short and longer period.
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The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates

Autores: Baele G, Derdelinckx I, Drummond A, Lemey P, Rambaut A, Suchard MA, Van Laethem K, Van Wijngaerden E, Vandamme AM, Vrancken B
Ano de Publicação: 2014
Journal: PLoS Computational Biology
Link: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003505

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete.
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Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic

Autores: Albert J, Balotta C, Boucher C, De Munter P, Derdelinckx I, Ferreira F, Gomez-Lopez A, Khouri R, Kostrikis LG, Kücherer C, Li G, Littsola K, Nielsen C, Paredes R, Pineda-Peña AC, Schrooten Y, Stanojevic M, Trovão NS, Van Laethem K, Van Ranst M, Van Wijngaerden E, Vandamme AM, Vercauteren J, Vinken L, Wensing A
Ano de Publicação: 2014
Journal: PLoS One
Link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101738

We aimed to study epidemic trends and predictors for transmitted drug resistance (TDR) in our region, its clinical impact and its association with transmission clusters. We included 778 patients from the AIDS Reference Center in Leuven (Belgium) diagnosed from 1998 to 2012. Resistance testing was performed using population-based sequencing and TDR was estimated using the WHO-2009 surveillance list.
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Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

Autores: Abecasis AB, Albert J, Åsjö B, Balotta C, Beshkov D, Boucher CA, Camacho RJ, Clotet B, Coughlan S, Frentz D, Griskevicius A, Grossman Z, Hamouda O, Horban A, Jørgensen LB, Kolupajeva T, Korn K, Kostrikis LG, Kücherer C, Liitsola K, Linka M, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Struck D, Van de Vijver DA, Van Wijngaerden E, Vercauteren J, Wensing AM
Ano de Publicação: 2014
Journal: Bmc Infectious Diseases
Link: http://www.biomedcentral.com/1471-2334/14/407

One out of ten newly diagnosed patients in Europe was infected with a virus carrying a drug resistant mutation. We analysed the patterns over time for transmitted drug resistance mutations (TDRM) using data from the European Spread program.
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