A5039280845- Genomics and Phylogenetic Studies
- HIV Research and Treatment
- Influenza Virus Research Studies
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- Viral Infections and Vectors
- Viral gastroenteritis research and epidemiology
- Hepatitis C virus research
- Evolution and Paleontology Studies
- Animal Virus Infections Studies
- HIV/AIDS Research and Interventions
- Plant Virus Research Studies
- HIV/AIDS drug development and treatment
- Animal Disease Management and Epidemiology
- Virology and Viral Diseases
- Mosquito-borne diseases and control
- Hepatitis B Virus Studies
- Zoonotic diseases and public health
- Yersinia bacterium, plague, ectoparasites research
- Viral Infections and Outbreaks Research
- Rabies epidemiology and control
- Respiratory viral infections research
- Bayesian Methods and Mixture Models
Rega Institute for Medical Research
2016-2025
KU Leuven
2016-2025
Global Virus Network
2022-2024
Université Libre de Bruxelles
2023
Royal Meteorological Institute of Belgium
2023
Boston University
2023
University Medical Center Utrecht
2023
Université Paris Cité
2020
Centre National de la Recherche Scientifique
2020
Université Paris-Saclay
2020
The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular reconstruction with complex discrete continuous trait evolution, divergence-time dating, coalescent demographic models in an efficient statistical engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of...
As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted light their genetic histories. Unfortunately, inference historical dispersal or migration patterns mainly restricted to model-free heuristic approaches that provide little insight into temporal setting spatial dynamics. The introduction probabilistic models evolution, however, offers unique opportunities engage this statistical endeavor. Here we introduce Bayesian...
Abstract Summary: RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this includes four analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), tests hot-spots, range matrix visualizing over-all patterns within datasets recombination-aware ancestral sequence reconstruction. Complementary to high degree flow automation, also has highly interactive detailed graphical user interface that enables more focused hands-on...
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged late 2020 despite previously high levels infection. Genome sequencing viruses sampled Manaus between November and January 2021 revealed the emergence circulation a novel SARS-CoV-2 variant concern. Lineage P.1 acquired 17 mutations, including trio spike protein (K417T, E484K, N501Y) associated with increased binding to human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular...
Recent developments in marginal likelihood estimation for model selection the field of Bayesian phylogenetics and molecular evolution have emphasized poor performance harmonic mean estimator (HME). Although these studies shown merits new approaches applied to standard normally distributed examples small real-world data sets, not much is currently known concerning computational issues methods when fitting complex evolutionary population genetic models empirical sets. Further, yet seen...
A Family of Languages English is part the large Indo-European language family, which includes Celtic, Germanic, Italic, Balto-Slavic, and Indo-Iranian languages. The origin this family hotly debated: one hypothesis places north Caspian Sea in Pontic steppes, from where it was disseminated by Kurgan semi-nomadic pastoralists; a second suggests that Anatolia, modern-day Turkey, source, radiated with spread agriculture. Bouckaert et al. (p. 957 ) used phylogenetic methods modeling to assess...
Research aimed at understanding the geographic context of evolutionary histories is burgeoning across biological disciplines. Recent endeavors attempt to interpret contemporaneous genetic variation in light increasingly detailed geographical and environmental observations. Such interest has promoted development phylogeographic inference techniques that explicitly aim integrate such heterogeneous data. One promising involves reconstructing history on a continuous landscape. Here, we present...
Thirty years after the discovery of HIV-1, early transmission, dissemination, and establishment virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that 1920s Kinshasa (in what is now Democratic Republic Congo) was focus transmission source pre-1960 pandemic viruses elsewhere. Location dating estimates were validated using earliest archival sample, also Kinshasa. The epidemic histories group M nonpandemic O...
Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in world. Because limited available data, assessments impact nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced reproduction number from >3 to 1 1.6 São Paulo and Rio de Janeiro. Sequencing 427 new genomes analysis geographically representative genomic dataset identified >100...
Recent implementations of path sampling (PS) and stepping-stone (SS) have been shown to outperform the harmonic mean estimator (HME) a posterior simulation-based analog Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection demographic molecular clock models. Almost simultaneously, averaging approach was developed that avoids conditioning on single but averages over set relaxed This returns estimates probability each which one can estimate Bayes...
Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine (BCoV), show remarkable antigenic similarities. In this study, we report the first complete sequence (30,738 nucleotides) prototype HCoV-OC43 strain (ATCC VR759). Complete open reading frame (ORF) analyses were performed in comparison to BCoV genome....
Effective population size is fundamental in genetics and characterizes genetic diversity. To infer past dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective over time. Among the most successful a Gaussian Markov random field (GMRF) model single gene locus. Here, we present generalization GMRF that allows analysis multilocus data. Using simulated demonstrate improved performance our method to recover true...
Abstract Summary: SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial–temporal diffusion. The software maps phylogenies annotated with both discrete continuous spatial information can export high-dimensional posterior summaries keyhole markup language (KML) for animation of the diffusion through time in virtual globe software. In addition, implements Bayes factor calculation evaluate support hypotheses...
Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral represents an integral part these analyses. Here, we present a complete overhaul the reconstruction dynamics software, now called SpreaD3 emphasize use data-driven documents, as analysis and package that primarily complements Bayesian inference BEAST ( http://beast.bio.ed.ac.uk...
In this study we date the introduction of HIV-2 into human population and estimate epidemic history subtype A in Guinea-Bissau, putative geographic origin HIV-2. The evolutionary simian immunodeficiency virus sooty mangabey /HIV-2 lineage was reconstructed by using available database sequences with known sampling dates, a timescale for calculated maximum likelihood methods. most recent common ancestor strains estimated to be 1940 ± 16 that B 1945 14. addition used coalescent theory past...
Information on global human movement patterns is central to spatial epidemiological models used predict the behavior of influenza and other infectious diseases. Yet it remains difficult test which modes dispersal drive pathogen spread at various geographic scales using standard data alone. Evolutionary analyses genome sequences increasingly provide insights into dynamics viruses, but date they have largely neglected wealth information mobility, mainly because no statistical framework exists...
Abstract The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real time. Early analyses these revealed low variation, a finding is consistent with recently emerging outbreak, but which raises question whether such are sufficiently informative for phylogenetic inferences evolutionary rates scales. phylodynamic threshold key concept refers to point at sufficient molecular change has accumulated...
Accurate understanding of the global spread emerging viruses is critical for public health responses and anticipating preventing future outbreaks. Here we elucidate when, where, how earliest sustained severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission networks became established in Europe North America. Our results suggest that rapid early interventions successfully prevented introductions virus from taking hold Germany United States. Other, later China to both Italy...
Influenza viruses undergo continual antigenic evolution allowing mutant to evade host immunity acquired previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend approaches cartography, and simultaneously characterize genetic by modeling diffusion over a shared phylogeny. Using HI data from lineages A/H3N2, A/H1N1, B/Victoria B/Yamagata, determine...
Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market Wuhan, China, was identified as a likely source of cases early reports, but later this conclusion became controversial. We show here that earliest known COVID-19 from December 2019, including those without reported direct links, were geographically centered on market. report...