News

Our new study about epidemiological hypothesis testing using phylogeographic and phylodynamic approaches

On September 21 2020 by Simon Dellicour
Our new study on landscape phylogeography has been accepted for publication in Nature Communications. In this study, we illustrate how phylogeographic and phylodynamic and analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example. Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. In our new study, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. Read more...

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

On June 16 2020 by Simon Dellicour
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on Belgium, one of the countries with the highest spatial density of sequenced SARS-CoV-2 genomes. Read more...

Ongoing epidemiological analyses of COVID-19 in Belgium

On April 19 2020 by Simon Dellicour & Marius Gilbert
The Spatial Epidemiology Lab is actively involved in several real-time analyses dedicated to the COVID-19 epidemic in Belgium. Here is an overview of ongoing analyses and preliminary results. All the scripts written and used to perform these analyses are available on the following GitHub repo. Please note that the content of this page (and GitHub repo) will be regularly updated to rapidly share updated or new results. Spatial analyses are performed in collaboration with the research teams of Catherine Linard (UNamur), Sophie Vanwambeke (UCL), and Niel Hens (UHasselt), and phylogenetic analyses are performed in collaboration with the research teams of Piet Maes and Guy Baele from the Rega Institute (KU Leuven), as well as the teams of Marie-Pierre Hayette, Vincent Bours and Keith Durkin (ULiège). Read more...

Unravelling the dispersal dynamics and ecological drivers of the African swine fever outbreak in Belgium

On April 17 2020 by Simon Dellicour
Our new study on the dispersal dynamics and ecological drivers of the African swine fever outbreak in Belgium has been accepted for publication in Journal of Applied Ecology. In this study, we present and apply a novel analytical framework that uses occurrence data to investigate the impact of environmental factors on the wavefront progression of epidemics and biological invasions. African swine fever is a devastating disease of domestic pigs and wild boars caused by African swine fever virus (ASFV). Read more...

New publication on COVID-19 in The Lancet

On February 19 2020 by Marius Gilbert
Egypt, Algeria and Republic of South Africa are the African countries most at risk for coronavirus COVID-19 importation in the continent, due to high air traffic with the contaminated Chinese provinces. But these countries are also among the best equipped on the continent to quickly detect and deal with new cases. In other African countries, the risk of importation is lower, but health organization deficiencies raise concerns about rapid spread. Read more...

A novel approach to incorporate heterogeneous sampling probabilities in phylogeographic inference

On November 21 2019 by Simon Dellicour
Our new article presenting a method to incorporate heterogeneous sampling probabilities in continuous phylogeographic inference has been accepted for publication in Bioinformatics. In this study, we present how to take advantage of external data (such as outbreak locations) to inform priors of sampling coordinates. We then apply this new method to analyse the circulation of highly pathogenic avian influenza H5N1 clades in the Mekong region. The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i. Read more...

A new paper in Science on antimicrobial resistance in low and middle countries

On September 20 2019 by Marius Gilbert
The paper aimed to produce a first global overview of antimicrobial resistance in low and middle-income countries, based on the compilation of thousands of point-prevalence surveys. The paper, published in Science describes temporal trends in the levels of resistance in farm animals, and provides a first global map of where antimicrobial resistance is the highest. The paper is lead by Thomas Van Boeckel, a former member of the lab, who now leads the Health Geography and Policy Group at ETH Zurich, and was carried out in collaboration with researchers from Princeton university and CDDEP. Read more...

New publication on methodological developments in landscape phylogeography

On September 01 2019 by Simon Dellicour
Our new article on landscape phylogeography has been accepted for publication in Molecular Ecology. In this study, we applied different post-hoc landscape phylogeographic approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran. Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially-explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Read more...

New publication on the future global distribution of Aedes aegypti and Aedes albopictus

On March 01 2019 by Marius Gilbert
Since a few years, we have been involved in the development of method to measure the rate of spread of biolgical invasions. More specifically, we published a new method to quantify the local velocity of the front wave of an invasion, and applied this method to measure the rate of spread of several bluetongue epidemics. Recently, the sampe method was applied to describe the invasion by Aedes aegypti and Aedes albopictus in US and in Europe in a large collaborative study lead by Moritz Kraemer, at the university of Oxford. Read more...

New publication on methodological developments in landscape genetics

On March 01 2019 by Simon Dellicour
Our article titled “Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments” has recently been published in Heredity. In this study, we describe and use a landscape genetic workflow to compare spatial patterns of genetic variability and the impact of environmental factors on genetic differentiation. Red deer and wild boar are two major game species whose populations are managed and live in areas impacted by human activities. Read more...