At the Spatial Epidemiology Lab (SpELL), we study the effect of spatial factors on the emergence, spread, persistence and evolution of diseases and invasive species. The understanding of key spatial factors, such as climatic, ecological or anthropogenic variables, and their integration into spatial and/or molecular approaches is used to predict the geographical distribution of risk and the environmental factors impacting the dispersal history and dynamic of pathogen spreads, which can contribute to better targetted prevention, surveillance and control measures. We also work toward the development, improvement and application of methods in spatial modelling of biological invasions, ecological niche modelling for risk mapping, and landscape phylogeography. The SpELL is also involved in the assembly of large-scale data sets on farm animals and in studies dedicated to the conservation of insect pollinators.
On May 29 2025 by Fabiana Gámbaro & Simon Dellicour
African swine fever virus (ASFV) is a highly virulent DNA virus that causes African swine fever, a severe hemorrhagic disease affecting domestic and wild pigs, leading to significant animal health burdens and economic losses. Initially limited to the sub-Saharan African region, ASFV genotype II has spread globally and is now a major concern in Africa, Europe, Asia, the Pacific and, more recently, the Caribbean. In this study, we performed phylogenetic and phylogeographic analyses using newly sequenced ASFV genomes from Lithuania, combined with previously available complete genomes, to investigate the spatiotemporal dispersal dynamics of ASFV genotype II in Europe. Read more...
On May 15 2025 by Simon Dellicour
In Europe, highly pathogenic avian influenza (HPAI) virus continues to circulate in avian wildlife and undergo frequent reassortment, sporadic introductions in domestic birds, and spillover to mammals. An H5N1 clade 2.3.4.4b reassortant, EA-2023-DG, affecting wild and domestic birds was detected in western Europe in November 2023. Six of its RNA segments came from the EA-2021-AB genotype, but the PB2 and PA segments originated from low pathogenicity avian influenza viruses. In this new study, we analysed the genesis and spread of this reassortant genotype in western Europe. Read more...
On May 07 2025 by Simon Dellicour
The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. In a new comprehensive study, we employed phylogenetic inference while accounting for recombination of bat sarbecoviruses and found that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses showed bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. Read more...
Spatially-explicit phylogeographic analyses can be used to reconstruct the dispersal history of viral lineages. Over the last years, we started exploiting such phylogeographic reconstructions to investigate the impact on environmental factors on the dispersal dynamic of viral lineages (dispersal velocity, dispersal position, and dispersal frequency). Furthermore, we also aim to use phylogeographic reconstruction to assess hypothetical intervention strategies in the context of viral epidemics.
See moreWe further develop and applies methodologies to conduct ecological niche modelling for the risk mapping of infectious diseases. Our research initially focused on avian influenza, with a particular emphasis on the role of agro-ecological factors on its emergence and persistence, but we have then also worked on other important livestock diseases such as bluetongue, bovine tuberculosis, and Nipah virus infections. More recently, we have conducted studies dedicated to the impact of climate and land-use changes on the distribution of pathogens of OneHealth importance such as the Lassa virus in Africa and the West Nile virus in Europe.
See moreInvading organisms spreading though an heterogeneous landscape are difficult to study using conventional statistical models. We aim to review existing methods, to develop new methodologies to study those type of data, and to compare all methods in their capacity to detect the influence of landscape heterogeneity on the pattern of spread. In particular, we have developed an analytical framework that allows testing the impact of continuous environmental layer as well as barriers on a wavefront progression.
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