I am an assistant professor in Microbial Ecology and Evolution at the University of Groningen (the Netherlands). I obtained my Pharm.D. from the University of Tours (France) and my Ph.D. from the University Pierre-et-Marie Curie (Paris, France). I then did a postdoc at the University of Leuven (Belgium).
My research aims to characterize evolutionary pressures and dynamics that impact the evolution of viruses across scales, from within- to between-hosts, from small transmission chains to epidemics and from deep to recent evolutionary processes. Because viral evolution takes place at the same time scale as viral ecological processes, its study can uncover some insights into virus ecology: How do they spread? Where do they come from? What is their host range? All critical pieces of information to understand and manage their impact on us, on our domesticated animals and plants, on our ecosystems and even on our whole biosphere.
To explore these questions, I use an integrated combination of “wet” (controlled experiments, fieldwork, high-throughput sequencing) and “dry” (bioinformatics, phylodynamics, modeling, and simulations) approaches.
Do you want to know more about my team (Virus Ecology and Evolution) and its research? Please visit our official page hosted on the University of Groningen’s website.
Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing [Nature Communications]
In this study, we showcase how you can use state-of-the-art phylogeography and phylodynamics to infer epidemiological parameters and test hypotheses, using the well covered West Nile virus emergence in northern America.
S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, O. G. Pybus & P. Lemey (2020) Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing. Nature Communications. In press.
Measles virus and rinderpest virus divergence dated to the sixth century BCE [Science]
In this work, we take advantage of the full-length genome sequence of a measles morbillivirus from 1912 to explore anew the origin and emergence of measles using phylogenetics. This study lead us to estimate a divergence date around the 6th century BCE, a time when human settlements started hosting more inhabitants.
A. Düx*, S. Lequime*, L. V. Patrono, B. Vrancken, S. Boral, J. F. Gogarten, A. Hilbig, D. Horst, K. Merkel, B. Prepoint, S. Santibanez, J. Schlotterbeck, M. A. Suchard, M. Ulrich, N. Widulin, A. Mankertz, F. H. Leendertz, K. Harper, P. Lemey* & S. Calvignac-Spencer* (2020) Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science 368(6497): 1367-1370.
Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes [PLoS Genetics]
In this work, we explore the evolutionary constraints acting on dengue virus upon infection of its mosquito vector Aedes aegypti. We characterized an infection bottleneck and strong purifying selection, as well as an impact of vector genotype on within-host genetic diversity.
S. Lequime, A. Fontaine, M. Ar Gouilh, I. Conclois-Moltini & L. Lambrechts (2016) Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PLoS Genet. 12(6): e1006111.