Welcome to the Lequime lab

Virus Ecology and Evolution

Every living organism, from bacteria and archaea to plants and humans, is expected to harbor several viruses. These obligate cellular parasites represent one of the most diverse biological entities known to us, and we just began to explore this diversity.

RNA viruses are characterized by a relatively small genome size of around 10-30 kb, a high mutation rate about one million times higher than their hosts, and big population size. These features translate into considerable genetic diversity within each host, better pictured by the existence of a population of variants (micro-evolution). Because of these features, evolutionary rates of viruses (macro-evolution) are usually several hundreds of times faster than for prokaryotes or eukaryotes.

Our 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, we use an integrated combination of "wet" (controlled experiments, field work, high-throughput sequencing) and "dry" (bioinformatics, phylodynamics, modeling and simulations) approaches.