Viral genomes contain a lot of information. About viruses themselves, of course, but also about how they evolved and spread in space and time. It can even tell us some things about their hosts…
Every living organism, from bacteria 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.
Our interest is mostly focused on RNA viruses. They 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 tries 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 this evolution takes place at the same time scale as their ecological processes, we can also uncover some insights into their ecology: How do they spread? Where do they come from? What is their host range?
To answer these questions, we use an integrated combination of experimental, observational, and computational approaches. We mostly study members of the Flavivirus genus. Indeed, albeit a relatively conserved set of genetic and structural features, its members infect a wide range of hosts (such as primates, rodents, birds, fishes, arthropods and nematodes; sometimes even several groups at once) and present the full array of symbiotic interactions with their host (from pathogenic to mutualistic) as well as infection dynamics (from acute to chronic). Moreover, they count some important human pathogens, such as Zika, dengue, or yellow fever viruses.