You can find our full list of publications here: Full list of publications
My research aims to harness genomics and the characterization of evolutionary processes to better understand the ecology of RNA viruses across scales, from within- to between hosts, from small transmission chains to epidemics, and from deep to recent evolutionary processes. My group focuses on RNA viruses infecting eukaryotes, from unicellular organisms to whales. While I work on a wide range of hosts, I have a special place in my heart for insects (including mosquitoes).
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.
Constraints on within-host evolution
Because of their high mutation rate, within their hosts, viruses exist as a population of variants. This “swarm” is shaped by important constraints from their environment (i.e. the host, other viruses, etc.).
We aim to disentangle these different constraints and characterize how they act on virus evolution.
- Lequime et al. (2016) Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes PLoS Genetics 12(6):e1006111 doi: 10.1371/journal.pgen.1006111
- Mongelli et al. (2022) Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nature Ecology & Evolution 6: 565-578. doi: 10.1038/s41559-022-01697-z
Ancient virus evolution
- Düx°, Lequime° et al. (2020) Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science 368(6497):1367-1370doi: 10.1126/science.aba9411
- Patrono et al. (2022) Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nature Communications 13(1): 2314 doi: 10.1038/s41467-022-29614-9
Viral ecology using genomics
Because RNA viruses evolve so quickly, their evolution occurs at the same timescale as their ecological (or epidemiological) processes. By reconstructing the evolutionary of a set of viral genomic sequences, we can infer some insights into their ecology, e.g. how do they spread, and where from? What are the factors that favor the spread?
- Dellicour et al. (2020) Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications 11(1):5620 doi: 10.1038/s41467-020-19122-z
Endogenous viral elements
Endogenous viral elements are full or partial integrations of viral genetic material in their hosts’ genomes. These integrations sometimes bring new functionsn, but they are a clue of the ancient history of viruses, i.e., “genomic fossils”
- Li et al. (2022) Endogenous viral elements in shrew genomes provide insights into Pestivirus ancient history. Molecular Biology and Evolution 39(10): msac190 doi: 10.1093/molbev/msac190
- Brait et al. (2024) A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data. Virus Evolution 10(1): vead088 doi: 10.1093/ve/vead088
- Brait, Hackl & Lequime (2025) detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data. Molecular Ecology Resources e14083 doi: 10.1111/1755-0998.14083
Factors influencing viral transmission
With tiny viruses, it’s sometimes easy to lose the big picture. Here we aim to connect insights collaborators and we get through experimental and field-derived work into bigger scales models for the eco/epidemiology and evolution of viruses. Can we use these models to understand what happened, happens, and will happen in eco/epidemiology of viruses?
- Lequime et al. (2020) nosoi: A stochastic agent-based transmission chain simulation framework in R. Methods in Ecology and Evolution 11:1002-1007 doi: 10.1111/2041-210X.13422
- Lequime et al. (2020) Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus. PLoS Pathogens 16(12):e1009068 doi: 10.1371/journal.ppat.1009068