Research in danger : This website and this work have been made possible by the freedom of research that tenured positions and recurrent funding guarantee. All this is threatened by the LPPR legislation that the French government wants to impose on us. For more details, see for example the analysis of the Jean-Pierre Vernant Group or the official report from the CESE..*



Our team gathers researchers, assistant professors, PhD candidates, students, engineers, both tenured and non-tenured, who work on modelling the ecology and evolution of infectious diseases.

Our expertise, both in biology and in mathematical\(^*\), statistical and computational tools, allows us to study the population aspects of the COVID-19 pandemic, which we have been doing since March 12, 2020.

This site brings together our work on the subject (mostly in French).

Tenured staff

Non-tenured staff

  • Thomas Bénéteau, PhD candidate funded by the Ligue contre le Cancer

  • Corentin Boennec, engineer in data science funded by the Occitanie Region and the ANR under the PhyEpi project

  • Gonché Danesh, PhD candidate funded by the Fondation pour la Recherche Médicale

  • Baptiste Elie, PhD candidate funded by the ENS Paris-Saclay

  • Bastien Reyné, PhD candidate funded by the University of Montpellier

  • Quentin Richard, CNRS post-doctoral fellow CNRS

ETE : Expérimental and theoretical evolution

The ecology and evolution of host-parasite\(^{**}\) interactions are indissociable and we study them by adopting both a theoretical approach and an experimental approach.

The main questions we try to address revolve around the evolution of the life-history traits of hosts and their parasites. Our experimental approaches range from characterizing the effect of point mutations to characterizing complex phenotypic effects. We also develop mathematical approaches based on conceptual models or on more applied models to analyse data.

The team also analyses clinical and epidemiological data originating from human infectious diseases such as those caused by HIV, dengue, hepatitis C virus and human papillomaviruses (HPV). We are particularly interested in analysing phylogenies originating from virus sequence data.

Finally, the team develops conceptual models to study the dynamics and evolution of infectious diseases. The models are usually based on dynamical systems that capture the epidemiology or the parasite within-host dynamics.

\(^*\): It is interesting to note that infectious disease epidemiology, population dynamics (human and non-human) and evolutionary biology all share a common methodological cornerstone, namely invasion analysis, of which the now famous basic reproductive number, \(\mathcal{R}_0\), is the ambassador. For a recent perspective on the generality of this analysis and the similarities between the theory of these three fields, see Hurford et al. 2009 (Journal of the Royal Society Interface).
\(^{**}\): In the broadest sense, any biological entity that lives and reproduces at the expense of another (the host). This term therefore encompasses viruses, bacteria, pathogenic unicellular eukaryotes, and helminths.


These reports are primarily for academic purposes. They cannot replace any national or international guidelines or expertise. In particular, the assumptions made are often deliberately simplified for the sake of clarity.

  • October 26, 2020 : Report 13 (in French) which estimates doubling times of the COVID-19 epidemics in France using hospital admission data, with a stratification per region and per department.

  • August 27, 2020: Report 12 (in French) which explores theoretical scenarios concerning SARS-CoV-2 virulence evolution based on examples from other viruses.

  • August 17, 2020: Report 11 (in French) which complements Report 10 about the potential role of G6PD deficit in explaining observed COVID-19 virulence between men and women.

  • July 30, 2020: version 2 (in English) of the software Rt to estimate the temporal reproduction number in different countries.

  • July 30, 2020 : version 2 (in english) of the software COVIDSIM to model the spread of the epidemic in France and the effect of public health measures.

  • June 24, 2020: Report 10 on co-morbidities and sex-specific effects (in French), which explores the extent to which the apparent variations in COVID-19 virulence observed between men and women could be explained by co-morbidities, in particular the G6PD deficiency.

  • June 2, 2020: Report 9 on modelling (in French), which presents the results from the preprint in English which is currently being reviewed.

  • May 20, 2020: Report on stochasticity (in French), which explores the most likely dates for the origin of the epidemic. Source files can be dowloaded as .zip file.

  • April 22, 2020: Summary report (in French) more accessible to a wide audience. Source files can be dowloaded as .zip files.

  • April 17, 2020: software and detailed note on the basic reproduction number (Rt, in French).

  • April 9, 2020: Report 6 (French version is older) using phylodynamics to detect temporal variations in epidemic spread in France.

  • April 7, 2020: Report 5 (in French for now) on the limits and delays in estimating the basic reproduction number in France. Source files can be dowloaded as .zip files.

  • April 6, 2020: software and detailed note on modelling the epidemics (COVIDSIM-FR).

  • March 30, 2020: Report 4 (in French for now) on phylodynamics of the French sequences. Source files can be dowloaded as .zip files.

  • March 24, 2020: Report 3 on a model of COVID-19 spread (R0 calculation and control). Source files can be dowloaded as .zip files.

  • March 17, 2020: Report 2 on herd immunity and total epidemic size. Source files can be dowloaded as .zip files.

  • March 14, 2020: Report 1 on the basic (\(\mathcal{R}_0\)) and efficient reproduction numbers (\(\mathcal{R}(t)\)) of the COVID-19 epidemics in France (updated on March 31). Source files can be dowloaded as .zip files.


These softwares are academic outputs. They cannot replace any national or international guidelines or expertise. In particular, the assumptions made are often deliberately simplified for the sake of clarity.

  • An estimator for the temporal reproduction number (Rt2) in various countries and French departments based on different types of times series.

  • An online simulator (COVIDSIM2) allowing to see the effect of flexible control measures (with variations in intensity and length).


Scientific work


  • Samuel Alizon (2021, Science) Superspreading genomes [PDF}].

  • Gonché Danesh, Baptiste Elie,Yannis Michalakis, Mircea T. Sofonea, Antonin Bal, Sylvie Behillil, Grégory Destras, David Boutolleau, Sonia Burrel, Anne-Geneviève Marcelin, Jean-Christophe Plantier, Vincent Thibault, Etienne Simon-Loriere, Sylvie van der Werf, Bruno Lina, Laurence Josset, Vincent Enouf, Samuel Alizon (2020, medRxiv) Early phylodynamics analysis of the COVID-19 epidemics in France [PDF], version 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology.

Submitted manuscripts

  • [preprint] Thomas Bénéteau, Baptiste Elie, Mircea T. Sofonea, Samuel Alizon (2020, medRxiv) Estimating dates of origin and end of COVID-19 epidemics [PDF]

  • [preprint] Bastien Reyné, Christian Selinger, Mircea T Sofonea, Stéphanie Miot, Amandine Pisoni, Edouard Tuaillon, Jean Bousquet, Hubert Blain, Samuel Alizon (2020, medRxiv) Wearing masks and establishing COVID-19 areas reduces secondary attack risk in nursing homes [PDF]

  • [preprint] Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea T. Sofonea (2020, medRxiv) Rt2: computing and visualising COVID-19 epidemics temporal reproduction number [PDF]

  • [preprint] Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T. Sofonea, Ramsès Djidjou-Demasse (2020, medRxiv) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic [PDF]

  • [preprint] Mircea T. Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, Yannis Michalakis, Samuel Alizon (2020, medRxiv) Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France [PDF]

  • [preprint] Ramsès Djidjou-Demasse, Yannis Michalakis, Marc Choisy, Mircea T. Sofonea, Samuel Alizon (2020, medRxiv) Optimal COVID-19 epidemic control until vaccine deployment [PDF]

Media (in English)

  • Beaten back, the coronavirus regains strength in France (The New York Times,17 Aug 2020)

  • Céline Carret (2020) 10 Questions and 4 experts on Corona, EMBO Molecular Medicine, in press

  • Pablo Rougerie (2020) Health Feedback The first SARS-CoV-2 infections in humans occurred during fall 2019, but not enough evidence exists to confirm a global spread before early 2020


Since Apr 30, 2020, we are supported by the région Occitanie in the context of its call « Urgence Recherche Covid-19 ». The French National Research Agency will support the other half of the project since Jun 16, 2020.

For the tenured researchers, our institutions (CNRS, IRD, Université de Montpellier) still trust us to choose our research subjects and provide us with some basic support. On the other hand, for those with a precarious position, this work is done at the expenses of other funded projects or in addition to their thesis or internship subjects. Without these other projects, this work could not have been carried out (at least not on this scale).

We are also grateful to the South Green platform, which gives us access to the itrop high-performance computer of the IRD in Montpellier (more details on

Finally, this work was also made possible by the availability of data related to the epidemic by Santé Publique France and the GISAID - Global Initiative on Sharing All Influenza Data initiative and to French and international laboratories for sharing viral genomic sequences.