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..*

Team

Presentation

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 Beneteau, PhD candidate funded by the Ligue contre le Cancer

  • Corentin Boennec, ex-engineer in statistics and computer sciences funded by the Occitanie Region and the ANR under the PhyEpi project, now PhD candidate in Toulouse

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

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

  • Alexander Massey, engineer in statistics and computer sciences funded by the Occitanie Region and the ANR under the PhyEpi project

  • Claudia Ximena Restrepo Ortiz, engineer from the KIM data of the University of Montpellier

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

  • Quentin Richard, ex-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.

Reports

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.

  • December 23, 2021 : Report 16 (in French) which explores two scenarios of omicron spread using mathematical modelling.

  • December 17, 2021 : Report 15 (in French) which estimates the spread of the Omicron variant in France using screening and sequencing data (updated on Dec 20).

  • February 17, 2021 : Report 14 (in French) which estimates the spread of the first variants of concern in France.

  • 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.

Softwares

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.

We thanl the French Institute for Bioinformatics and the bioinfo IRD server for hosting us!

Publications

Scientific work

Peer-reviewed

  • Mircea T Sofonea, Bénédicte Roquebert, Vincent Foulongne, David Morquin, Laura Verdurme, Sabine Trombert-Paolantoni, Mathilde Roussel, Jean-Christophe Bonetti, Judith Zerah, Stéphanie Haim-Boukobza, Samuel Alizon (2022, Emerging Infectious Diseases) Analyzing and modeling the spread of SARS-CoV-2 Omicron lineages BA.1 and BA.2 in France (September 1, 2021, to February 28, 2022). [PDF]

  • Baptiste Elie, Emmanuel Lecorche, Mircea T Sofonea, Sabine Trombert-Paolantoni, Laura Verdurme, Jérémie Guedj, Vincent Foulongne, Stéphanie Haim-Boukobza, Bénédicte Roquebert, Samuel Alizon (2022, Journal of Medical Virology) Variant-specific SARS-CoV-2 within-host kinetics. [PDF]

  • Bastien Reyné, Quentin Richard, Christian Selinger, Mircea T. Sofonea, Ramsès Djidjou-Demasse, Samuel Alizon (2022, MMNP) Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics [PDF]

  • Samuel Alizon, Christian Selinger, Mircea T Sofonea, Haim-Boukobza S, Giannoli J-M, Ninove L, Pillet S, Vincent T, Rougemont A de, Tumiotto C, Solis M, Stephan R, Bressollette-Bodin C, Salmona M, L’Honneur A-S, Behillil S, Lefeuvre C, Dina J, Hantz S, Hartard C, Veyer D, Delagreverie HM, Fourati S, Visseaux B, Henquell C, Lina B, Foulougne V, Burrel S. (2022, Eurosurveillance) Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values [PDF]

  • [review] Samuel Alizon, Mircea T. Sofonea (2021, Journal of Evolutionary Biology). SARS-CoV-2 virulence evolution: avirulence theory, immunity, and trade-offs [PDF]

  • Olivier Thomine, Samuel Alizon, Marc Barthelemy, Corentin Boenec, Mircea T. Sofonea (2021, eLife). Emerging dynamics from high-resolution spatial numerical epidemics. [PDF]

  • Bénédicte Roquebert, Stéphanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, Vincent Foulongne, Sonia Burrel, Samuel Alizon, Mircea T Sofonea (2021, International Journal of Infectious Diseases) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France [PDF]

  • [forum] Yannis Michalakis, Mircea T. Sofonea, Samuel Alizon, Ignacio G Bravo (2021, Trends in Microbiology) SARS-CoV-2 viral RNA levels are not “viral load”. [PDF]

  • [editorial] Mircea T.Sofonea, Samuel Alizon (2021, Anaesthesia Critical Care & Pain Medicine) Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France.

  • Christian Selinger, Marc Choisy, Samuel Alizon (2021, International Journal of Infectious Diseases) Predicting COVID-19 incidence in French hospitals using human contact network analytics. [PDF]

  • Samuel Alizon, Stephanie Haim-Boukobza, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, Emmanue Lecorche, Benedicte Roquebert, Mircea T. Sofonea (2021, Eurosurveillance) Rapid spread of the SARS-CoV-2 δ variant in some French regions in June 2021. [PDF]

  • Thomas Beneteau, Baptiste Elie, Mircea T. Sofonea, Samuel Alizon (2021, Peer Community Journal) Estimating dates of origin and end of COVID-19 epidemics [PDF]

  • Bénédicte Roquebert, Sabine Trombert-Paolantoni, Stéphanie Haim-Boukobza, Emmanuel Lecorche, Laura Verdurme, Vincent Foulongne, Mircea T Sofonea, Samuel Alizon (2021, Eurosurveillance) The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021 [PDF]

  • [editorial] Mircea T.Sofonea, Corentin Boennec, Yannis Michalakis, Samuel Alizon (2021, Anaesthesia Critical Care & Pain Medicine) Two waves and a high tide: the COVID-19 epidemic in France [PDF]

  • Bastien Reyné, Christian Selinger, Mircea T Sofonea, Stéphanie Miot, Amandine Pisoni, Edouard Tuaillon, Jean Bousquet, Hubert Blain, Samuel Alizon (2021, International Journal of Epidemiology) Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities [PDF]

  • Mircea T. Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, Yannis Michalakis, Samuel Alizon (2021, Epidemics) Memory is key in capturing COVID-19 epidemiological dynamics [PDF]

  • Stéphanie Haim-Boukobza, Bénédicte Roquebert, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, Vincent Foulongne, Christian Selinger, Yannis Michalakis, Mircea T Sofonea, Samuel Alizon (2021, Emerging Infectious Diseases) Detecting rapid spread of SARS-CoV-2 variants, France, January 26–February 16, 2021 [PDF]

  • Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T. Sofonea, Ramsès Djidjou-Demasse (2021, PLoS Computational Biology) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic [PDF]

  • [perspective] 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 (2021, Peer Community Journal) Early phylodynamics analysis of the COVID-19 epidemics in France [PDF].

Submitted manuscripts

  • [preprint] Bastien Reyné, Mircea T. Sofonea, Samuel Alizon (2022, medRxiv) Modelling long-term COVID-19 hospital admission dynamics using immune protection waning data [PDF]

  • [preprint] Gonche Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert, Benoit Visseaux, Stephanie Haim-Boukobza, Samuel Alizon (2022, bioRxiv ) COVFlow: virus phylodynamics analyses from selected SARS-CoV-2 sequences [PDF ]

  • [preprint] Mircea T Sofonea, Bénédicte Roquebert, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, Mathilde Roussel, Stéphanie Haim-Boukobza, Samuel Alizon (2022, medRxiv) From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021). [PDF]

  • [preprint] Corentin Boennec, Samuel Alizon, Mircea T. Sofonea (2021, medRxiv) Anticipating the hospital burden of future COVID-19 epidemic waves. [PDF]

  • [preprint] Baptiste Elie, Emmanuel Lecorche, Mircea T Sofonea, Sabine Trombert-Paolantoni, Laura Verdurme, Jérémie Guedj, Vincent Foulongne, Stéphanie Haim-Boukobza, Bénédicte Roquebert, Samuel Alizon (2021, medRxiv) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. [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] 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)

  • Is the Covid-19 pandemic ‘over’? Biden’s bold declaration raises questions (France 24, 20 Sept 2022)

  • France: Vaccination alone won’t be enough to break the fourth Covid wave, researcher says (RFI, 20 Jul 2021)

  • Europe wields the stick to boost vaccination as Delta variant spreads (Financial Times, 16 Jul 2021)

  • SARS-CoV-2 variants have higher transmissibility and a longer infectious period (News Medical, 31 May 2020)

  • 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

Support

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 bioinfo.ird.fr).

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.