Modelling the COVID-19 epidemics

Disclaimer

These reports are primarily for educational 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.

This work was performed by modellers from the ETE team in the MIVEGEC department (CNRS, IRD, University of Montpellier).

To date, this work has not received any dedicated funding and is designed to be independent from any private or public entity.

Reports

• March 14, 2020: Report 1 on the basic (R0) and efficient reproduction numbers (R) of the COVID-19 epidemics in France (updated on March 31). Raw files and R scripts can be downloaded as a .zip file.

• March 17, 2020: Report 2 on herd immunity and total epidemic size. Raw files and R scripts can be downloaded as a .zip file.

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

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

• • 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 downloaded as a .zip file.

• • April 9, 2020 : Report 6 (in French for now) on the phylodynamic of COVID-19 in France : temporal variations of the epidemic growth. Source files can be downloaded as a .zip file.
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  • Arpil 17, 2020: software and detailed note on the basic reproduction number (Rt, in French).
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  • April 22 , 2020 : Repport 7 summary (in French), more accessible for the general public, with different scenario of lockdown exit. Source files can be downloaded as a .zip file.
  • May 20, 2020 : Repport 8 (in french), using stochastics modelling to explore the original date of the epidemic and how many days would be needed in order to have the epidemic completly disapearing.

Scientific works

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

Some useful links about COVID-19 epidemiology

• Epidemic status is accessible through this government website
• Visualise the epidemics worlwide via a site from John Hopkins University
• Compilation of detailed epidémiological data by the MIDAS consortium
• Reports from the modeling groupe at Imperial College (and WHO partner)
• Models and analyses from the Centre for the Mathematical Modelling of Infectious Diseases at at the London School of Hygiene & Tropical Medicine, with a regular update on COVID-19 transmission in different countries.
• A flexible web application allowing to epidemiology outbreaks designed by Alison Hill.
• Nextstrain: beautiful phylogenetic analyses
• Discussions and analyses in phylodynamics

The team

The ETE modeling group ETE is composed of Samuel Alizon, Thomas Bénéteau, Marc Choisy, Gonché Danesh, Ramsès Djidjou-Demasse, Baptiste Elie, Yannis Michalakis, Bastien Reyné, Quentin Richard, Christian Selinger, Mircea Sofonea.