Emerging dynamics from high-resolution spatial numerical epidemics

Abstract
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Abstract

Simulating nationwide realistic individual movements with a detailed geographical structure can help optimize public health policies. However, existing tools have limited resolution or can only account for a limited number of agents. We introduce Epidemap, a new framework that can capture the daily movement of more than 60 million people in a country at a building-level resolution in a realistic and computationally efficient way. By applying it to the case of an infectious disease spreading in France, we uncover hitherto neglected effects, such as the emergence of two distinct peaks in the daily number of cases or the importance of local density in the timing of arrival of the epidemic. Finally, we show that the importance of super-spreading events strongly varies over time.

Data availability

The raw data associated with the 100 simulations performed and the Rscripts used to generate the figures are available from theZenodo repository at https://zenodo.org/record/5542171 ( results.zip ).

The following data sets were generated

(2021) Emerging dynamics from high-resolution spatial numerical epidemics
Zenodo, doi:10.5281/zenodo.5542171.

https://doi.org/10.5281/zenodo.5542171

Article and author information

Author details

Olivier Thomine

Aix-Marseille Université / CNRS LIS, Marseille, France

For correspondence
olivier.thomine@protonmail.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4847-3224
Samuel Alizon

IRD/MIVEGEC, Montpellier, France

For correspondence
samuel.alizon@ird.fr

Competing interests
The authors declare that no competing interests exist.
Corentin Boennec

IRD/MIVEGEC, Montpellier, France

For correspondence
corentin.boennec@ird.fr

Competing interests
The authors declare that no competing interests exist.
Marc Barthelemy

Institut de physique théorique, Saclay, France

For correspondence
marc.barthelemy@ipht.fr

Competing interests
The authors declare that no competing interests exist.
Mircea Sofonea

Montpellier University, Montpellier, France

For correspondence
mircea.sofonea@umontpellier.fr

Competing interests
The authors declare that no competing interests exist.

Funding

Région Occitanie Pyrénées-Méditerranée

Samuel Alizon

Agence Nationale de la Recherche (PhyEpi project)

Samuel Alizon

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.