Section: Mathematical & Computational Biology
Topic: Biophysics and computational biology, Health sciences, Demography

Bayesian investigation of SARS-CoV-2-related mortality in France

Duchemin, Louis1; Veber, Philippe1; Boussau, Bastien1 
1 Université de Lyon, Université Lyon1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France

Corresponding author(s): Boussau, Bastien (bastien.boussau@univ-lyon1.fr)

10.24072/pcjournal.84 - Peer Community Journal, Volume 2 (2022), article no. e6.

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The SARS-CoV-2 epidemic in France has focused a lot of attention as it has had one of the largest death tolls in Europe. It provides an opportunity to examine the effect of the lockdown and of other events on the dynamics of the epidemic. In particular, it has been suggested that municipal elections held just before lockdown was ordered may have helped spread the virus. In this manuscript we use Bayesian models of the number of deaths through time to study the epidemic in 13 regions of France. We found that the models accurately predict the number of deaths 2 to 3 weeks in advance, and recover estimates that are in agreement with recent models that rely on a different structure and different input data. In particular, the lockdown reduced the viral reproduction number by ≈ 80%. However, using a mixture model, we found that the lockdown had had different effectiveness depending on the region, and that it had been slightly more effective in decreasing the reproduction number in denser regions. The mixture model predicts that 2.08 (95% CI: 1.85-2.47) million people had been infected by May 11, and that there were 2567 (95% CI: 1781-5182) new infections on May 10. We found no evidence that the reproduction numbers differ between week-ends and week days, and no evidence that the reproduction numbers increased on the election day. Finally, we evaluated counterfactual scenarios showing that ordering the lockdown 1 to 7 days sooner would have resulted in 19% to 76% fewer deaths, but that ordering it 1 to 7 days later would have resulted in 21% to 266% more deaths. Overall, the predictions of the model indicate that holding the elections on March 15 did not have a detectable impact on the total number of deaths, unless it motivated a delay in imposing the lockdown.
Published online:
DOI: 10.24072/pcjournal.84
Type: Research article

Duchemin, Louis 1; Veber, Philippe 1; Boussau, Bastien 1

1 Université de Lyon, Université Lyon1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Duchemin, Louis; Veber, Philippe; Boussau, Bastien. Bayesian investigation of SARS-CoV-2-related mortality in France. Peer Community Journal, Volume 2 (2022), article  no. e6. doi : 10.24072/pcjournal.84. https://peercommunityjournal.org/articles/10.24072/pcjournal.84/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100001

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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