Monitoring the reproductive number of COVID-19 in France: Comparative estimates from three datasets

Christophe Bonaldi (1) , Anne Fouillet (1) , Cécile Sommen (1) , Daniel Lévy-Bruhl (2) , Juliette Paireau (2, 3)

1 Direction appui, traitements et analyses de données - Data Support, Processing and Analysis Division [Santé publique France, Saint-Maurice]
2 Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice]
3 Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases

Background: The effective reproduction number (R t ) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of R t during an outbreak is a major indicator used to monitor changes in disease transmission and assess the effectiveness of interventions. The estimation of R t usually requires the identification of infected cases in the population, which can prove challenging with the available data, especially when asymptomatic people or with mild symptoms are not usually screened. The purpose of this study was to perform sensitivity analysis of R t estimates for COVID-19 surveillance in France based on three data sources with different sensitivities and specificities for identifying infected cases. Methods: We applied a statistical method developed by Cori et al. to estimate R t using (1) confirmed cases identified from positive virological tests in the population, (2) suspected cases recorded by a national network of emergency departments, and (3) COVID-19 hospital admissions recorded by a national administrative system to manage hospital organization. Results: R t estimates in France from May 27, 2020, to August 12, 2022, showed similar temporal trends regardless of the dataset. Estimates based on the daily number of confirmed cases provided an earlier signal than the two other sources, with an average lag of 3 and 6 days for estimates based on emergency department visits and hospital admissions, respectively. Conclusion: The COVID-19 experience confirmed that monitoring temporal changes in R t was a key indicator to help the public health authorities control the outbreak in real time. However, gaining access to data on all infected people in the population in order to estimate R t is not straightforward in practice. As this analysis has shown, the opportunity to use more readily available data to estimate R t trends, provided that it is highly correlated with the spread of infection, provides a practical solution for monitoring the COVID-19 pandemic and indeed any other epidemic.

Domaines: Santé publique et épidémiologie

Christophe Bonaldi, Anne Fouillet, Cécile Sommen, Daniel Lévy-Bruhl, Juliette Paireau. Monitoring the reproductive number of COVID-19 in France: Comparative estimates from three datasets. PLoS ONE, 2023, 18 (10), pp.e0293585. ⟨10.1371/journal.pone.0293585⟩. ⟨pasteur-04388729⟩