Abstract
Background
The effective reproduction number (Rt) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of Rt during an outbreak is a major indicator used to monitor changes in disease transmission and assess the effectiveness of interventions. The estimation of Rt 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 Rt 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 Rt 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
Rt 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 Rt 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 Rt is not straightforward in practice. As this analysis has shown, the opportunity to use more readily available data to estimate Rt 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.
Publisher
Public Library of Science (PLoS)
Reference27 articles.
1. Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study.;A Camacho;PLoS Curr.,2015
2. The Effective Reproduction Number as a Prelude to Statistical Estimation of Time-Dependent Epidemic Trends.;H Nishiura;Mathematical and Statistical Estimation Approaches in Epidemiology. Dordrecht: Springer Netherlands,2009
3. Association of Public Health Interventions with the Epidemiology of the COVID-19 Outbreak in Wuhan;A Pan;China. JAMA,2020
4. Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft.;J Scire;Swiss Med Wkly.,2020
5. Report 13: Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries.;NM Ferguson;Imp Coll COVID-19 Response Team.,2020