Data-driven multiscale dynamical framework to control a pandemic evolution with non-pharmaceutical interventions

• Published in: PloS one 2023-01, Vol.18 (1), p.e0278882
• Main Authors: Reingruber, Jürgen, Papale, Andrea, Ruckly, Stéphane, Timsit, Jean-Francois, Holcman, David
• Format: Article
• Language: English
• Subjects: Age; Asymptomatic; Availability; Biology and Life Sciences; Calibration; Changing environments; Computer applications; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - prevention & control; COVID-19 vaccines; Data mining; Disease transmission; Environmental changes; Epidemics; Epidemiologic methods; Evolution; Forecasts and trends; France; Health care industry; Herd immunity; Hospital care; Hospitalization; Hospitals; Humans; Infections; Intensive care; Mathematical models; Medicine and Health Sciences; Methods; Pandemics; Pandemics - prevention & control; Parameters; People and Places; Pharmaceuticals; Retirement homes; SARS-CoV-2; Simulation; Statistical methods; Statistics; Transition probabilities; Vaccines; Websites
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0278882

Before the availability of vaccines, many countries have resorted multiple times to drastic social restrictions to prevent saturation of their health care system, and to regain control over an otherwise exponentially increasing COVID-19 pandemic. With the advent of data-sharing, computational approaches are key to efficiently control a pandemic with non-pharmaceutical interventions (NPIs). Here we develop a data-driven computational framework based on a time discrete and age-stratified compartmental model to control a pandemic evolution inside and outside hospitals in a constantly changing environment with NPIs. Besides the calendrical time, we introduce a second time-scale for the infection history, which allows for non-exponential transition probabilities. We develop inference methods and feedback procedures to successively recalibrate model parameters as new data becomes available. As a showcase, we calibrate the framework to study the pandemic evolution inside and outside hospitals in France until February 2021. We combine national hospitalization statistics from governmental websites with clinical data from a single hospital to calibrate hospitalization parameters. We infer changes in social contact matrices as a function of NPIs from positive testing and new hospitalization data. We use simulations to infer hidden pandemic properties such as the fraction of infected population, the hospitalisation probability, or the infection fatality ratio. We show how reproduction numbers and herd immunity levels depend on the underlying social dynamics.