Spatialized epidemiological forecasting applied to Covid-19 pandemic at departmental scale in France

In this paper, we present a spatialized extension of a SIR model that accounts for undetected infections and recoveries as well as the load on hospital services. The spatialized compartmental model we introduce is governed by a set of partial differential equations (PDEs) defined on a spatial domain with complex boundary. We propose to solve the set of PDEs defining our model by using a meshless numerical method based on a finite difference scheme in which the spatial operators are approximated by using radial basis functions. Such an approach is reputed as flexible for solving problems on complex domains. Then we calibrate our model on the French department of Isère during the first period of lockdown, using daily reports of hospital occupancy in France. Our methodology allows to simulate the spread of Covid-19 pandemic at a departmental level, and for each compartment. However, the simulation cost prevents from online short-term forecast. Therefore, we propose to rely on reduced order modeling to compute short-term forecasts of infection number. The strategy consists in learning a time-dependent reduced order model with few compartments from a collection of evaluations of our spatialized detailed model, varying initial conditions and parameter values. A set of reduced bases is learnt in an offline phase while the projection on each reduced basis and the selection of the best projection is performed online, allowing short-term forecast of the global number of infected individuals in the department. The original approach proposed in this paper is generic and could be adapted to model and simulate other dynamics described by a model with spatially distributed parameters of the type diffusion–reaction on complex domains. Also, the time-dependent model reduction techniques we introduced could be leveraged to compute control strategies related to such dynamics. •We introduced a spatialized SIR model with diffusion operators to better take local transmission of the infection into account.•We developed a meshless RBF-FD numerical method for its simulation.•We calibrated our model over the first wave of Covid-19 in France.•We built a metamodel from a set of evaluations of the detailed model.•We aggregated models obtained by changing the number of elements kept in the reduced basis, the aggregated model has a more robust behavior with respect to changes in the sanitary rules.