A Spatiotemporal Epidemic Model to Quantify the Effects of Contact Tracing, Testing, and Containment

We introduce a novel modeling framework for studying epidemics that is specifically designed to make use of fine-grained spatiotemporal data. Motivated by the current COVID-19 outbreak and the availability of data from contact or location tracing technologies, our model uses marked temporal point processes to represent individual mobility patterns and the course of the disease for each individual in a population. We design an efficient sampling algorithm for our model that can be used to predict the spread of infectious diseases such as COVID-19 under different testing and tracing strategies, social distancing measures, and business restrictions, given location or contact histories of individuals. Building on this algorithm, we use Bayesian optimization to estimate the risk of exposure of each individual at the sites they visit, the percentage of symptomatic individuals, and the difference in transmission rate between asymptomatic and symptomatic individuals from historical longitudinal testing data. Experiments using measured COVID-19 data and mobility patterns from Tubingen, a town in the southwest of Germany, demonstrate that our model can be used to quantify the effects of tracing, testing, and containment strategies at an unprecedented spatiotemporal resolution. To facilitate research and informed policy-making, particularly in the context of the current COVID-19 outbreak, we are releasing an open-source implementation of our framework at this https URL.