A Bayesian Spatio-Temporal Extension to Poisson Auto-Regression: Modeling the Disease Infection Rate of COVID-19 in England

Abstract: The COVID-19 pandemic provided many modeling challenges to investigate the evolution of an epidemic process over areal units. A suitable encompassing model must describe the spatio-temporal variations of the disease infection rate of multiple areal processes while adjusting for local and global inputs. We develop an extension to Poisson Auto-Regression that incorporates spatio-temporal dependence to characterize the local dynamics while borrowing information among adjacent areas. The specification includes up to two sets of space-time random effects to capture the spatio-temporal dependence and a linear predictor depending on an arbitrary set of covariates. The proposed model, adopted in a fully Bayesian framework and implemented through a novel sparse-matrix representation in Stan, provides a framework for evaluating local policy changes over the whole spatial and temporal domain of the study. It has been validated through a substantial simulation study and applied to the weekly COVID-19 cases observed in the English local authority districts between May 2020 and March 2021. The model detects substantial spatial and temporal heterogeneity and allows a full evaluation of the impact of two alternative sets of covariates: the level of local restrictions in place and the value of the Google Mobility Indices. The paper also formalizes various novel model-based investigation methods for assessing additional aspects of disease epidemiology.