Modelling and predicting the spatio-temporal spread of COVID-19, associated deaths and impact of key risk factors in England

COVID-19 caseloads in England have passed through a first peak, and at the time of this analysis appeared to be gradually increasing, potentially signalling the emergence of a second wave. To ensure continued response to the epidemic is most effective, it is imperative to better understand both retrospectively and prospectively the geographical evolution of COVID-19 caseloads and deaths at small-area resolution, identify localised areas in space–time at significantly higher risk, quantify the impact of changes in localised population mobility (or movement) on caseloads, identify localised risk factors for increased mortality and project the likely course of the epidemic at high spatial resolution in coming weeks. We applied a Bayesian hierarchical space–time SEIR model to assess the spatiotemporal variability of COVID-19 caseloads (transmission) and deaths at small-area scale in England [Middle Layer Super Output Area (MSOA), 6791 units] and by week (using observed data from week 5 to 34 of 2020), including key determinants, the modelled transmission dynamics and spatial–temporal random effects. We also estimate the number of cases and deaths at small-area resolution with uncertainty projected forward in time by MSOA (up to week 51 of 2020), the impact mobility reductions (and subsequent easing) have had on COVID-19 caseloads and quantify the impact of key socio-demographic risk factors on COVID-19 related mortality risk by MSOA. Reductions in population mobility during the course of the first lockdown had a significant impact on the reduction of COVID-19 caseloads across England, however local authorities have had a varied rate of reduction in population movement which our model suggest has substantially impacted the geographic heterogeneity in caseloads at small-area scale. The steady gain in population mobility, observed from late April, appears to have contributed to a slowdown in caseload reductions towards late June and subsequent start of the second wave. MSOA with higher proportions of elderly (70+ years of age) and elderly living in deprivation, both with very distinct geographic distributions, have a significantly elevated COVID-19 mortality rates. While non-pharmaceutical interventions (that is, reductions in population mobility and social distancing) had a profound impact on the trajectory of the first wave of the COVID-19 outbreak in England, increased population mobility appears to have significantly contributed to the second wave. A number of contiguous small-areas appear to be at a significant elevated risk of high COVID-19 transmission, many of which are also at increased risk for higher mortality rates. A geographically staggered re-introduction of intensified social distancing measures is advised and limited cross MSOA movement if the magnitude and geographic extent of the second wave is to be reduced.