Peter Congdon1. 1. School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
Abstract
BACKGROUND: The evolution of the COVID-19 epidemic has been accompanied by efforts to provide comparable international data on new cases and deaths. There is also accumulating evidence on the epidemiological parameters underlying COVID-19. Hence, there is potential for epidemic models providing mid-term forecasts of the epidemic trajectory using such information. The effectiveness of lockdown or lockdown relaxation can also be assessed by modelling later epidemic stages, possibly using a multiphase epidemic model. METHODS: Commonly applied methods to analyse epidemic trajectories or make forecasts include phenomenological growth models (e.g., the Richards family of densities) and variants of the susceptible-infected-recovered (SIR) compartment model. Here, we focus on a practical forecasting approach, applied to interim UK COVID data, using a bivariate Reynolds model (for cases and deaths), with implementation based on Bayesian inference. We show the utility of informative priors in developing and estimating the model and compare error densities (Poisson-gamma, Poisson-lognormal, and Poisson-log-Student) for overdispersed data on new cases and deaths. We use cross validation to assess medium-term forecasts. We also consider the longer-term postlockdown epidemic profile to assess epidemic containment, using a two-phase model. RESULTS: Fit to interim mid-epidemic data show better fit to training data and better cross-validation performance for a Poisson-log-Student model. Estimation of longer-term epidemic data after lockdown relaxation, characterised by protracted slow downturn and then upturn in cases, casts doubt on effective containment. CONCLUSIONS: Many applications of phenomenological models have been to complete epidemics. However, evaluation of such models based simply on their fit to observed data may give only a partial picture, and cross validation against actual trends is also valuable. Similarly, it may be preferable to model incidence rather than cumulative data, although this raises questions about suitable error densities for modelling often erratic fluctuations. Hence, there may be utility in evaluating alternative error assumptions.
BACKGROUND: The evolution of the COVID-19 epidemic has been accompanied by efforts to provide comparable international data on new cases and deaths. There is also accumulating evidence on the epidemiological parameters underlying COVID-19. Hence, there is potential for epidemic models providing mid-term forecasts of the epidemic trajectory using such information. The effectiveness of lockdown or lockdown relaxation can also be assessed by modelling later epidemic stages, possibly using a multiphase epidemic model. METHODS: Commonly applied methods to analyse epidemic trajectories or make forecasts include phenomenological growth models (e.g., the Richards family of densities) and variants of the susceptible-infected-recovered (SIR) compartment model. Here, we focus on a practical forecasting approach, applied to interim UK COVID data, using a bivariate Reynolds model (for cases and deaths), with implementation based on Bayesian inference. We show the utility of informative priors in developing and estimating the model and compare error densities (Poisson-gamma, Poisson-lognormal, and Poisson-log-Student) for overdispersed data on new cases and deaths. We use cross validation to assess medium-term forecasts. We also consider the longer-term postlockdown epidemic profile to assess epidemic containment, using a two-phase model. RESULTS: Fit to interim mid-epidemic data show better fit to training data and better cross-validation performance for a Poisson-log-Student model. Estimation of longer-term epidemic data after lockdown relaxation, characterised by protracted slow downturn and then upturn in cases, casts doubt on effective containment. CONCLUSIONS: Many applications of phenomenological models have been to complete epidemics. However, evaluation of such models based simply on their fit to observed data may give only a partial picture, and cross validation against actual trends is also valuable. Similarly, it may be preferable to model incidence rather than cumulative data, although this raises questions about suitable error densities for modelling often erratic fluctuations. Hence, there may be utility in evaluating alternative error assumptions.