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Bayesian inference for high-dimensional discrete-time epidemic models: spatial dynamics of the UK COVID-19 outbreak
Chris P Jewell, Alison C Hale, Barry S Rowlingson, Christopher Suter, Jonathan M Read, Gareth O Roberts
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Stochastic epidemic models which incorporate interactions between space and human mobility are a key tool to inform prioritisation of outbreak control to appropriate locations. However, methods for fitting such models to national-level population data are currently unfit for purpose due to the difficulty of marginalising over high-dimensional, highly-correlated censored epidemiological event data. Here we propose a new Bayesian MCMC approach to inference on a spatially-explicit stochastic SEIR meta-population model, using a suite of novel model-informed Metropolis-Hastings samplers. We apply this method to UK COVID-19 case data, showing real-time spatial results that were used to inform UK policy during the pandemic.
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