Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update

Seth Flaxman; Swapnil Mishra; Axel Gandy; H Juliette T Unwin; Helen Coupland; Thomas A Mellan; Harrison Zhu; Tresnia Berah; Jeffrey W Eaton; Pablo N P Guzman; Nora Schmit; Lucia Callizo; Imperial College COVID-19 Response Team; Charles Whittaker; Peter Winskill; Xiaoyue Xi; Azra Ghani; Christl A. Donnelly; Steven Riley; Lucy C Okell; Michaela A C Vollmer; Neil M. Ferguson; Samir Bhatt

arXiv · 2004.11342

Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update

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Abstract

Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler.

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Seth Flaxman, Swapnil Mishra, Axel Gandy, H Juliette T Unwin, Helen Coupland, Thomas A Mellan, Harrison Zhu, Tresnia Berah, Jeffrey W Eaton, Pablo N P Guzman, Nora Schmit, Lucia Callizo, Imperial College COVID-19 Response Team, Charles Whittaker, Peter Winskill, Xiaoyue Xi, Azra Ghani, Christl A. Donnelly, Steven Riley, Lucy C Okell, Michaela A C Vollmer, Neil M. Ferguson, Samir Bhatt. 2020-04-23. Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update. https://arxiv.org/abs/2004.11342

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