Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number
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Published version
Author(s)
Type
Journal Article
Abstract
The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provide a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R<1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks. Here, focusing on the dynamics of the first wave (March–June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the time course of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.
Date Issued
2022-01-17
Date Acceptance
2022-01-01
Citation
Statistical Methods in Medical Research, 2022
ISSN
0962-2802
Publisher
SAGE Publications
Journal / Book Title
Statistical Methods in Medical Research
Copyright Statement
© The Author(s) 2022
License URL
Sponsor
UKRI MRC COVID-19 Rapid Response Call
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000749890000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
MC_PC19025
Subjects
Science & Technology
Life Sciences & Biomedicine
Physical Sciences
Health Care Sciences & Services
Mathematical & Computational Biology
Medical Informatics
Statistics & Probability
Mathematics
COVID-19
severe acute respiratory syndrome coronavirus 2
mathematical modelling
Markov chain Monte Carlo
Bayesian inference
epidemiology
growth rate
reproduction number
short-term forecasts
COMPUTATION
MODELS
Publication Status
Published
Date Publish Online
2022-01-17