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Philos Trans A Math Phys Eng Sci ; 380(2233): 20210301, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-1992459

ABSTRACT

We present a method for rapid calculation of coronavirus growth rates and [Formula: see text]-numbers tailored to publicly available UK data. We assume that the case data comprise a smooth, underlying trend which is differentiable, plus systematic errors and a non-differentiable noise term, and use bespoke data processing to remove systematic errors and noise. The approach is designed to prioritize up-to-date estimates. Our method is validated against published consensus [Formula: see text]-numbers from the UK government and is shown to produce comparable results two weeks earlier. The case-driven approach is combined with weight-shift-scale methods to monitor trends in the epidemic and for medium-term predictions. Using case-fatality ratios, we create a narrative for trends in the UK epidemic: increased infectiousness of the B1.117 (Alpha) variant, and the effectiveness of vaccination in reducing severity of infection. For longer-term future scenarios, we base future [Formula: see text] on insight from localized spread models, which show [Formula: see text] going asymptotically to 1 after a transient, regardless of how large the [Formula: see text] transient is. This accords with short-lived peaks observed in case data. These cannot be explained by a well-mixed model and are suggestive of spread on a localized network. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Subject(s)
Coronavirus , Epidemics , Epidemics/prevention & control , Reproduction , United Kingdom/epidemiology
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