Bayesian inference across multiple models suggests a strong increase in lethality of COVID-19 in late 2020 in the UK.

Patrick Pietzonka,William Bankes,Robert L Jack,Erik Brorson,Michael E Cates,Ronojoy Adhikari,Jeffrey Shaman

doi:10.1371/journal.pone.0258968

Patrick Pietzonka, William Bankes + Show 5 more

Open Access

https://doi.org/10.1371/journal.pone.0258968

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Abstract

We apply Bayesian inference methods to a suite of distinct compartmental models of generalised SEIR type, in which diagnosis and quarantine are included via extra compartments. We investigate the evidence for a change in lethality of COVID-19 in late autumn 2020 in the UK, using age-structured, weekly national aggregate data for cases and mortalities. Models that allow a (step-like or graded) change in infection fatality rate (IFR) have consistently higher model evidence than those without. Moreover, they all infer a close to two-fold increase in IFR. This value lies well above most previously available estimates. However, the same models consistently infer that, most probably, the increase in IFR preceded the time window during which variant B.1.1.7 (alpha) became the dominant strain in the UK. Therefore, according to our models, the caseload and mortality data do not offer unequivocal evidence for higher lethality of a new variant. We compare these results for the UK with similar models for Germany and France, which also show increases in inferred IFR during the same period, despite the even later arrival of new variants in those countries. We argue that while the new variant(s) may be one contributing cause of a large increase in IFR in the UK in autumn 2020, other factors, such as seasonality, or pressure on health services, are likely to also have contributed.

Highlights

The alpha variant B.1.1.7 of the SARS-CoV-2 virus first emerged in the UK in September 2020
As we have centred the prior for the factor of change in infection fatality rate (IFR) to the value 1, the prior always decreases with a change in IFR, but this reduction of the prior is overbalanced by quite some margin by the increased likelihood derived from data
We have reported evidence for an increase in lethality of COVID-19 in the UK in late autumn 2020

Summary

Introduction

The alpha variant B.1.1.7 of the SARS-CoV-2 virus first emerged in the UK in September 2020. It is well known to be more infectious than the prior UK strain and for this reason, in the following months, it became dominant in the UK itself, but rapidly took hold in a number of other countries (including the USA) where it soon became the dominant variant [1]. It is less certain whether B.1.1.7 led to more severe cases of COVID-19, resulting in turn in a higher fatality rate [2, 3].

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