The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices
Authors: Nightingale Emily S. , Abbott Sam , Russell Timothy W. ,   CMMID Covid-19 Working Group, Rees Eleanor M. , Eggo Rosalind M. , Quaife Matthew , Sun Fiona Yueqian , Pearson Carl A. B. , Prem Kiesha , Munday James D. , Meakin Sophie R. , Medley Graham , van Zandvoort Kevin , Edmunds W. John , Rosello Alicia , Funk Sebastian , O’Reilly Kathleen , Quilty Billy J. , Procter Simon R. , Gimma Amy , Kucharski Adam J. , Deol Arminder K. , Emery Jon C. , Bosse Nikos I. , Gibbs Hamish P. , Simons David , Hué Stéphane , Jarvis Christopher I. , Klepac Petra , Liu Yang , Foss Anna M. , Diamond Charlie , Villabona-Arenas C. Julian , Endo Akira , Houben Rein M. G. J. , Flasche Stefan , Russell Timothy W. , Clifford Samuel , Knight Gwenan M. , Hellewell Joel , Davies Nicholas G. , Atkins Katherine E. , Tully Damien C. , Auzenbergs Megan , Jit Mark , Lowe Rachel , Medley Graham F. , Brady Oliver J. 
Published: April 2022

Abstract
Background
The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (“pillar 1”) before expanding to community-wide symptomatics (“pillar 2”). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths.

Methods
We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020–30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.

Results
A model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000–420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%.

Conclusions
Limitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.