An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence

Mario Morvan, Anna Lo Jacomo, Celia Souque, Matthew J. Wade, Till Hoffmann, Koen Pouwels, Chris Lilley, Andrew C. Singer, Jonathan Porter, Nicholas P. Evens, David I. Walker, Joshua T. Bunce, Andrew Engeli, Jasmine Grimsley, Kathleen M. O’Reilly () and Leon Danon
Additional contact information
Mario Morvan: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Anna Lo Jacomo: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Celia Souque: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Matthew J. Wade: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Till Hoffmann: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Koen Pouwels: NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England
Chris Lilley: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Andrew C. Singer: UK Centre for Ecology & Hydrology
Jonathan Porter: National Monitoring, Starcross
Nicholas P. Evens: National Monitoring, Starcross
David I. Walker: Centre for Environment, Fisheries and Aquaculture Science
Joshua T. Bunce: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Andrew Engeli: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Jasmine Grimsley: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Kathleen M. O’Reilly: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)
Leon Danon: UK Health Security Agency (Formerly part of the Joint Biosecurity Centre, Department of Health and Social Care)

Nature Communications, 2022, vol. 13, issue 1, 1-9

Abstract: Abstract Accurate surveillance of the COVID-19 pandemic can be weakened by under-reporting of cases, particularly due to asymptomatic or pre-symptomatic infections, resulting in bias. Quantification of SARS-CoV-2 RNA in wastewater can be used to infer infection prevalence, but uncertainty in sensitivity and considerable variability has meant that accurate measurement remains elusive. Here, we use data from 45 sewage sites in England, covering 31% of the population, and estimate SARS-CoV-2 prevalence to within 1.1% of estimates from representative prevalence surveys (with 95% confidence). Using machine learning and phenomenological models, we show that differences between sampled sites, particularly the wastewater flow rate, influence prevalence estimation and require careful interpretation. We find that SARS-CoV-2 signals in wastewater appear 4–5 days earlier in comparison to clinical testing data but are coincident with prevalence surveys suggesting that wastewater surveillance can be a leading indicator for symptomatic viral infections. Surveillance for viruses in wastewater complements and strengthens clinical surveillance, with significant implications for public health.

Date: 2022
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DOI: 10.1038/s41467-022-31753-y

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