Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jul 15:200:117214.
doi: 10.1016/j.watres.2021.117214. Epub 2021 May 8.

Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK

Luke S Hillary  1 , Kata Farkas  2 , Kathryn H Maher  3 , Anita Lucaci  4 , Jamie Thorpe  2 , Marco A Distaso  5 , William H Gaze  6 , Steve Paterson  4 , Terry Burke  3 , Thomas R Connor  7 , James E McDonald  8 , Shelagh K Malham  9 , David L Jones  10
Affiliations

Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK

Luke S Hillary et al. Water Res. .

Abstract

SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiology (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease, particularly within urban centres. Here, we present a longitudinal analysis (March-July 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK (total population equivalent 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community in large urban centres, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this association was weaker in areas with lower confirmed COVID-19 case numbers. Further, sequence analysis of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants observed in wastewater reflected similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus' prevalence, and can inform public health policy decisions. Although, greater understanding of the factors that affect SARS-CoV-2 RNA concentration in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures.

Keywords: Coronavirus outbreak; Infection control; Municipal wastewater; Public health; Sewage surveillance.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Image, graphical abstract
Graphical abstract
Fig 1
Fig. 1
(a) Temporal trend of the recorded number of COVID-19 infections and deaths at six urban centres in the UK and the corresponding levels of SARS-CoV-2 in wastewater. The coloured triangles represent levels of SARS-CoV-2 in influent wastewater, with open triangles being below LoD. Grey triangles represent the number of COVID-19 reported deaths and the solid line represents the number of COVID-19 cases reported in each study region. The dashed and dotted horizontal lines represent the assay LoQ (scaled to 1180 genome copies/ 100 ml) and LoD (180 genome copies/ 100 ml) respectively, scaled for a sample volume of 100 mL. The dashed vertical line represents the imposition of UK-wide lockdown measures. (b) Correlation of SARS-CoV-2 RNA concentration (CoV) in influent wastewater with COVID-19 related cases and deaths at six urban centres in the UK. Pie charts represent Spearman correlation ρ where p < 0.05 with fullness indicating degree of correlation and colour representing positive (white) or negative (black) correlations.
Fig 2
Fig. 2
Effects of varying the number of days between wastewater sampling date and clinical testing date (x axis) and the number of days over which to sum cases over (y axis) on the strength of correlation between wastewater SARS-CoV-2 concentration and local authority positive tests. Quantities are shown where a false discovery rate corrected p-value was below 0.05.
Fig 3
Fig. 3
Coverage of the SARS-CoV-genome from reads recovered from wastewater samples. a) Frequency of the proportion of the genome sequenced at 50 × depth or greater. b) Coverage across the genome, median plotted in dark grey, interquartile ranges in purple and a smoothed GAM spline in green. c) Proportion of the genome sequenced relative to the estimated number of genome copies estimated from (RT)-qPCR. Note that sequence was obtained in several samples where the (RT)-qPCR for this locus was negative, reflecting the ability of the protocol to sequence genomes of low copy number. d) The number of SNP and indel sites detected relative to the proportion of the genome that was sequenced at 50 × or higher.
Fig 4
Fig. 4
Comparison of the mean number of SNP/ INDELs sites divided by genome coverage to (a) positive tests in the previous 7 days in the local authority, (b) sample date, (c) WWTP site and (d) log10 population equivalent.
See this image and copyright information in PMC

References

    1. Ahmed W., Angel N., Edson J., Bibby K., Bivins A., O'Brien J.W., Choi P.M., Kitajima M., Simpson S.L., Li J., Tscharke B., Verhagen R., Smith W.J.M., Zaugg J., Dierens L., Hugenholtz P., Thomas K.V., Mueller J.F. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Sci. Total Environ. 2020;728 doi: 10.1016/j.scitotenv.2020.138764. - DOI - PMC - PubMed
    1. Ahmed W., Bertsch P.M., Bibby K., Haramoto E., Hewitt J., Huygens F., Gyawali P., Korajkic A., Riddell S., Sherchan S.P., Simpson S.L., Sirikanchana K., Symonds E.M., Verhagen R., Vasan S.S., Kitajima M., Bivins A. Decay of SARS-CoV-2 and surrogate murine hepatitis virus RNA in untreated wastewater to inform application in wastewater-based epidemiology. Environ. Res. 2020;191 doi: 10.1016/j.envres.2020.110092. - DOI - PMC - PubMed
    1. Ahmed W., Bivins A., Bertsch P.M., Bibby K., Gyawali P., Sherchan S.P., Simpson S.L., Thomas K.V., Verhagen R., Kitajima M., Mueller J.F., Korajkic A. Intraday variability of indicator and pathogenic viruses in 1-h and 24-h composite wastewater samples: implications for wastewater-based epidemiology. Environ. Res. 2021;193 doi: 10.1016/j.envres.2020.110531. - DOI - PMC - PubMed
    1. Ahmed W., Tscharke B., Bertsch P.M., Bibby K., Bivins A., Choi P., Clarke L., Dwyer J., Edson J., Nguyen T.M.H., O'Brien J.W., Simpson S.L., Sherman P., Thomas K.V., Verhagen R., Zaugg J., Mueller J.F. SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: a temporal case study. Sci. Total Environ. 2021;761 doi: 10.1016/j.scitotenv.2020.144216. - DOI - PMC - PubMed
    1. Aleta A., Martín-Corral D., Pastore y Piontti A., Ajelli M., Litvinova M., Chinazzi M., Dean N.E., Halloran M.E., Longini I.M., Jr, Merler S., Pentland A., Vespignani A., Moro E., Moreno Y. Modelling the impact of testing, contact tracing and household quarantine on second waves of COVID-19. Nat. Hum. Behav. 2020;4:964–971. doi: 10.1038/s41562-020-0931-9. - DOI - PMC - PubMed