SARS-CoV-2 Genome Quantification in Wastewaters at Regional and City Scale Allows Precise Monitoring of the Whole Outbreaks Dynamics and Variants Spreading in the Population

Overview

Journal Sci Total Environ

Date 2021 Dec 13

PMID 34896511

Citations 26

Authors

S Wurtzer

P Waldman

M Levert

N Cluzel

J L Almayrac

C Charpentier

S Masnada

M Gillon-Ritz

J M Mouchel

Y Maday

M Boni

V Marechal

L Moulin

Affiliations

Soon will be listed here.

Abstract

SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several "waves" of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.

Citing Articles

Wastewater-Based Epidemiological Surveillance in France: The SUM'EAU Network.

Jourdain F, Toro L, Senta-Loys Z, Deryene M, Mokni W, Azevedo Da Graca T Microorganisms. 2025; 13(2).

PMID: 40005648 PMC: 11857653. DOI: 10.3390/microorganisms13020281.

Wastewater-based epidemiology: deriving a SARS-CoV-2 data validation method to assess data quality and to improve trend recognition.

Saravia C, Putz P, Wurzbacher C, Uchaikina A, Drewes J, Braun U Front Public Health. 2024; 12:1497100.

PMID: 39735750 PMC: 11674844. DOI: 10.3389/fpubh.2024.1497100.

Multisite community-scale monitoring of respiratory and enteric viruses in the effluent of a nursing home and in the inlet of the local wastewater treatment plant.

Manoha C, Dequiedt A, Thery L, Marotel M, Pez F, Vouillon B Appl Environ Microbiol. 2024; 90(11):e0115824.

PMID: 39387558 PMC: 11577779. DOI: 10.1128/aem.01158-24.

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis.

Veneri C, Brandtner D, Mancini P, Bonanno Ferraro G, Iaconelli M, Suffredini E Food Environ Virol. 2024; 16(4):449-457.

PMID: 38918335 PMC: 11525314. DOI: 10.1007/s12560-024-09607-1.

SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic.

DAoust P, Hegazy N, Ramsay N, Yang M, Dhiyebi H, Edwards E Sci Data. 2024; 11(1):656.

PMID: 38906875 PMC: 11192951. DOI: 10.1038/s41597-024-03414-w.

References

Weidhaas J, Aanderud Z, Roper D, VanDerslice J, Gaddis E, Ostermiller J . Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds. Sci Total Environ. 2021; 775:145790. PMC: 7879159. DOI: 10.1016/j.scitotenv.2021.145790. View

Sun K, Viboud C . Impact of contact tracing on SARS-CoV-2 transmission. Lancet Infect Dis. 2020; 20(8):876-877. PMC: 7185949. DOI: 10.1016/S1473-3099(20)30357-1. View

Ogorzaly L, Gantzer C . Development of real-time RT-PCR methods for specific detection of F-specific RNA bacteriophage genogroups: application to urban raw wastewater. J Virol Methods. 2006; 138(1-2):131-9. DOI: 10.1016/j.jviromet.2006.08.004. View

Ferretti L, Wymant C, Kendall M, Zhao L, Nurtay A, Abeler-Dorner L . Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing. Science. 2020; 368(6491). PMC: 7164555. DOI: 10.1126/science.abb6936. View

ODriscoll M, Ribeiro Dos Santos G, Wang L, Cummings D, Azman A, Paireau J . Age-specific mortality and immunity patterns of SARS-CoV-2. Nature. 2020; 590(7844):140-145. DOI: 10.1038/s41586-020-2918-0. View

Schmittgen T, Livak K . Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008; 3(6):1101-8. DOI: 10.1038/nprot.2008.73. View

Haramoto E, Kitajima M, Kishida N, Konno Y, Katayama H, Asami M . Occurrence of pepper mild mottle virus in drinking water sources in Japan. Appl Environ Microbiol. 2013; 79(23):7413-8. PMC: 3837739. DOI: 10.1128/AEM.02354-13. View

Medema G, Heijnen L, Elsinga G, Italiaander R, Brouwer A . Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands. Environ Sci Technol Lett. 2023; 7(7):511-516. DOI: 10.1021/acs.estlett.0c00357. View

Kishimoto M, Tsuchiaka S, Rahpaya S, Hasebe A, Otsu K, Sugimura S . Development of a one-run real-time PCR detection system for pathogens associated with bovine respiratory disease complex. J Vet Med Sci. 2017; 79(3):517-523. PMC: 5383171. DOI: 10.1292/jvms.16-0489. View

10.

Wurtzer S, Marechal V, Mouchel J, Maday Y, Teyssou R, Richard E . Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. Euro Surveill. 2020; 25(50). PMC: 7812418. DOI: 10.2807/1560-7917.ES.2020.25.50.2000776. View

11.

Yang J, Zheng Y, Gou X, Pu K, Chen Z, Guo Q . Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis. Int J Infect Dis. 2020; 94:91-95. PMC: 7194638. DOI: 10.1016/j.ijid.2020.03.017. View

12.

Di Domenico L, Sabbatini C, Pullano G, Levy-Bruhl D, Colizza V . Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France. Euro Surveill. 2021; 26(15). PMC: 8167415. DOI: 10.2807/1560-7917.ES.2021.26.15.2100272. View

13.

Prevost B, Lucas F, Goncalves A, Richard F, Moulin L, Wurtzer S . Large scale survey of enteric viruses in river and waste water underlines the health status of the local population. Environ Int. 2015; 79:42-50. DOI: 10.1016/j.envint.2015.03.004. View

14.

Mizumoto K, Kagaya K, Zarebski A, Chowell G . Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020. Euro Surveill. 2020; 25(10). PMC: 7078829. DOI: 10.2807/1560-7917.ES.2020.25.10.2000180. View

15.

Corman V, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D . Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020; 25(3). PMC: 6988269. DOI: 10.2807/1560-7917.ES.2020.25.3.2000045. View

16.

Harvey W, Carabelli A, Jackson B, Gupta R, Thomson E, Harrison E . SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7):409-424. PMC: 8167834. DOI: 10.1038/s41579-021-00573-0. View

17.

Bertrand I, Challant J, Jeulin H, Hartard C, Mathieu L, Lopez S . Epidemiological surveillance of SARS-CoV-2 by genome quantification in wastewater applied to a city in the northeast of France: Comparison of ultrafiltration- and protein precipitation-based methods. Int J Hyg Environ Health. 2021; 233:113692. PMC: 7847400. DOI: 10.1016/j.ijheh.2021.113692. View

18.

Ahmed W, Tscharke B, Bertsch P, Bibby K, Bivins A, Choi P . 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. 2020; 761:144216. PMC: 7718102. DOI: 10.1016/j.scitotenv.2020.144216. View

19.

Stachler E, Kelty C, Sivaganesan M, Li X, Bibby K, Shanks O . Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement. Environ Sci Technol. 2017; 51(16):9146-9154. PMC: 7350147. DOI: 10.1021/acs.est.7b02703. View

20.

Wurtzer S, Prevost B, Lucas F, Moulin L . Detection of enterovirus in environmental waters: a new optimized method compared to commercial real-time RT-qPCR kits. J Virol Methods. 2014; 209:47-54. DOI: 10.1016/j.jviromet.2014.08.016. View