Skip to main navigation menu Skip to main content Skip to site footer

Original article

Vol. 152 No. 2526 (2022)

Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study

  • Claudia Bagutti
  • Monica Alt Hug
  • Philippe Heim
  • Laura Maurer Pekerman
  • Evelyn Ilg Hampe
  • Philipp Hübner
  • Simon Fuchs
  • Miodrag Savic
  • Tanja Stadler
  • Ivan Topolsky
  • Pelin Icer Baykal
  • David Dreifuss
  • Niko Beerenwinkel
  • Sarah Tschudin Sutter
DOI
https://doi.org/10.4414/SMW.2022.w30202
Cite this as:
Swiss Med Wkly. 2022;152:w30202
Published
27.06.2022

Summary

AIMS OF THE STUDY: Wastewater-based epidemiology has contributed significantly to the comprehension of the dynamics of the current COVID-19 pandemic. Its additional value in monitoring SARS-CoV-2 circulation in the population and identifying newly arising variants independently of diagnostic testing is now undisputed. As a proof of concept, we report here correlations between SARS-CoV-2 detection in wastewater and the officially recorded COVID-19 case numbers, as well as the validity of such surveillance to detect emerging variants, exemplified by the detection of the B.1.1.529 variant Omicron in Basel, Switzerland.

METHODS: From July 1 to December 31, 2021, wastewater samples were collected six times a week from the inflow of the local wastewater treatment plant that receives wastewater from the catchment area of the city of Basel, Switzerland, comprising 273,075 inhabitants. The number of SARS-CoV-2 RNA copies was determined by reverse transcriptase-quantitative PCR. Spearman’s rank correlation coefficients were calculated to determine correlations with the median seven-day incidence of genome copies per litre of wastewater and official case data. To explore delayed correlation effects between the seven-day median number of genome copies/litre wastewater and the median seven-day incidence of SARS-CoV-2 cases, time-lagged Spearman’s rank correlation coefficients were calculated for up to 14 days. RNA extracts from daily wastewater samples were used to genotype circulating SARS-CoV-2 variants by next-generation sequencing.

RESULTS: The number of daily cases and the median seven-day incidence of SARS-CoV-2 infections in the catchment area showed a high correlation with SARS-CoV-2 measurements in wastewater samples. All correlations between the seven-day median number of genome copies/litre wastewater and the time-lagged median seven-day incidence of SARS-CoV-2 cases were significant (p<0.001) for the investigated lag of up to 14 days. Correlation coefficients declined constantly from the maximum of 0.9395 on day 1 to the minimum of 0.8016 on day 14. The B.1.1.529 variant Omicron was detected in wastewater samples collected on November 21, 2021, before its official acknowledgement in a clinical sample by health authorities.

CONCLUSIONS: In this proof-of-concept study, wastewater-based epidemiology proved a reliable and sensitive surveillance approach, complementing routine clinical testing for mapping COVID-19 pandemic dynamics and observing newly circulating SARS-CoV-2 variants.

References

  1. Ahmed W, Angel N, Edson J, Bibby K, Bivins A, O’Brien JW, et al. 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 Aug;728:138764. https://doi.org/10.1016/j.scitotenv.2020.138764
  2. Medema G, Heijnen L, Elsinga G, Italiaander R, Brouwer A. Presence of SARS-Coronavirus-2 in sewage. Environ Sci Technol Lett. 2020;7:511–6. https://doi.org/10.1021/acs.estlett.0c00357
  3. Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, et al. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. mSystems. 2020 Jul;5(4):e00614–20. https://doi.org/10.1128/mSystems.00614-20
  4. La Rosa G, Mancini P, Bonanno Ferraro G, Veneri C, Iaconelli M, Bonadonna L, et al. SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring. Sci Total Environ. 2021 Jan;750:141711. https://doi.org/10.1016/j.scitotenv.2020.141711
  5. Kitajima M, Ahmed W, Bibby K, Carducci A, Gerba CP, Hamilton KA, et al. SARS-CoV-2 in wastewater: state of the knowledge and research needs. Sci Total Environ. 2020 Oct;739:139076. https://doi.org/10.1016/j.scitotenv.2020.139076
  6. Zhu Y, Oishi W, Maruo C, Saito M, Chen R, Kitajima M, et al. Early warning of COVID-19 via wastewater-based epidemiology: potential and bottlenecks. Sci Total Environ. 2021 May;767:145124. https://doi.org/10.1016/j.scitotenv.2021.145124
  7. Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, et al. Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples. medRxiv. 2021. https://doi.org/https://doi.org/10.1101/2021.01.08.21249379
  8. Kitajima M, Sassi HP, Torrey JR. Pepper mild mottle virus as a water quality indicator. NPJ Clean Water. 2018;1(1):1–9. https://doi.org/10.1038/s41545-018-0019-5
  9. D’Aoust PM, Mercier E, Montpetit D, Jia JJ, Alexandrov I, Neault N, et al. Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence. Water Res. 2021 Jan;188:116560. https://doi.org/10.1016/j.watres.2020.116560
  10. Feng S, Roguet A, McClary-Gutierrez JS, Newton RJ, Kloczko N, Meiman JG, et al. Evaluation of Sampling, Analysis, and Normalization Methods for SARS-CoV-2 Concentrations in Wastewater to Assess COVID-19 Burdens in Wisconsin Communities. ACS ES&T Water. 2021;1(8):1955–65. https://doi.org/10.1021/acsestwater.1c00160
  11. FOPH. Reporting systems for infectious diseases requiring notification Federal Office of Public Health FOPH. Available from: https://www.bag.admin.ch/bag/de/home/krankheiten/infektionskrankheiten-bekaempfen/meldesysteme-infektionskrankheiten/meldepflichtige-ik/meldeformulare.html. (Accessed May 1, 2022)
  12. ARTICnetwork. Real-Time Molecular Epidemiology for Outbreak Response. Available from: https://artic.network/ (Accessed May 1, 2022)
  13. Posada-Céspedes S, Seifert D, Topolsky I, Jablonski KP, Metzner KJ, Beerenwinkel N. V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinformatics. 2021 Jan;37(12):1673–80. https://doi.org/10.1093/bioinformatics/btab015
  14. Chen C, Nadeau S, Yared M, Voinov P, Xie N, Roemer C, et al. CoV-Spectrum: Analysis of Globally Shared SARS-CoV-2 Data to Identify and Characterize New Variants. Bioinformatics. 2021 Dec;38(6):1735–7. https://doi.org/10.1093/bioinformatics/btab856; Epub ahead of print.
  15. Chen X, Huang Z, Wang J, Zhao S, Wong MC, Chong KC, et al. Ratio of asymptomatic COVID-19 cases among ascertained SARS-CoV-2 infections in different regions and population groups in 2020: a systematic review and meta-analysis including 130 123 infections from 241 studies. BMJ Open. 2021 Dec;11(12):e049752. https://doi.org/10.1136/bmjopen-2021-049752
  16. Yuan C, Wang H, Li K, Tang A, Dai Y, Wu B, et al. SARS-CoV-2 viral shedding characteristics and potential evidence for the priority for faecal specimen testing in diagnosis. PLoS One. 2021 Feb;16(2):e0247367. https://doi.org/10.1371/journal.pone.0247367
  17. Zheng S, Fan J, Yu F, Feng B, Lou B, Zou Q, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ. 2020 Apr;369:m1443. https://doi.org/10.1136/bmj.m1443
  18. Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020 May;581(7809):465–9. https://doi.org/10.1038/s41586-020-2196-x
  19. Schmitz BW, Innes GK, Prasek SM, Betancourt WQ, Stark ER, Foster AR, et al. Enumerating asymptomatic COVID-19 cases and estimating SARS-CoV-2 fecal shedding rates via wastewater-based epidemiology. Sci Total Environ. 2021 Dec;801:149794. https://doi.org/10.1016/j.scitotenv.2021.149794
  20. Kirby AE, Welsh RM, Marsh ZA, Yu AT, Vugia DJ, Boehm AB, et al.; New York City Department of Environmental Protection. Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater - United States, November-December 2021. MMWR Morb Mortal Wkly Rep. 2022 Jan;71(3):103–5. https://doi.org/10.15585/mmwr.mm7103a5
  21. Martin J, Klapsa D, Wilton T, Zambon M, Bentley E, Bujaki E, et al. Tracking SARS-CoV-2 in sewage: evidence of changes in virus variant predominance during COVID-19 pandemic. Viruses. 2020 Oct;12(10):1144. https://doi.org/10.3390/v12101144
  22. Izquierdo-Lara R, Elsinga G, Heijnen L, Munnink BB, Schapendonk CM, Nieuwenhuijse D, et al. Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium. Emerg Infect Dis. 2021 May;27(5):1405–15. https://doi.org/10.3201/eid2705.204410
  23. Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, et al. Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. MBio. 2021 Jan;12(1):e02703–20. https://doi.org/10.1128/mBio.02703-20
  24. Nemudryi A, Nemudraia A, Wiegand T, Surya K, Buyukyoruk M, Cicha C, et al. Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater. Cell Rep Med. 2020 Sep;1(6):100098. https://doi.org/10.1016/j.xcrm.2020.100098
  25. Heijnen L, Medema G. Surveillance of influenza A and the pandemic influenza A (H1N1) 2009 in sewage and surface water in the Netherlands. J Water Health. 2011 Sep;9(3):434–42. https://doi.org/10.2166/wh.2011.019
  26. Hellmér M, Paxéus N, Magnius L, Enache L, Arnholm B, Johansson A, et al. Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks. Appl Environ Microbiol. 2014 Nov;80(21):6771–81. https://doi.org/10.1128/AEM.01981-14
  27. Manor Y, Handsher R, Halmut T, Neuman M, Bobrov A, Rudich H, Vonsover A, Shulman L, Kew O, Mendelson E. Detection of poliovirus circulation by environmental surveillance in the absence of clinical cases in Israel and the Palestinian authority. J Clin Microbiol. 1999 Jun;37(6):1670-5. doi: https://doi.org/10.1128/JCM.37.6.1670-1675.1999. PMID: 10325305; PMCID: PMC84919.

Most read articles by the same author(s)