Department Urban Water Management

SARS-CoV-2 in Wastewater

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Team

Project description

Wastewater based epidemiology provides insights into the disease burden and disease dynamics of the current COVID-19 pandemic. Through surveillance of wastewater for the presence of SARS-CoV-2 RNA at wastewater treatment plants throughout Switzerland, wastewater complements other epidemiological indicators, such as reported cases, to help inform COVID-19 disease dynamics.  SARS-CoV-2 RNA in wastewater also provides insights into the circulation of Variants of Concern through targeted detection of signature mutations as well as through whole genome sequencing.  In this project, we continue to develop, apply, and evaluate methods for sensitive and specific detection of SARS-CoV-2 and other pathogens in wastewater to help inform disease dynamics.

Project history

Update December 2021

We are monitoring the wastewater for the relative proportion (percentage) of signature mutations of the Delta Variant (S:L452R) and the Alpha/Omicron Variants (HV69/70). The data are available here and a visualization can be found here.

Update June 2021

Based on the wastewater data, our ETHZ project partners (Group cEvo, BSSE) estimated the effective reproductive number Re, i.e. the number of people an infected individual will infect over time. These estimates are visualized here with a direct comparison of estimates based on clinical cases. 

Update May 2021

Extracts of wastewater samples are sequenced at the FGCZ. With bioinformatics tools, our ETHZ project partners (Group Computational Biology, BSSE) estimate the prevalence of different genomic variants of SARS-​CoV-2. The results for six wastewater treatment plants for B.1.1.7, B.1.351, P.1 and B.1.617* are presented here.

Update April 2021

The AbwasSARS-CoV-2 Project launched in February 2021 in collaboration with the FOPH (see Point de Presse, 9 March 2021, Link zu Video from minute 15:36, German). In this project, we are collecting and quantifying SARS-CoV-2 RNA from six wastewater treatment plants across Switzerland daily (see Figure 2; results here).

Figure 2: Locations of the six wastewater treatment plants being investigated in the FOPH's AbwasSARS-CoV-2 project, with information on the size of the catchment areas. Together, these treatment plants collect and treat the wastewater of almost 1 million inhabitants.

Updates are normally provided once or twice per week (depending on frequency of sample shipment and processing capacity not all locations are updated on the same day).  The following links direct you to the data measured at the wastewater treatment plants (currently only in German):

Overview  all  wastewater treatment plants

Altenrhein ARA Altenrhein

Chur ARA Chur

Laupen ARA Sensetal

Lausanne STEP Vidy

Lugano CDA Lugano

Zürich ARA Werdhölzli

Update October 2020

After an intense period of method development and data collection, we are happy to now provide:

Near-real-time measurements for the two wastewater treatment plants, ARA Werdhölzli in Zürich and STEP Vidy in Lausanne: graph for Zurich and graph for Lausanne  [these graphs are not updated any longer after the April update, see new links above]

Our protocols for sample preparation: ultrafiltration protocol (updated version here) and extraction protocol

Answers to frequently asked questions (see link to FAQ)

Original project description June 2020

Application of Wastewater-based Epidemiology to SARS-CoV-2 Detection

Wastewater provides potential insights into improved understanding of the disease burden and disease dynamics of the current COVID-19 pandemic. Although COVID-19 is a respiratory disease, a substantial portion of people shed signatures of the virus (RNA) in their feces. By collecting and analyzing wastewater samples for these signatures, we can determine whether or not, and to what extent, people within a wastewater treatment plant catchment area are infected with the virus. We may also be able to detect the virus circulating in communities via wastewater before clinical case data is available, due to the lag between symptoms and confirmed testing results.

Figure 1. At the beginning of the first wave, we collected samples from 12 wastewater treatment plants (green circles) and continued with Lausanne and Zurich. Samples from 19 large wastewater treatment plants (bold circles) would cover 2.5 million people.

In this study, we (the laboratories of Tim Julian and Christoph Ort, Eawag; Tamar Kohn and Xavier Fernandez Cassi, EPFL) are analyzing wastewater influent samples from Lausanne, Zurich, and Ticino for the presence and quantity of SARS-CoV-2 from the start of the outbreak (late February) to the present. We will integrate the data into models of disease trajectory, in hopes that we can contribute to insights about the disease in Switzerland. Furthermore, we will develop and improve methods for the detection of SARS-CoV-2 at very low concentrations to help develop and improve an early warning system for the emergence or re-emergence of the disease.

Publications

Huisman, J.S.,  Scire, J., Caduff, L., Fernandez-Cassi, X., Ganesanandamoorthy, P.,  Kull, A.,  Scheidegger, A., Stachler, E., Boehm, A.B., Hughes, B., Knudson, A., Topol, A., Wigginton, K.R., Wolfe, M.K., Kohn, T., Ort, C., Stadler, T., Julian, T.R. (2022). Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environ. Health Perspect. 130:5. https://doi.org/10.1289/EHP10050

Caduff L., Dreifuss D., Schindler T., Devaux A.J., Ganesanandamoorthy P., Kull A., Stachler E., Fernandez-Cassi X., Beerenwinkel N., Kohn T., Ort C., Julian T.R. (2022). Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. Euro Surveill. 27(10). https://doi.org/10.2807/1560-7917.ES.2022.27.10.2100806

Fernandez-Cassi X., Scheidegger A., Bänziger C., Cariti F., Tuñas Corzon A., Ganesanandamoorthy P., Lemaitre J.C., Ort C., Julian T.R., Kohn T. (2021). Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high. Water Res. 200: 117252. https://doi.org/10.1016/j.watres.2021.117252