The grey area ━ at the bottom of the charts shows values below the approximate method detection limit. Trimmed averages may appear within this range when they include samples where the target wasn't detected, as these are recorded as 0.
These plots show trimmed averages of concentrations of N, S, and ORF1a over time in settled solids with a line for each wastewater treatment plant in SCAN. The data are plotted both as gene concentrations in copies per gram dry weight (right column), and those concentrations normalized by PMMoV copies per gram dry weight (left column).
Our analysis suggests that both the concentrations of the SARS-CoV-2 genes and those concentrations normalized by PMMoV are proportional to laboratory confirmed COVID-19 incidence rates in the sewersheds. Further, the relationship between these wastewater measures and COVID-19 incidence rates is consistent between the sewersheds in our study. That means a higher wastewater value at one plant compared to another suggests COVID-19 incidence rates are higher in that plants sewershed compared to the others.
To choose which plants to view on the plots, select or deselect the names of the plants you want to visualize. When the plant name is greyed out, it means that the data from that plant are not shown on the plot.
For more information about data shown here, please see the about page.
These data were collected as part of the SCAN (sewer coronavirus alert network) project based out of Stanford University.
SCAN: Sewer Coronavirus Alert Network
Wastewater treatment plant sites
There are 9 wastewater treatment plants participating in this project including plants in San Jose, Gilroy, Sunnyvale, and Palo Alto in Santa Clara County, Silicon Valley Clean Water in San Mateo County, Oceanside in San Francisco County, Davis and UC Davis in Yolo County, and Sacramento in Sacramento County. The plants each serve between approximately 10,000 and over 1,000,000 people living in their sewersheds. There is one experimental, pilot wastewater treatment plant that serves a sub-sewershed located within Stanford University called Codiga. Sewerage from approximately 10,000 people passes through the Codiga collection point.
- The pink area near Sacramento is the Sacramento sewershed.
- The purple area near Sacramento is the Davis sewershed.
- The brown area near Sacramento is the UC Davis sewershed.
- The red area near San Francisco is the Oceanside sewershed.
- The pink area on the peninsula is Silicon Valley Clean Water sewershed in San Mateo County.
- The purple area on the peninsula is the Palo Alto sewershed.
- The yellow area is the Sunnyvale sewershed.
- The green area is San Jose sewershed.
- The blue area is the Gilroy sewershed.
- Not shown is the area of the Codiga sub-sewershed which is part of the Palo Alto sewershed.
Settled solids from wastewater are collected from wastewater treatment plants by dedicated staff each day. Samples are “grab” samples from the primary clarifier at most plants with the following exceptions: 1) San Jose provides a manually collected composite sample from the primary clarifier; 2) UC Davis, Codiga, and Gilroy collect a 24-hour composite sample from their influent and then let it settle to generate a sample of settled solids. Plants finish their sample collection in the morning of each day and label the sample with the date when they cap the sample with the following exceptions: 1) Palo Alto collects their grab sample at 14:00 the day before the sample is picked up because that is the time of day when their primarily clarifier settled solids waste stream is thickest. They then hold the sample at 4°C until it is picked up the next day; the sample is labeled with the date it was collected. 2) San Jose labels their sample with the previous day’s date because that is the date for which the majority of the composite sample was collected. All samples are held at 4°C prior to analysis.
Daily samples are retrieved from the participating wastewater treatment plants by Dalmatian Couriers and transported to Verily’s industrial laboratory. Samples generally arrive by 12:00. At the lab, they are processed for three SARS-CoV-2 genomic RNA targets: N, S, and ORF1a genes using digital RT-PCR. Results are reported as copies per dry weight of solids. Additionally, we measure pepper mild mottle virus (PMMoV) as a fecal strength control and results for this target are reported per gram dry weight. Prior to nucleic acid extraction, samples are spiked with a vaccine strain of bovine coronavirus (BCoV) in order to measure the recovery of BCoV in each sample. Results are ready within 24 hours of sample drop off and uploaded to this site and distributed to stakeholders.
Laboratory analyses are available on protocols.io:
Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria B Boehm 2021. High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses. protocols.io Link.
Aaron Topol, Marlene Wolfe, Krista Wigginton, Bradley White, Alexandria B Boehm 2021. High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA. protocols.io Link
Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria B. Boehm. 2021. High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR. protocols.io Link.
These protocols are described in, and based on analyses in these pre-prints and publications:
Jana S. Huisman, Jérémie Scire, Lea Caduff, Xavier Fernandez-Cassi, Pravin Ganesanandamoorthy, Anina Kull, Andreas Scheidegger, Elyse Stachler, Alexandria B. Boehm, Bridgette Hughes, Alisha Knudson, Aaron Topol, Krista R. Wigginton, Marlene K. Wolfe, Tamar Kohn, Christoph Ort, Tanja Stadler, Timothy R. Julian. 202X. Wastewater-based estimation of the effective reproductive number of SARS-CoV-2. medRxiv 2021.04.29.21255961; doi: 10.1101/2021.04.29.21255961 Link.
M. K. Wolfe, A. Archana, D. Catoe, M. M. Coffman, S. Dorevich, K. E. Graham, S. Kim, L. Mendoza Grijalva, L. Roldan-Hernandez, A. I. Silverman, N. Sinnott-Armstrong, D. J. Vugia, A. T. Yu, W. Zambrana, K. R. Wigginton, A. B. Boehm. 2021. Scaling of SARS-CoV-2 RNA in settled solids from multiple wastewater treatment plants to compare relative incidence of laboratory-confirmed COVID-19 in their sewersheds. Environmental Science & Technology Letters, 8, 5, 398- 404. Link.
K. E. Graham, S. K. Loeb, M. K. Wolfe, D. Catoe, N. Sinnott-Armstrong, S. Kim, K. M. Yamahara, L. M. Sassoubre, L. M. Mendoza, L. Roldan-Hernandez, L. Li, K. Langenfeld, K. R. Wigginton, A. B. Boehm. 2021. SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed. Environmental Science & Technology, 55, 488-498. Link.
Adrian Simpson, Aaron Topol, Bradley White, Marlene Wolfe, Krista Wigginton, Alexandria B Boehm. Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids. PeerJ 9:e11933.; doi: 10.1101/2021.05.04.21256611. Link.
M. K. Wolfe, A. Topol, A. Knudson, A. Simpson, B. J. White, D. J. Vugia, A. T. Yu, L. Li, M. Balliet, P. Stoddard, G. S. Han, K. R. Wigginton, A. B. Boehm. 2021. High frequency, high throughput quantification of SARS-CoV-2 RNA in wastewater settled solids at eight publicly owned treatment works in Northern California shows strong association with COVID-19 incidence. mSystems, 6(5), e00829-21. DOI: doi/10.1128/mSystems.00829-2. Link.
What is plotted
The Overview plots show consensus smoothing of the SARS-CoV-2 gene (N gene, S gene, and ORF1a gene) concentrations normalized by PMMoV concentrations in the solids. The resultant ratio is unitless. Normalizing the SARS-CoV-2 genes by PMMoV conceptually corrects for measurement-to-measurement changes in RNA recovery and fecal strength. This assumes that RNA recovery from PMMoV is similar to that of SARS-CoV-2 RNA, and that PMMoV adequately controls for fecal strength of the sample. The trimmed average uses 5 consecutive samples, first eliminating the maximum and minimum among the 5 samples and then taking the mean. The smoothing is centered, so the values for Jan 10th will be based on Jan 8th, 9th, 10th, 11th, and 12th. For the most recent two days of data, it will just use the 3 or 4 values available. The y-axis shows a linear scale.
The Location Drilldown shows all data collected for each sample. The errors on each point represent standard deviations from the digital RT-PCR measurement and include Poisson error as well as variation among 10 replicate wells. The normalized, as well as unnormalized, SARS-CoV-2 targets are shown. The reported ratio error is propagated from the errors on the SARS-CoV-2 gene and PMMoV gene measurements assuming that the relative error is additive among the numerator and denominator. The quality control data included for each site shows the bovine coronavirus recovery, as well as the concentration measured of PMMoV in copies per gram dry weight of solids.
This document provides additional information about what specific factors lead to variability in this dataset, how these differ from the types of variability we expect in clinical case or syndromic data, and what actions have been taken to mitigate those sources of variability.
Data Licensing and Use
This project is run by Alexandria Boehm, Krista Wigginton, and Marlene Wolfe. If you want to use these data or have questions about these data, please contact us (firstname.lastname@example.org, email@example.com, firstname.lastname@example.org). Data visualization created by Zan Armstrong.
During the COVID-19 pandemic, we are making the wastewater data on this website available. Except where noted, content on this site is licensed under CC BY-NC 4.0. By accessing or copying any part of the database, the user accepts the terms of this license. Anyone seeking to use the database for other purposes is required to contact Alexandria Boehm to obtain permission.
Our team has made every effort to ensure the accuracy of the information. However, the database may contain typographic errors or inaccuracies and may not be complete or current at any given time. Licensees further agree to assume all liability for any claims that may arise from or relate in any way to their use of the database and to hold our team harmless from any such claims.