Level thresholds for SARS-CoV-2 were calculated based on correlating case rates and normalized wastewater concentration levels in Ann Arbor over the 2021-2022 year. The wastewater concentration levels correspond approximately to case rates as follows:
1 = 50 or less weekly cases/100K
2 = 51 to 200 weekly cases/100K
3 = 201 to 400 weekly cases/100K
4 = 401 weekly cases/100K or more
Level thresholds for all other organisms are based on quartile cutoffs of available measurements, and are subject to change as more analysis is completed.
We present SARS-CoV2 and other viral pathogens as wastewater concentrations that have been normalized to account for the amount of human material that is in the sample. We normalize using the concentration of Pepper mild mottle virus (PMMoV) measured in the same sample. This virus is harmless to humans and is shed in stool.
The seven-sample average is colored according to the relative “level” of the organism detected.
“Trend” is a modification of the CDC’s Incidence Trend calculation, which was presented by Matt Lozier (document here).
If the “Trend” metric falls into “decline”, then a counter begins to count the number of days the metric is in decline.
The trend variable calculation that is presented on the Trends & Comparison page is calculated following the methodology presented by the Sentinel Wastewater Epidemiology Evaluation Project run by the Michigan Department of Health and Human Services.
7-Sample Trend = First, the seven sample rolling average for the given gene is calculated. Then the seven sample average value from 7 samples ago is subtracted from the current seven sample average. This value is divided by the seven sample average from 7 samples ago and multiplied by 100.
14-Sample Trend = First, the fourteen sample rolling average for the given gene is calculated. Then the fourteen sample average value from 14 samples ago is subtracted from the current fourteen sample average. This value is divided by the fourteen sample average from 14 samples ago and multiplied by 100.
Both trend values are categorized as:
Case data are from the Michigan Disease Surveillance System (MDSS), the Michigan Department of Health and Human Services’ web based communicable disease reporting system. Cases are attributed to date of illness onset. If illness onset date is unavailable, date of testing is used. If date of testing is unavailable, date of referral to MDSS is used. Date attributions are subject to change over time as better data become available. Both probable and confirmed status cases are available for display. Confirmed cases only include individuals with a positive diagnostic laboratory test for COVID-19. Probable cases include individuals with COVID-19 symptoms and an epidemiological link to a confirmed case or a positive serology test, but do not have a positive diagnostic laboratory test.
Cases were assigned to a given wastewater catchment area only if they had associated location data included in their case report. This information for cases is associated with the individual’s residential address, so this does not account for any travel into or out of the catchment area.
COVID-19 case data is presented as a 7-Day Average Number of Cases per Day, per 100,000 Population. If this value for a day is < 10, then the value is not displayed (censored).
Estimated Populations of Wastewater Catchment Areas
|Wastewater Catchment Area||Estimated Population||Source|
|Ann Arbor||121093||ACS 5Y Estimate 2020 - City|
|Flint||95999||ACS 5Y Estimate 2020 - City|
|Jackson||90000||State of Michigan SWEEP|
|Tecumseh||8680||State of Michigan SWEEP|
|Ypsilanti||330000||State of Michigan SWEEP|
Google Trend information is pulled periodically as a potential correlate of disease occurrence.
This information is presented at a weekly, state-wide level only. The organism specific search terms used are:
Influenza A “flu symptoms”, “influenza”, “flu”, “influenza symptoms”
Mpox “mpox symptoms”, “mpox”, “monkeypox symptoms”, “monkeypox”
Norovirus “norovirus symptoms”, “norovirus”, “stomach flu”, “stomach flu symptoms”
RSV “rsv symptoms”, “rsv”
SARS-CoV-2 “covid”, “covid symptoms”
We use the following methods to extract, concentrate, and quantify SARS-CoV-2 in wastewater.
Influent Methodology from Flood, M. T., D’Souza, N., Rose, J. B., & Aw, T. G. (2021). Methods evaluation for rapid concentration and quantification of SARS-CoV-2 in raw wastewater using droplet digital and quantitative RT-PCR. Food and environmental virology, 13(3), 303-315. (with modifications)
Norovirus GII is detected using influent samples prepared using the method described above, but with the primers from the following paper. Kageyama, Tsutomu, et al. “Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR.” Journal of clinical microbiology 41.4 (2003): 1548-1557.
Extraction from settled solids is used to detect RSV, IFA, and Mpox. The method for sample processing is described in the paper below. Kim, Sooyeol, et al. “SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works.” Environmental science: water research & technology 8.4 (2022): 757-770.
The primers used for IFA, RSV, and Mpox are from the following papers.
Wolfe, Marlene K., et al. “Wastewater-based detection of two influenza outbreaks.” Environmental Science & Technology Letters 9.8 (2022): 687-692.
Hughes, Bridgette, et al. “Respiratory syncytial virus (RSV) RNA in wastewater settled solids reflects RSV clinical positivity rates.” Environmental Science & Technology Letters 9.2 (2022): 173-178.
Wolfe, Marlene K., et al. “Use of Wastewater for Mpox Outbreak Surveillance in California.” New England Journal of Medicine (2023).
Record of the changes made to this dashboard (history starting March 2023).
17 March 2023
21 March 2023
27 March 2023
28 March 2023
Pathogenic microorganisms that infect humans are commonly shed in feces, urine, saliva, and skin. The shed organisms can eventually end up in municipal wastewater, where they can be detected and quantified. Such measurements can provide helpful information for public health officials regarding community health.
In the 1960s, epidemiologists began using wastewater to track and contain polio outbreaks. These early efforts relied on culture-based methods to detect polioviruses in the wastewater. In the 1980s, Hepatitis A was monitored in wastewater using hybridization techniques with radioactive cDNA probes. Broader wastewater pathogen detection techniques began in the 1990s with the advent of polymerase chain reaction (PCR) technology. PCR-based methods have been widely used for SARS-CoV-2 surveillance.
Normalizing the sample - Human inputs within a single community’s wastewater can be diluted during stormwater events or other changes in wastewater inputs. Likewise, comparing pathogen concentrations in the wastewaters between different community sewersheds can be complicated by different wasteawter compositions, such as the amount and types of industries in the sewershed. Normalizing ultimately helps account for the number of individuals that contribute to the wastewater sample and thus facilitates comparing organism concentrations measured over time in the same sewershed and between sewersheds. Potential normalization factors include concentrations of of Pepper Mild Mottle virus, crAssphage, Bacteroides HF183, or Lachnospiraceae Lachno3 in the wasteawter. Normalizing by wastewater flow rate and sewershed population, as well as chemical concentrations, have also been proposed.
Sample collection method and frequency - Wastewater collected as a grab sample represents a single point in time, whereas composite samples represent wastewater levels over a specified period of time (often 24 hours). Sample collection frequency can affect the ability to observe trends in wastewater–samples collected and analyzed at a higher frequency (e.g., daily samples) provide more information on disease dynamics in a community than samples collected and analyzed at a lower frequency collection (e.g, weekly samples).
The laboratory detection method used - Methods used to quantify organisms in wastewater can be culture-based or molecular-based. Culture-based methods require a live, or infectious organism to be detected and quantified. PCR-based methods require the targeted regions of the genome to be intact so that they can be detected and quantified. PCR methods do not relay information about the infectiou state of the organism, but they are relatively quick and specific. With PCR-based methods, pathogen wastewater concentrations can be measured and reported within 1-2 days of when the organisms were shed. Different methods have different limits of detection.
The persistence of the organism in the environment - The temperature of the environment, along with the presence of other chemicals and organisms in the environment, may impact the amount of the infectious/live organism or its genome that can be detected.
Wastewater-based epidemiology methods have detection limits that depend on the amount of organisms people shed during an infection and the methods used to recover and detect the organism.
SARS-CoV-2, or the virus that causes COVID-19, is shed in stool during infections. We can therefore quantify SARS-CoV-2 RNA in wastewater to get a sense of a community’s COVID-19 burden. Most efforts to quantify SARS-CoV-2 concentrations in wastewater focus on the liquid fraction of wastewater. Methods have also been developed to measure SARS-CoV-2 RNA in the solid fractions of wastewater and there is evidence that solids fractions contain higher concentrations of SARS-CoV-2 than the liquid fraction (see links below). Focusing on solids can therefore improve detection limits. Although our team currently measures SARS-CoV-2 in liquid influent samples, we plan to incorporate solids measurements in the future.
https://pubs.rsc.org/en/content/articlehtml/2022/ew/d1ew00826a - Solids Vs Influent (example 1)
https://pubmed.ncbi.nlm.nih.gov/33283515/ - Solids Vs Influent (example 2)
Sinclair RG, Choi CY, Riley MR, Gerba CP. Pathogen surveillance through monitoring of sewer systems. Adv Appl Microbiol. 2008;65:249-269. doi:10.1016/S0065-2164(08)00609-6
Centers for Disease Control and Prevention - Wastewater Testing Methods
Centers for Disease Control and Prevention - Sampling Strategy
State of Michigan Sentinel Wastewater Epidemiology Evaluation Project (SWEEP) - SARS-CoV-2
University of California San Diego COVID-19 Monitoring Dashboard with Wastewater Monitoring for SARS-CoV-2
Centers for Disease Control and Prevention Tracking SARS-CoV-2 in the United States