Testing for SARS-CoV-2

Testing for Norovirus

Catchment Area Maps

Ann Arbor WWTP

Flint WWTP

Jackson WWTP

Tecumseh WWTP

Ypsilanti WWTP

About Testing Wastewater for Viruses & Bacteria

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.

History and Methods

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 in Wastewater

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.

SARS-CoV-2 Wastewater Metrics

We report the SARS-CoV-2 data for each of our locations in two different ways. First, we report concentrations as gene copies per mL of wasteawter. This data does not account for the amount of human fecal material that is in the sample and can therefore be impacted by stormwater events, the recovery of RNA from our sample, etc. We also present SARS-CoV-2 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 motile virus (PMMoV) measured in the same sample. This virus is harmless to humans and is shed in stool.

COVID-19 Case Data

  • 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 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

Overview Trend Calculation

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-Day Trend = First, the seven day rolling average for the given gene is calculated. Then the seven day average value from 7 days ago is subtracted from the current seven day average. This value is divided by the seven day average from 7 days ago and multiplied by 100.

14-Day Trend = First, the fourteen day rolling average for the given gene is calculated. Then the fourteen day average value from 14 days ago is subtracted from the current fourteen day average. This value is divided by the fourteen day average from 14 days ago and multiplied by 100.

Both trend values are categorized as:


SARS-CoV-2 Methods

We use the following methods to extract, concentrate, and quantify SARS-CoV-2 in wastewater.

  • Extraction and Concentration

  • Quantification

  • 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)


Additional Wastewater Dashboards