Tapping into Wastewater Testing to Predict Virus Surges

By Christina P. Hooton

A pathogen can move silently through a community before making its presence known. Contagious people may experience delayed symptoms or be asymptomatic, unknowingly infecting others. Suddenly, many people are sick with the same illness. Heading off a virus before it becomes a problem at a city or state level requires knowing people are sick before they do. Achieving this kind of prescience seems somewhat unlikely, but wastewater, an abundant and accessible resource, has recently become a popular place to look for warning signs.

Researchers and communities all over the world have been trying to understand the effectiveness of wastewater-based epidemiology in predicting surges in COVID-19 cases. Because someone infected with the virus starts shedding it in their stool before experiencing symptoms, wastewater testing may help us anticipate an increase in cases earlier than clinical test results.1 And, like clinical testing, detection is possible in both symptomatic and asymptomatic patients.

The technique is not new. In 2013, a wild polio epidemic was detected using environmental surveillance of sewage in Israel.This type of monitoring at a national level is beginning to take shape in the United States in response to the pandemic. The Centers for Disease Control and Prevention (CDC) and the U.S. Department of Health and Human Services created the National Wastewater Surveillance System (NWSS) to better understand the extent of SARS-CoV-2 infections in communities. Eventually, state, tribal, local, and territorial health departments will be able to submit their wastewater testing data through a portal, and the data will be summarized and interpreted to help inform public health actions. Additionally, the CDC is allocating $33 million for public health laboratories to start conducting wastewater testing.

Testing the Power of Wastewater

Two University of Minnesota Medical School researchers have been studying the effectiveness of wastewater testing in predicting COVID-19 case increases across their state. Assistant professors Glenn Simmons Jr., PhD, and Richard Melvin, PhD, collected and analyzed samples from wastewater treatment plants in 19 Minnesota cities from May 2020 through August 2020. The team initially began testing on-campus residence hall sewage to predict and prevent COVID-19 outbreaks among students and eventually set their sights on something with broader impacts. They specifically sought to understand what would happen in a large region with diverse populations over a long period of time. A preprint version of their study is available on medRxiv and is currently undergoing peer review.

They were able to detect the presence of SARS-CoV-2 RNA in the wastewater of cities with populations ranging from 500 to over 1 million people 15 to 17 days before new clinical cases were confirmed. Since they scaled up from sampling 19 cities once per week to sampling 44 cities twice per week, this window has narrowed to between 10 and 14 days.3

“Looking at the wastewater, you see what’s going to happen in the future with clinical cases. And that has happened consistently since wastewater testing has been going on in our lab,” said Dr. Simmons.

This type of information is especially valuable in areas where access to testing varies. Dr. Simmons said he first approached this project from an equity perspective, asking what they could do about the fact that the availability of individualized testing varied. “In Duluth, we have different pockets of folks that have different circumstances. Drive-thru testing is very convenient, but what about for people who don’t have cars?” he posed. Some cases could go undetected.

"Looking at the wastewater, you see what’s going to happen in the future with clinical cases."

Creating a Steady Flow of Data

Initiating a research project like the one in Minnesota required participation and buy-in from multiple wastewater treatment plants in different locations. Additionally, they needed sufficient lab staff to process the samples, a resource that was in short supply during that period of the pandemic. They recruited recent graduates to work in their lab and solicited participation from wastewater treatment plants through the Minnesota Environmental Science and Economic Review Board website.

Once the framework was in place, composite samples were collected by plant personnel on a weekly, and eventually biweekly, basis, and shipped to the lab overnight on wet ice. Upon receipt, lab personnel sterilized the sample tubes and pasteurized the samples in preparation for RNA extraction. The extracted RNA samples were then tested for SARS-CoV-2.

Extracting Meaningful Information

Collecting wastewater from a variety of cities meant there would be a significant number of variables affecting the concentration of pathogens. These include the presence of industry and variations in the size and flow rate of each wastewater facility.

To account for the variations at each facility, the researchers used Pepper Mild Mottle Virus as a standard. This pepper virus is the most abundant RNA virus in human feces and remains stable in a variety of environmental conditions.They measured the impact of system variations on pepper virus concentration levels and ranked each facility accordingly.

Additionally, the team needed to normalize the raw data to turn it into digestible information suitable for public consumption. They created Melvin’s Index, a simplified value for tracking virus levels compared to the pepper virus.

Moving Forward with Wastewater Testing

While wastewater testing is proving to be an effective tool in tracking the rise and fall of virus cases, there is still information it can’t provide. Dr. Simmons mentioned the limitations in approximating how many people are infected based on wastewater alone. The number of variables makes it a complex guessing game.

Clinical testing is still the most accurate way to count virus cases. However, if a significant enough increase in the virus is seen in wastewater before clinical cases start to rise, resources can be allocated to the affected areas.

This happened recently in Davis, California. Health officials and researchers saw a potential rise in cases thanks to wastewater surveillance, and local officials sent out alerts and encouraged people in the affected neighborhoods to get tested. Paired with patient sampling, they were able to determine that the Delta variant was in the mix.5

Variants are another piece of the puzzle Dr. Simmons and his team would like to integrate into their studies through the end of the year. And there is potential for future viruses. Influenza, for example, was successfully detected in wastewater during the 2009 H1N1 pandemic, according to a Netherlands study. “One of our desires is that this system stays in place, and we just change out what we’re looking at. Or we create a panel of different targets that we’re looking at whether it’s some other emergent tropical disease, like Nipah virus or chikungunya, or SARS,” said Dr. Simmons.

He points out that by providing surveillance data about new and emerging viruses in small doses as it becomes available to us through techniques like wastewater testing, we’re creating an ongoing conversation with people and helping them to better understand the science without overwhelming them. This type of dialogue and transparency will continue to be a crucial part of dealing with public health crises now and in the future.


  1. Jones D.L., Baluja M.Q., Graham D.W., Corbishley A., McDonald J.E., Malham S.K., et al. (2020). Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. Sci Total Environ, 749. https://doi.org/10.1016/j.scitotenv.2020.141364
  2. Brouwer, A.F., Eisenberg, J.N.S., Eisenberg, M.C., Grotto, I., Hindiyeh, M., Koopman, J.S., Manor, Y., Pomeroy, C.D., Shulman, L. M., (2018). Epidemiology of the silent polio outbreak in Rahat, Israel, based on modeling of environmental surveillance data. Proceedings of the National Academy of Sciences, 115(45). https://doi.org/10.1073/pnas.1808798115
  3. Chaudhry, N., Freese, R., Georgewill, O., Melvin, R.G. & Simmons, G.E. (2021). Predictive power of SARS-CoV-2 wastewater surveillance for diverse populations across a large geographical range. medRxiv. https://doi.org/10.1101/2021.01.23.21250376
  4. Kitajima, M., Sassi, H.P. & Torrey, J.R. (2018). Pepper mild mottle virus as a water quality indicator. npj Clean Water, 1, Article 19. https://doi.org/10.1038/s41545-018-0019-5
  5. Abbott, B. (2021, July 25). Wastewater Helps Health Officials Spot Covid-19 Warning Signs. TheWall Street Journal.https://www.wsj.com/articles/wastewater-helps-health-officials-spot-covid-19-warning-signs-11627214400