Awash with Potential: Using Wastewater Surveillance to Shore Up Public Health

Wastewater surveillance. It’s not the most glamorous-sounding job on the planet, but it has the potential to save lives, turning an “Ewww” moment into an “Aha!” one.

Here’s the scoop on poop:

Many people infected with SARS-CoV-2, the virus that causes COVID-19, shed viruses in their feces, even if they are asymptomatic. Feces, and any other excretions that go down the drain, end up in wastewater, also known as sewage. That wastewater flows through the community’s sanitation system to a wastewater treatment plant where a small sample can be collected and tested for signs of the COVID-19 virus and other infectious diseases.

Samples can be taken anywhere along the sewer system, from manholes to settling tanks at the plant. Because the virus shows up in waste before people feel sick and often before they get a diagnostic test, the result is an early-warning detection system that can alert public health officials to the ebbs and flows of a potential or definitive outbreak.

Alexandria Boehm, PhD | Lead investigator, SCAN project

Wastewater testing in San José, California

Sewer Coronavirus Alert Network (SCAN)

“As people wondered whether Omicron would eventually arrive in the United States, our data showed it was already here,” said Alexandria Boehm, PhD, an investigator leading the Sewer Coronavirus Alert Network, or SCAN. “We shared those results with our state and county public health partners within a week of the World Health Organization designating Omicron a virus of concern, giving them more information to guide their responses.”

Funded by the CDC Foundation since early 2021, SCAN analyzes daily samples from a dozen wastewater plants for SARS-CoV-2 and specific variants. In partnership with the Valley Medical Center Foundation and California Department of Public Health, the work has expanded to include sampling for the common respiratory virus RSV as well as influenza. Data are posted daily on a public website.


Healthy Davis Together

Elsewhere in Northern California, the city of Davis and the University of California Davis implemented wastewater surveillance as part of Healthy Davis Together (HDT), a COVID-19 emergency response project for which the CDC Foundation provides support for communications and media. HDT brings together the city government, the university and community members to collaborate on efforts to reduce the spread of COVID-19. HDT leveraged SCAN for citywide monitoring and engaged the University of California Davis’ environmental engineering department to sample and analyze results at the neighborhood level as well. The Davis campus and University of California Merced launched a joint center of excellence to use SCAN’s methods in eight other communities.

HDT developed resources to assist the Davis community—and beyond. Materials made available to all include a step-by-step guide on using wastewater monitoring as an effective public health tool to track trends and prevent the spread of COVID-19.


Video: Healthy Davis Together Wastewater Monitoring Overview

National Wastewater Surveillance System

While the concept of testing wastewater for pathogens is not new, the pandemic has underscored the need for more coordinated efforts across the country and around the world. In September 2020, the Centers for Disease Control and Prevention (CDC) launched the National Wastewater Surveillance System to bolster collection and analysis of wastewater. CDC works with health departments to build partnerships and implement systems for tracking wastewater surveillance and sharing out data. In January 2022, CDC added a wastewater surveillance tab to its comprehensive COVID Data Tracker to aggregate data from more than 400 testing sites across the country.

In Nebraska, the CDC Foundation COVID-19 Corps epidemiologist Zizwa Mwafulirwa, MBBS, spends many hours poring over data from the Nebraska Wastewater Surveillance System project, which is part of the CDC’s National Wastewater Surveillance System.

Nebraska started collecting samples in December 2021 and is actively growing its network of sampling sites across the state. According to Mwafulirwa, “We hope the Nebraska Wastewater Surveillance System will serve to guide the Nebraska Department of Health and Human Services in implementing public health responses in real time.”

Mwafulirwa noted that detecting SARS-CoV-2 in wastewater samples will be an early indicator of disease risk in Nebraskan communities; guide timely communication; serve as early warning to disproportionally affected groups/communities such as long-term care facility residents and staff; inform targeted and equitable resource allocation like pop-up testing and contact tracing; and guide public awareness and community response especially with non-pharmaceutical interventions like mask mandates and social distancing.

Zizwa Mwafulirwa, MBBS | CDC Foundation epidemiologist

A wasterwater surveillance system in Houston, Texas

Paz Ramirez, RN | CDC Foundation case investigator

Houston Wastewater Monitoring Project

In Texas, the CDC Foundation is partnering with the Houston Health Foundation and the Houston Health Department on a wastewater monitoring project. Wastewater data helps the health department more quickly identify emerging outbreaks or hotspots needing interventions. The department targets areas of Houston with higher concentrations of the virus in wastewater for increased COVID-19 vaccination, testing, outreach and education. Houston is the fourth largest city in the United States, so identifying high-risk areas is key to resource management and mitigation efforts.

Paz Ramirez, RN, a CDC Foundation case investigator working as a staff epidemiologist at the Houston Health Department, monitors outbreaks at schools. She says the health department uses wastewater samples drawn from nearby manholes to predict an outbreak in a particular school or zip code. “If they see an increase in the wastewater’s viral load, a surge usually follows,” she said.


Fortifying the Public Health Toolkit

Wastewater surveillance complements other disease detection and mitigation measures such as masking, hand hygiene, lab and at-home diagnostic testing. It works across the entire community served by the sewage system; it offers a way to monitor infections broadly regardless of community access to and participation in diagnostic testing, thereby increasing health equity. It may become even more important as laboratory-confirmed COVID-19 testing is replaced by at-home, self-administered rapid tests. While the scientific techniques used to search for infectious disease targets in wastewater are like those used for clinical testing, wastewater monitoring doesn’t pinpoint exactly which residents are infected.

If they see an increase in the wastewater’s viral load, a surge usually follows.

To ensure that this powerful and cost-effective tool becomes part of the public health toolkit in more communities requires establishing partnerships among wastewater treatment plants and the local governments that oversee them, public health officials and groups with expertise and capacity to analyze samples quickly and cost effectively. Communities from Davis to Houston to Nebraska are showing those partnerships can work in identifying infection hot spots and controlling communicable diseases.

“We have seen the exciting potential of wastewater surveillance grow in scale and utility during the pandemic,” said CDC Foundation President and CEO Judy Monroe, MD, during the organization’s Lights, Camera, Action: The Future of Public Health National Summit Series. “It’s a concrete example of how we can harness the power of today’s technology to collect and analyze data needed from a variety of sources to inform health practice and policy and realize the vision of health equity.”


Photos via City of Houston Health Department and City of San José Environmental Services Department



This article is supported by the Centers for Disease Control and Prevention (CDC) of the U.S. Department of Health and Human Services (HHS) as part of a financial assistance award totaling $68,939,536 with 100 percent funded by CDC/HHS. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement by, CDC/HHS or the U.S. Government.

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