By Aaron Peacock, PhD

At this writing, the COVID-19 pandemic has been with us for over 20 months, resulting in over 45 million cases of infection and over 738,000 deaths in the United States, sobering figures with a harrowing impact on society as a whole. Although controversial, the institution of local, state and federal vaccination mandates have been credited, in some quarters, with helping to stifle the spread of the SARS-CoV-2 virus across large swaths of the country. Encouragingly, the nation recorded a dramatic drop (29 percent)[1] in the number of daily new COVID-19 cases and hospitalizations during September.

Despite this positive news, public health authorities caution that the country has not turned the corner on the COVID-19 epidemic, which recently surpassed the 1918 Spanish flu as the deadliest disease event in US history.[2] The virus, they emphasize, remains a threat due (in part) to a large population of people who are not vaccinated and the risk posed by emerging SARS-CoV-2 variants.

Unmasked shortcomings
In the ongoing battle against COVID-19, epidemiological surveillance is critical in monitoring infection trends, as well as promulgating effective preventive and control measures. The pandemic, according to an abundance of voices within the public health community, unmasked several shortcomings in the country’s disease surveillance,[3] such as inadequate diagnostic capacity, insufficient contact tracing and fragmented data systems. During the pandemic, we learned that weak surveillance of cases and insufficient national capacity to integrate data for timely adjustment of public health measures undermines intervention strategies intended to control community transmission. Handicapped by these and other limitations, researchers and scientists gravitated toward expedient strategies, measures and approaches to monitor and control the rapid spread of COVID-19. One approach that has gained notable traction in the US and abroad involves using community wastewater (sewage) to measure the prevalence of SARS-CoV-2 in a given population.

Surveillance tool
Commonly referred to as wastewater-based epidemiology (WBE) or sewer surveillance, the method monitors community-level infection trends by analyzing SARS-CoV-2 through biological markers in wastewater entering treatment plants or within the collection system. In years past, sewer surveillance was used to detect various disease agents,[4] including poliovirus, hepatitis B and norovirus. More recently, it has been employed to understand community-level drug use (e.g., opioids).

SARS-CoV-2, like most infectious diseases, can be shed in the stool of infected persons, including asymptomatic individuals. According to estimates, SARS-CoV-2 can be detected in human feces anywhere from four to 10 days before the onset of symptoms, giving public health officials valuable time to contain the spread of the virus in a given community. Noting that municipal sewage collection systems serve nearly 80 percent of US households, the Centers for Disease Control and Prevention (CDC), an early and strong proponent of WBE, pinpoints several advantages offered by this surveillance tool, such as:

  • Quantitative SARS-CoV-2 measurements in untreated sewage can provide information on changes in total SARS-CoV-2 infection in the community contributing to that wastewater treatment plant
  • Depending on the frequency of testing, sewage surveillance may be a leading indicator of changes in COVID-19 burden in a community
  • SARS-CoV-2 RNA detection in sewage serves as a COVID-19 indicator that is independent of healthcare-seeking behaviors and access to clinical testing

The CDC stresses that a multidisciplinary approach is essential for communities in establishing successful wastewater surveillance initiatives. As such, the federal agency urges interested communities to identify and engage qualified local partners to assist in sample collection, environmental testing and public health action.

US EPA’s A Compendium of U.S. Wastewater Surveillance to Support COVID-19 Public Health Response report[5] identifies 14 states with large-scale SARS-CoV-2 wastewater surveillance programs, along with 160 local communities or academic institutions conducting wastewater surveillance. Released earlier this year, the document utilizes case studies to highlight the inner workings of surveillance programs in Indiana, Michigan, Ohio, New Mexico, Arizona, New Jersey and other states featured in the insightful and informative report.

Sampling and testing
For most community-level wastewater surveillance programs, samples are typically collected[6] at the influent of a wastewater treatment plant. Other smaller scale programs sample at locations throughout the collection system, including at lift stations or from manholes that carry sewage from individual buildings. Wastewater samples are analyzed for the presence of SARSCoV-2 using a nucleic acid–based reverse transcription polymerase chain reaction (RT-PCR) assay for gene markers that are unique to the virus.

Generally, state and local programs send wastewater samples to commercial or university laboratories for analysis. Most universities carry out testing in on-campus testing facilities. In some cases, wastewater testing programs send samples to multiple laboratories as part of an interlaboratory comparison to validate and improve analytical methods. For the most part, many state, local and university wastewater surveillance programs communicate their results to the public in real-time via online data dashboards.

Currently, there is no official method for monitoring SARS CoV-2 in wastewater. It is, however, imperative for commercial testing operations to adhere to the highest possible quality standards to ensure the accuracy and integrity of wastewater test results. The CDC and other oversight agencies have suggested data quality requirements and method controls, including spike recovery and multiple qPCR runs, to ensure data integrity.

Early warning signal
It is important to underscore that wastewater surveillance for SARS-CoV-2 is a developing field and researchers are still learning about the dynamics of viral shedding in feces and viral persistence in wastewater. Going forward, more data on the prevalence and concentrations of SARS-CoV-2 shed in the feces of infected individuals is needed to better understand the relationship between SARS-CoV-2 concentrations in wastewater and the number of individuals infected with COVID-19.[7]

In the meantime, the interest in wastewater testing as an early warning signal for COVID-19 continues to grow. The ability to monitor populations at scale at a low cost, coupled with the health and environmental data provided by wastewater testing, allows community leaders to take proactive action against the highly contagious virus. Across the country, scores of community institutions, such as nursing homes, colleges and universities and public schools, are utilizing wastewater testing to control the spread of COVID-19.

1. Berger, Eric. “Signs of encouragement as US sees drop in Covid cases and hospitalizations.” The Guardian. cases-hospitalizations-drop
2. McKeever, Amy. “COVID-19 surpasses 1918 flu as deadliest pandemic in U.S. History.” National Geographic. is-now-the-deadliest-pandemic-in-us-history
3. Morgan, Oliver W.; Aguilera, Ximena, et al. “Disease surveillance for the COVID-19 era: time for bold changes.” US National Library of Medicine National Institutes of Health.
4. US EPA. A Compendium of U.S. Wastewater Surveillance to Support COVID-19 Public Health Response.
5. US EPA. A Compendium of U.S. Wastewater Surveillance to Support COVID-19 Public Health Response.
6. US EPA. A Compendium of U.S. Wastewater Surveillance to Support COVID-19 Public Health Response.
7. US EPA. A Compendium of U.S. Wastewater Surveillance to Support COVID-19 Public Health Response.

About the author
Dr. Aaron Peacock, Director of Molecular Biology at Microbac Laboratories, is an environmental scientist with 25 years of experience specializing in microbial molecular diagnostics. He has worked extensively in the development, evaluation and implementation of new technologies for molecular-based surveillance and forensics.

About the company
Microbac Laboratories, Inc. ( operates the largest network of privately held testing facilities in the United States, providing broad analytical offerings and testing insights across the environmental, food and life science markets. A family-run company with more than 50 years of experience honing its craft, the company is on a mission to improve the world around us, one test at a time. To contact Microbac, please visit



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