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November 19, 2023

You can tell a lot about someone’s health from their body’s waste. If you are fighting an infectious illness, you flush away more than yesterday’s lunch. It may be off-putting, but checking wastewater for infectious disease has become an important tool that scientists and public health officials can use to respond to and prevent new infectious disease outbreaks.

When a new virus, SARS-CoV-2, led to the COVID-19 pandemic, this pragmatic tool was needed on a much larger scale than had previously been attempted. This need led to coordination and collaboration between many federal agencies and partners, including the USGS, to increase the infectious disease surveillance capacity within the U.S.

After a truly herculean effort undertaken over the last half of 2021, USGS scientists contributed valuable science that will continue to help increase wastewater surveillance capabilities for COVID-19 and future infectious disease outbreaks.

Because symptomatic and asymptomatic people infected with SARS-CoV-2 shed viral RNA, or ribonucleic acid, in their waste, testing wastewater for the virus gives a clear, noninvasive picture of the prevalence of SARS-CoV-2 in a population.

Man and Woman in full protective gear work on samples in a lab.
Luke Iwanowicz (left) Christine Densmore (right) perform RNA extractions in the Biosafety Level-3 lab

What’s more, viral RNA is detectable in wastewater days before it is detected by other sampling methods, like those deep nose swabs we’ve probably all experienced at least once by now. Sampling wastewater can also fill in gaps where clinical tests are lacking.

The result of such wastewater sampling gives public health officials a powerful peek into the level of infection in a community. With that knowledge, local public health officials can prepare medical services and enact measures to lower disease spread before outbreaks grow larger.

In 2020, as the COVID-19 pandemic grew, so too did the prudence of a coordinated wastewater surveillance program.

The Centers for Disease Control and Prevention (CDC) and the U.S. Department of Health and Human Services (HHS), in collaboration with the USGS and other agencies throughout the federal government, initiated the National Wastewater Surveillance System (NWSS). The data generated by the NWSS helps public health officials to better understand the extent of SARS-CoV-2 infection in communities.

The USGS has supported wastewater research for over 20 years. Much of this research occurs through the Drinking Water and Wastewater Infrastructure Integrated Science Team. USGS wastewater studies have made key contributions to the scientific literature, including how chemicals in human wastewater effluent spread, affect animals and enter drinking water supplies. In addition, the USGS has scientific infrastructure in place on a national scale allowing the agency to quickly respond to sampling and analytical needs.

By mid-2021, it was apparent that a very large surge in COVID-19 infections was imminent, a result of a new strain of the virus—the Delta variant. Wastewater surveillance was in place, but it wasn’t happening at the scale needed during this new surge.

In response, CDC officials worked with USGS leadership in July 2021 to increase the capacity of the country’s wastewater surveillance program. To address the need, in August 2021, the Department of the Interior apportioned funds from the Coronavirus Aid, Relief and Economic Security (CARES) Act to increase the USGS’s capacity to support NWSS efforts.

Man in personal protective gear collects a wastewater sample at night.
A USGS field team member retrieving the sample bottle from a time-based sampler onsite at a wastewater treatment facility.

USGS scientists who were already advising the NWSS, initiated the USGS COVID-19 Wastewater Surveillance project to support disease surveillance in wastewater at the community level and test protocols for frequent sampling.

Safety is paramount at the USGS, so a vital part of this study was ensuring all staff involved were trained in and followed strict safety procedures. In addition, USGS scientists processed the samples in a newly-constructed Biosafety Level-3 Laboratory—the highest biosafety level certification possible.

The study was testing the applicability of frequent sampling, which led to some long workdays, so having a large team with a protocol that included many opportunities to ensure quality of data was also important.

By September 7, 2021, the first wastewater samples were collected from two wastewater treatment facilities located in Colorado and Utah. Between September 8 and 30, USGS scientists processed a staggering 354 wastewater samples from 28 wastewater treatment facilities in six states.

To find SARS-CoV-2 viral RNA in a sample, they looked for 2 unique regions of viral RNA and checked for each of the two regions three times. They tested each sample in this way twice. Excluding weekends, that averages to over 41 tests per day!

USGS staff sent the CDC the laboratory results within 72 hours of sample collection so they could upload the data to the NWSS’s database and inform State Health Departments.

The extraordinary effort completed by USGS scientists to complete this study in such a short period of time paid off. USGS capabilities enhanced wastewater surveillance efforts, which could be used to track how viral RNA presence fluctuates both geographically and over time.

During the course of this project, the USGS also provided an additional service in wastewater surveillance during the Delta variant-caused COVID-19 surge by providing early viral detection for the communities sampled.

Stay tuned! The USGS and CDC will use the results of this study to evaluate the utility of frequent sampling in a wastewater surveillance program.

What’s next? Make the methodologies developed the best they can be!

The USGS provides “science for a changing world” and the bureau’s vision statement is to “lead the nation in 21st-century integrated research, assessments and prediction of natural resources and processes to meet society’s needs. The flexibility and responsiveness demonstrated by the USGS staff involved in this study are a great example of how we live up to those statements every day.


Glass bottle collect water from wastewater facility.
Image of a  flow-based composite sample being collected at one of the wastewater facilities to represent a 24-hour sample. 
Man in full protective gear filtering a sample in the lab.
Clay Raines performs primary filtration of pasteurized wastewater in the Biosafety Level-3 Lab
Man in personal protective gear fills out paperwork in a van.
Picture of Travis Smith at a wastewater facility filling out paperwork for samples collected that day in the lab van before shipping the same samples to the Leetown, WV lab.
Man and Woman in full protective gear work on samples in a lab.
Luke Iwanowicz (left) Christine Densmore (right) perform RNA extractions in the Biosafety Level-3 lab
Two men in full protective gear work on samples in a lab.
Purification of extracted RNA via vacuum manifold RNA column filtration in the BSL3 lab.
Hallway with people adding supplies to sample boxes.
The Logistics Team packs dozens of sample boxes to send to the field teams at multiple Science Centers across the country.

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