Wastewater provides a solution for monitoring omicron’s spread

Would you like to know if the omicron variant has arrived where you live? 

Two cities in northern California learned last Friday that they may have omicron in their communities, even before any residents’ clinical tests showed an omicron infection. At the same time, eight other cities found out omicron likely hasn’t arrived yet, and every other community in the United States could have that knowledge as well. That kind of public health radar is found in wastewater

COVID-19 virus markers can show up in sewage even before an infected person shows symptoms (and even though the wastewater itself isn’t infectious). Analyzing wastewater for the virus can detect a rise in COVID cases days before individuals’ tests show a trend. Armed with that information, public health officials can decide how to respond and how to deploy resources such as targeted individual testing.

The 10 cities have been analyzing their wastewater for a year, using the information they collect as a vital tool to slow the spread of COVID-19. Their collaboration with scientists from Stanford University, the University of Michigan, and Emory University and the life sciences research company Verily is called the Sewer Coronavirus Alert Network or SCAN.

One week after the World Health Organization identified a new “variant of concern,” SCAN began looking for a mutation present in almost all omicron genomes (and rarely present in other circulating variant genomes), giving these 10 communities an early sign that the variant likely has reached them.

Here is how it works: Municipal sewage treatment plants take samples of the solids that settle in their tanks and send them to a lab for testing. The results come back within 24 hours. That quick turnaround means public health officials can see how prevalent the virus and its variants are in a community, which foreshadows a rise in cases. 

By analyzing wastewater solids, which can carry 1,000 more COVID virus genes than liquid wastewater, SCAN estimates it can detect as few as two infected people among 100,000 served by a sewage system.

Established as a public health tool for decades, wastewater monitoring has evolved in the crucible of the current pandemic. This is the first time it has been deployed to find a respiratory, rather than intestinal, disease. With the SCAN methods and structure in place, these 10 communities quickly pivoted to monitoring for omicron. It’s easy to see how this rapid response could help in the face of new variants or even other pathogens in the future.

In most places, public health officials rely on the aggregated results from individuals’ COVID tests and hospitalizations. Widespread community testing, particularly of people who aren’t symptomatic, is logistically challenging, expensive and depends on people getting tested repeatedly. Neighborhoods and people who are underserved by the health care system often lack access to testing. With wastewater monitoring, no home, business, or neighborhood served by the sewage treatment system is left out. 

Ten cities shouldn’t be outliers on something as important as public health. The SCAN approach is scalable; the 10 treatment plants involved so far serve 10,000 to more than 1 million people. SCAN’s research and protocols are available to anyone online.

The pandemic has made it clear: A piecemeal approach won’t erase a public health threat; infections in one place spread to another. It is imperative for federal, state and local governments to work together to ensure that wastewater monitoring is a ready part of the public health toolbox and routinely available to support a robust response to outbreaks of known and emerging diseases. The Infrastructure Investment and Jobs Act offered a start with $25 million to train water and wastewater plant workers that could include sampling methods. We need additional support to make wastewater monitoring a common practice nationally. 

The real barriers are acceptance and infrastructure. While wastewater monitoring isn’t new, it also isn’t well known to all municipal and public health officials. Sampling, testing and analyzing sewage is relatively simple compared to widespread community testing, but they take expertise and some specialized equipment. We can do more to train people across the country to analyze wastewater and to interpret the data, as well as ensure access to the tools and technology needed.

The science is solid. The tools are available. We can be better prepared to combat the COVID-19 pandemic and to be ready for what’s to come. The real waste would be to fail to harness wastewater’s proven potential to protect health in our communities.

Alexandria Boehm, Ph.D., is a professor of civil and environmental engineering at Stanford University, a senior fellow at the Woods Institute for the Environment, and a principal investigator for the Sewer Coronavirus Alert Network (SCAN). Ekemini A. U. Riley, Ph.D., is founder and president of the Coalition for Aligning Science, serves as project lead for SCAN, and is a molecular biologist by training.