Early Discovery of Omicron in State Driven by Wastewater Studies

Omicron, the highly contagious coronavirus variant that swept across the globe this winter, was first reported to the World Health Organization by South Africa on Nov. 25, 2021.

That same day, a sample was collected from Merced wastewater. When it came back positive for the variant on Dec. 3, one of the omicron’s earliest detected arrivals in California was confirmed.

A UC Merced lab coordinated sampling and pick-up with the Merced and Modesto wastewater treatment plants for analyses of one of omicron’s unique gene mutations with Stanford University’s Sewer Coronavirus Alter Network (SCAN) project.

It was another victory for Professor Colleen Naughton’s team, which pioneered an online dashboard that tracks how communities around the world are using wastewater to track COVID-19. The dashboard and a Twitter account run by Naughton share the memorable moniker of COVIDPoops19. The Twitter account, with which Naughton retweets sewage tracking efforts around the world, has more than 5,000 followers.

The effectiveness of using wastewater to track disease is straightforward. Not everyone has been tested for coronavirus. But as the popular children’s book reminds us, everyone poops, and coronavirus can exit the body not just from the nose and mouth but through feces. That means wastewater samples can determine whether the virus is in a community, and at what level. Initial detections have preceded outbreaks by several days.

“It is not a replacement for clinical testing,” Naughton told Fresno TV station KSEE in early December. “But it is a powerful tool we can use to confirm if there is an increase or decrease in the spread.”

Epidemiology via wastewater has been so useful that the federal government created the National Wastewater Surveillance System, a network coordinated by the Centers for Disease Control and Prevention that taps into 400 testing sites across the nation.

"It's really exploded the field," Naughton said in an interview with CNN. "We did wastewater monitoring for other pathogens before this, like poliovirus, but it's really the amount of people involved in everything has really increased exponentially."

Naughton’s team is working on a COVID-19 early warning system for the region. Healthy Central Valley Together is patterned after an effort by UC Davis for the Davis community and Yolo County. The project combines wastewater surveillance with testing indoor air and certain surfaces in schools and other public places. Naughton partnered with Dr. Heather Bischel at UC Davis to establish a joint Center of Excellence with Ceres Nanosciences under the National Institutes of Health’s Rapid Acceleration of Diagnostics (RADxSM) initiative. With the Center of Excellence, Naughton and Bischel are able to process more wastewater samples in areas of need in the Central Valley with a rapid method that uses Nanotrap® Magnetic Virus Particles. The Naughton and Bischel labs partnered with Stanford University to add more Central Valley sites to their dashboard that presents fever-line graphs of coronavirus concentrations in selected communities. The dashboard includes Merced and Modesto. The Naughton lab also is part W-SPHERE, which provides a global data center, public health use cases, and visualizations of COVID-19 wastewater monitoring particularly for Low and Middle Income Countries. In addition, Naughton will expand wastewater testing to two additional underserved California communities by March 2022.