The Sewage Solution

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Women in white protective gear opens a device on a green lawn.
Smruthi Karthikeyan picks up wastewater samples from collection robots on the UC San Diego campus. Photo credit: Erik Jepsen/UC San Diego.

Fighting COVID-19 beneath the surface.

Throughout the pandemic, early detection and testing has been crucial to stemming the transmission of COVID-19. So when evidence emerged that people infected with COVID-19— with or without symptoms—shed the virus in their stool, UC San Diego researchers saw an opportunity for a novel early warning system. “The sewer seemed like the ‘happening’ place to look for it,” says Smruthi Karthikeyan, PhD, an environmental engineer and postdoctoral researcher who works in the lab of Rob Knight, PhD, at the School of Medicine.

Researchers in Knight’s lab are used to getting their hands dirty. The team has long studied the gut microbiome—unique communities of microbes that live in our gastrointestinal tracts. People all over the world participate in their research program, The Microsetta Initiative (aptly abbreviated “TMI”), by mailing fecal samples to Knight’s lab. The crowdsourced project has allowed the team to study many factors that might influence the makeup of a person’s gut microbiome and the many ways the microbiome influences our health.

By the summer of 2020, Karthikeyan, Knight and team were analyzing fecal samples closer to home—sewage flushed away by people in UC San Diego buildings—to look for the virus that causes COVID-19. One month after the system went online, the team detected a positive case on a then sparsely populated campus.

“At the time, we had just three wastewater samplers around campus, two by the hospital, which of course will be positive due to the patients being treated there, and one negative control by Revelle College,” Karthikeyan says. “I had packed up to leave the lab for the day when I saw that the Revelle sample was actually positive! That launched a thousand ships and put the whole surveillance team on overdrive.”

The campus community was notified within 14 hours, with targeted messages sent to people associated with the affected buildings, recommending that they be tested for the virus as soon as possible. More than 650 people were tested for COVID-19 that weekend. As a result, two asymptomatic individuals were diagnosed and self-isolated before an outbreak could occur.

The program only grew from there. The team now monitors wastewater from 350 UC San Diego buildings daily. Along with notifications, results are available on a public dashboard, and positive samples are also sequenced to track the emergence of new coronavirus variants such as Delta and Omicron.

After months of optimizing the process, the team can detect even a single infected person living or working in a large building of more than 500 people. Notifying the occupants of buildings with positive wastewater has been seen to increase COVID-19 testing rates as much as 13-fold, and researchers say the approach has enabled early detection of 85 percent of COVID-19 cases on campus.

Wastewater screening is an integral part of UC San Diego’s Return to Learn program, the evidence-based approach that has allowed the university to offer on-campus housing as well as in-person classes and research opportunities throughout most of the pandemic. The program has kept the university’s COVID-19 case rates much lower than those of other college campuses, maintaining a positivity rate of less than 1% throughout the 2020-2021 academic year.

“Our wastewater screening program demonstrates how different parts of UC San Diego can work together to keep campus safe,” says Knight, a professor of pediatrics and director of the Center for Microbiome Innovation. His team is now helping more universities, K-12 school districts and other organizations replicate their success with wastewater screening. Knight says the approach even has the potential to expand to other pathogens detectable in stool, such as flu.

Learn about COVID19 detection, intervention and risk mitigation at: