Smruthi Karthikeyan turned to wastewater to get ahead of COVID-19

Environmental engineer Smruthi Karthikeyan had spent just a couple of days working in her new lab at the University of California, San Diego when the state instituted its first coronavirus lockdown in March 2020.

She’d been brought on as a postdoc by biologist Rob Knight to develop new techniques for studying how microbes in complex ecosystems shape human health and vice versa. The COVID-19 pandemic quickly put a new spin on that mission.

Soon, the lab pivoted to support the coronavirus response. Infections were outpacing testing capacity in San Diego County, Karthikeyan says. Meanwhile, the university wanted to keep the campus open for its 10,000 students still living on campus and 25,000 workers. There had to be a way to monitor infections without requiring thousands of people to get tested all the time, Karthikeyan and colleagues thought.

Public health researchers had previously tested wastewater for pathogens as a way to spy on the movements of infectious agents in communities. Viruses, bacteria and parasites can show up in stool before people exhibit symptoms, giving clues to a coming outbreak. But no one had implemented such a system to track a respiratory virus before, and never at a scale of tens of thousands of people.

Karthikeyan was up for the challenge.

Bold idea

The wastewater monitoring system that Karthikeyan and colleagues developed and implemented at UC San Diego, reported July 7 in Nature, processes upward of 200 samples per day. Previous methods could process a maximum of eight samples, she says. What’s more, the system has identified newly spreading coronavirus variants up to two weeks earlier than clinical testing and accurately forecasted the mix of variants infecting students and staff.

That has given school officials more time to take action to keep infection rates low. During the study period from November 2020 to September 2021, the proportion of clinical tests that were positive was less than one percent, Karthikeyan says, dramatically lower than rates in the surrounding area and many other college campuses at the time.

Among the key players in the team’s monitoring system are 131 robots that collect wastewater samples throughout each day from 360 university buildings. Back at the lab, the samples are screened for viral RNA and results are fed into a publicly available online dashboard created as part of the project.

Karthikeyan’s team isn’t the only one using human waste to get a jump on COVID-19. But the scale of the monitoring “is a bit unprecedented,” says Ameet Pinto, an environmental engineer at Georgia Tech in Atlanta. During the study period, Karthikeyan and colleagues processed a total of nearly 20,000 samples. “That’s amazing,” he says.

A positive result triggers a campus-wide notification via smartphone app. For dorms, anyone who lives in the building is mandated to get tested for COVID-19, while anyone who may have recently been in the building is strongly encouraged to get…