85% of Campus COVID-19 Cases Detected Early by UC San Diego’s Wastewater Screening

Smruthi Karthikeyan, PhD (left) and Rob Knight, PhD (right) collect wastewater samples from collection robots on the UC San Diego campus. Credit: Erik Jepsen/UC San Diego

As part of the university’s Return to Learn program, wastewater screening has helped prevent outbreaks by detecting 85 percent of cases early, enabling timely testing, contact tracing and isolation.

People infected with SARS-CoV-2, the virus that causes COVID-19, are known to pass it in their stools, even if they don’t experience any symptoms. With that in mind, researchers at the University of California San Diego School of Medicine have been screening wastewater from campus buildings for signs of the virus since the summer of 2020, figuring the information could help prevent outbreaks.

Now they have data to back it up: When screening for SARS-CoV-2 in wastewater, the team showed they can detect even a single infected, asymptomatic person living or working in a large building. Notification to residents of any building with positive wastewater increased COVID-19 testing rates by as much as 13 times. Once a resident tested positive, isolation and contact tracing helped prevent further spread of the virus.

The approach enabled early detection of 85 percent of campus COVID-19 cases, researchers reported in the Aug. 10, 2021 issue of mSystems. In other words, wastewater samples tested positive before most individual diagnoses.

Approximately 10,000 students lived on the UC San Diego campus during the 2020-2021 academic year, with low COVID-19 cases due to the many risk mitigation, viral detection and intervention elements included in the Return to Learn program. Credit: Erik Jepsen/UC San Diego.

“University campuses especially benefit from wastewater monitoring as a means of preventing COVID-19 outbreaks, as they are fraught with largely asymptomatic populations and are potential hotspots for transmission that require frequent diagnostic testing,” said first author Smruthi Karthikeyan, PhD, an environmental engineer and postdoctoral researcher at the UC San Diego School of Medicine.

Karthikeyan led the study with senior author Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at UC San Diego.

Wastewater screening is an integral part of UC San Diego’s Return to Learn program, an evidence-based approach that has enabled the university to provide on-campus housing and personal tuition and research opportunities throughout most of the pandemic.

Return to Learn is built on three pillars: risk mitigation, viral detection and intervention. With approximately 10,000 students on campus during the 2020-2021 academic year, the program’s many components kept COVID-19 cases much lower than in the surrounding community and compared to most college campuses, with a positivity rate of less than 1 percent during that period. time. The Return to Learn program, including wastewater testing, has become a model for other universities, K-12 school districts, and regions.

Every morning, seven days a week, a team of students and staff in matching t-shirts ride golf carts across campus to collect sewer samples from 126 collection robots set up to guard 350 buildings. By 10 a.m., they return to Knight’s lab at the School of Medicine.

An online dashboard is tracking COVID-positive wastewater detection on the UC San Diego campus and making it available to the public. Credit: UC San Diego

There, Karthikeyan and team process the wastewater using a different kind of robot, which concentrates the virus using magnetic nanoparticles and then extracts RNA — the genetic material that makes up the genome of viruses such as SARS-CoV-2 — from the samples. Polymerase chain reaction (PCR) tests are used to look for the virus’ signature genes.

When the virus is detected, a campus-wide system sends automated but targeted messages to individuals involved in affected buildings, such as students, staff and faculty, advising them to be tested for the virus as soon as possible. The data is added to a public dashboard.

Since its inception, the team has been constantly working to optimize the process, Karthikeyan said. The current automated approach has drastically reduced the lead time from sample to result by a factor of 20; now five hours for 96 samples. By miniaturizing the samples, the researchers reduced processing costs to $13 per sample. Knight estimates that the approach exceeds the scale of comparable surveillance programs 10 to 100 times. The next step, he said, will be to deploy rapid methods to test for SARS-CoV-2 variants, including delta, in real time.

“This system shows how the many different parts of UC San Diego can work together as a system to keep the campus safe,” Knight said. “This work required advances not only in viral sample processing, but teams such as logistics, environmental health and safety, campus and health systems IT, facilities management, and many others, as well as leadership of the Return to Learn program to make this possible. to make. We are now helping other campuses and organizations replicate this success, which has potential not only for COVID-19, but for many other stool-borne pathogens, including flu, in the future.”

Reference: “Rapid, large-scale wastewater monitoring and automated reporting system enable early detection of nearly 85% of COVID-19 cases on a university campus” by Smruthi Karthikeyan, Andrew Nguyen, Daniel McDonald, Yijian Zong, Nancy Ronquillo, Junting Ren, Jingjing Zou , Sawyer Farmer, Greg Humphrey, Diana Henderson, Tara Javidi, Karen Messer, Cheryl Anderson, Robert Schooley, Natasha K. Martin and Rob Knight, Aug 10, 2021, mSystems.
DOI: 10.1128/mSystems.00793-21

Co-authors are: Andrew Nguyen, Daniel McDonald, Yijian Zong, Nancy Ronquillo, Junting Ren, Jingjing Zou, Sawyer Farmer, Greg Humphrey, Diana Henderson, Tara Javidi, Karen Messer, Cheryl Anderson, Robert Schooley, Natasha K. Martin, all at UC San Diego.