Early detection is one of the keys to reducing the spread of SARS-CoV-2 – the virus that causes COVID-19 – and a wastewater monitoring system developed by the UC San Diego Center for Microbiome Innovation (CMI) is proving to be an invaluable tool.
While symptoms of COVID-19 generally take four or five days to appear, traces of the virus can be detected much earlier. Once a person has been exposed to SARS-CoV-2, the virus replicates in the gastrointestinal tract and travels into stool, eventually reaching sewage systems from toilets and showers. By monitoring wastewater outflow, viral activity can be discovered near the onset of an infection, including presymptomatic and asymptomatic cases.
The Environmental Testing/Wastewater Work Group is led by Rob Knight, professor and director of the Center for Microbiome Innovation at UC San Diego; Smruthi Karthikeyan, postdoctoral researcher in the Department of Pediatrics; and Bob Neuhard, executive director of the Operational Strategic Initiatives, and serves as an integral component of UC San Diego’s Return to Learn Program. Using real-time quantitative polymerase chain reaction (RT-qPCR) analysis, wastewater samples are tested for genetic material unique to the coronavirus. The CMI integrates researchers and technologies to rapidly perform these tests on a large scale, enabling more efficient surveillance capacity for the university.
“Building capabilities to solve applied problems is where the Center for Microbiome Innovation excels,” according to Andrew Bartko, executive director of the CMI. “We strive to integrate the world-class expertise, technologies, and resources we have available into collaborative teams that yield impactful results.” Both the wastewater testing initiative and the Return to Learn program have garnered national acclaim, including recent coverage in the New York Times and Los Angeles Times.
The program began with six sample collection points during the summer and expanded to 52 sites in late November, with plans to reach 200 sites in the coming months. As the number of collection sites grow, the system will cover the entire campus and provide more granular data on where viral shedding is occurring. The increase in collection capacity has already paid dividends, as traces of the coronavirus were detected throughout late November and early December. When a positive sample is detected in wastewater, the university sends out an alert that encourages anyone who was in buildings where the virus was detected to get tested immediately. Infected students are then moved to isolated housing, preventing wider outbreaks and significantly reducing public spread of the virus.
This early detection has been vital to UC San Diego’s low infection rate, which has consistently been nearly an order of magnitude below San Diego County’s numbers. Even as the virus has surged throughout the county, UC San Diego has maintained a positivity rate of less than 1% among its student body.
With a continued focus on early detection and mitigation by studying the virus’s interaction with the microbiome, the CMI is committed to helping the university protect its community of students, faculty, and staff as they return to campus.
This piece was written by CMI’s contributing editor Cassidy Symons