Writing in the July 7, 2022 online issue of Nature, scientists and physicians at University of California San Diego and Scripps Research, with local and federal public health officials, describe how wastewater sequencing provided dramatic new insights into levels and variants of SARS-CoV-2 on campus and in the broader community — a key step to public health interventions in advance of COVID-19 case surges.
Importantly, the authors said the approach, deployed by UC San Diego as part of its Return to Learn efforts and then more broadly in the surrounding region, is a scalable, cheaper and faster way for communities and regions to detect the coronavirus and take appropriate actions.
“The coronavirus will continue to spread and evolve, which makes it imperative for public health that we detect new variants early enough to mitigate consequences,” said co-senior study author Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at UC San Diego.
“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation or the capacity to do sufficient testing and sequencing. We’ve shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community.”
Persons with COVID-19 shed the virus in their stool, whether or not they have symptoms. In the summer of 2020, Knight and colleagues leveraged that fact to begin robotic sampling of wastewater on the UC San Diego campus.
“The university’s Return to Learn program was conceived and built on three pillars: viral detection, risk mitigation and intervention,” said UC San Diego Chancellor and study co-author Pradeep K. Khosla. “Nothing like this had been done before. Sampling and detection efforts began modestly, but grew steadily with increased research capacity and experience. Currently, we’re monitoring almost 350 buildings on campus.”
The program has been a success. Students began returning to campus in mid-2020, with COVID-19 case rates far lower than in surrounding communities. In March 2021, wastewater surveillance went regional, with multiple samples sequenced each week from San Diego County’s primary wastewater treatment plant at Point Loma, with a catchment size of 2.3 million people.
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