Wastewater has become a useful way to monitor surges in specific areas, down to the variant
, director of the Center for Microbiome Innovation at the University of California, San Diego, and his team, along with scientists at Scripps Research, developed a system for picking out the genetic signatures of variants and determining the relative proportion of those variant strains in the wastewater samples they test. Identifying variants has been a challenge with wastewater samples, which contain not only SARS-CoV-2 but also myriad other bacteria, viruses, and pathogens.
To improve their chances of accurately identifying SARS-CoV-2 variants, the scientists focused on nearly 20,000 samples collected daily on the UC San Diego campus from 131 sites covering 360 buildings. They genetically sequenced a subset of SARS-CoV-2 virus they found in the positive samples and compared these sequences to those from positive COVID-19 tests from clinics on campus.
Those analyses allowed the researchers to determine, with just a few spoonfuls of wastewater, when COVID-19 infections among the 10,000 students living on campus and the 25,000 people spending time at the school trended upward—up to 14 days before testing on campus documented them. Because the team knew where the positive samples were collected, they could also pinpoint, down to the building, where infections were spreading.
With their new system for detecting variants, the researchers also found that they could pick up a wider variety of SARS-CoV-2 strains in the wastewater than sequencing of positive PCR tests from the campus clinics, providing a more accurate picture of the diversity of strains circulating in a community such as a college campus.
To track Omicron, which began spreading in the U.S. in late 2021, the team also collected data through February 2022, and documented the quick replacement of Delta by Omicron in their samples. Working with samples from the Point Loma wastewater treatment plant, near the UC San Diego campus, they were also able to detect Omicron on November 27; the first clinical identification of Omicron from tests on the school’s campus didn’t come until 10 days later, on December 8.
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