Wastewater testing is providing an early indicator of whether COVID-19 cases are increasing or decreasing in Santa Cruz County and beyond. Now, the process might become even more important amid concerns about variants of the disease.
Once or twice each week, biomolecular engineer David Bernick meets the head of Watsonville’s water quality lab in a grocery store parking lot. He takes a sample handoff, puts it on ice and brings it back to his own UC Santa Cruz lab for testing.
By the next day, Bernick says he has a pretty good idea of where Watsonville’s COVID-19 trajectory is headed — a trend that might not show up from swab tests for a handful of days, and in hospitals for weeks.
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His data is drawn from a test taken unwittingly by residents from across Watsonville with the flush of their toilets.
It relies on the fact that the SARS-CoV-2 virus, the virus that causes COVID-19, has been shown to shed through a carrier’s fecal matter even before — or in the absence of — the onset of symptoms.
A UCSC professor of molecular engineering, Bernick began testing Watsonville’s wastewater for traces of SARS-CoV-2 in September. After comparing his results to the coronavirus case curve that follows in its wake, he’s confident that wastewater testing could, and should, be put to even more use throughout the county.
“Prediction,” said Bernick, pointing out a trend line from his data that shows the immediate COVID-19 surge after Thanksgiving, and the continued rise through the New Year. “That’s what we really offer. . . . The Halloween spike, the Thanksgiving spike, the Christmas spike — I will tell you, this wasn’t our intention to be focusing on that.”
But he saw them all coming. “It just happened that that’s what we’re able to see.”
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Several cities around the world are also surveying their sewage for SARS-CoV-2: According to COVID-19 POOPS, a dashboard curated by the University of Merced, at least 900 sites in 45 countries are doing it, in addition to 189 universities. The University of Arizona credits the method as key to halting the spread of the pandemic as students returned to its dorms in August.
In Santa Cruz County, Bernick’s promising findings — and mounting concern about more infectious virus variants — are drawing renewed attention to the testing.
Local health officials are working with Bernick and the city governments to expand wastewater testing countywide, according to Dr. David Ghilarducci, Santa Cruz County’s deputy health officer. He sees potential uses not just for cities but targeted to schools, care facilities, and as a gauge for the presence of the new, more infectious virus variants from the UK and South Africa.
“It gives us an advanced warning when we expect clinical testing results to start climbing or dropping,” Ghilarducci said.
Search for virus variants
As of this week, the majority of Santa Cruz County residents are unwittingly taking the same COVID-19 test that Watsonville residents have been doing since the fall.
That’s because wastewater testing is resuming at the Santa Cruz wastewater treatment facility after a hiatus since the summer, according to Akin Babatola, the city’s laboratory and environmental compliance manager. The Santa Cruz plant processes waste for about 140,000 residents, more than half the county’s population. The Watsonville plant serves about 55,000 people.
Babatola said his focus now is on the more infectious COVID-19 variants from the UK and South Africa. He is working with an East Coast lab to secure markers to test for both of those variants — markers he hopes to have in hand as soon as next week. Testing will take place at the Santa Cruz wastewater plant, and also the county’s main jail, he said.
“Because of its high infectivity rate, I think it’s important to be able to communicate to the county immediately once we start seeing it, and how fast we’re seeing it, and what its relative concentration is in what you see,” Babatola said.
Bernick is also preparing his lab to test for the virus variants, and is hopeful to have tests running in a matter of weeks. Officials from Watsonville, Babatola, Ghilarducci and Bernick are in close communication about the results. The samples from both wastewater plants will be tested whenever the variant testing can begin, he said.
It’s not yet clear how useful the data will be, however, especially if the presence of the virus variants is small. “There is some question about detecting very small amounts, but it should become easier as these variants become more common,” said Ghilarducci.
How it works — and its imperfections
To monitor for the prevalence of the virus, wastewater samples can be collected from either centralized locations such as treatment facilities, or more targeted locations such as outside a particular dorm building. Samples are analyzed for presence and quantity of the virus. Researchers can then calibrate their findings based on the presence of another harmless contagion called pepper mild mottle virus that is reliably found in high levels across the population.
But their findings are only reliable to determine the coming case trend, according to Bernick — not the exact prevalence of the virus in the community. “As you get closer to a building, the answer to this question becomes binary: Is there, or isn’t there, SARS-CoV-2 being generated at this facility?” Bernick said.
Another limitation is that in areas with “largely transient” populations, such as those with high tourism, the viral load in sewage might not be a good indicator of how much infection is in the local community. Bababola, the Santa Cruz lab manager, saw that trend in action when the city was testing its wastewater earlier in 2020: when visitors flocked to Santa Cruz on weekends, they brought with them higher levels of the virus, he said.
Despite its lack of precision, the surveillance has several advantages, according to Ghilarducci. In addition to serving as a “leading indicator” of the trajectory of the virus, it also eliminates issues around access to — and deciding to take — PCR swab tests.
In other words, it’s a more representative sample.
“Essentially everybody in the area uses the bathroom at one point or another, and therefore they get represented in the sample,” Ghilarducci said. “So that’s one of the beauties of wastewater, is it’s not a selected subset, like clinical testing.
Buoyed by Bernick’s results, Watsonville is preparing to divide the city into four quadrants to test for variations in virus concentration across the population.
The results could help the city learn more about which neighborhoods, and demographics, are about to be hit the hardest, findings that could inform public outreach and other interventions, said Jackie McCloud, Watsonville’s environmental sustainability division manager.
“I’m pretty optimistic that it can be used for a lot of different measures,” McCloud said. “It can be an early predictor of where are we going to see COVID spikes in a community, as well as, okay, if we know we’re going to see it there, how do we arm our public health workforce, to be ready for that intake of patients?”
Bernick sees potential to zoom in even further and test the wastewater outflow from congregate settings like schools, nursing homes and or dorms. He has a proposal to bring the surveillance on campus at UCSC, as other universities have done.
“You as a parent, would you like to know that there’s no outbreaking happening in my school? Would you like to know that? We can know that, and it’s not very expensive,” Bernick said. Material costs in the range of $20 per test, he said, though some specialized training and PPE is required to collect the samples.
As Bernick sees it, collecting the data is the easy part. Figuring out what to do with it is harder.
For schools, the answers might be straightforward — whether temporary closure, mandatory testing or informing parents who can make choices for their families. In other cases, the range of interventions may be murkier.
“With all of this, the question that any person of authority needs to have an answer to is, if you had this data, what would you do?” Bernick said. “How would you change your behavior?”