Flushing the toilet tells Boise about COVID-19 case rates. Will it help detect variants?
There’s no longer a toilet paper craze, but the previously prized paper wipes still help Boise figure out community COVID-19 case rates and, possibly, variant prevalence.
The stool of about half the people infected with COVID-19 contains the virus, Amy Kirby, wastewater expert at the Centers for Disease Control and Prevention, said at an online conference.
“Few individuals get tested for COVID-19, but everybody uses the bathroom,” wrote Natalie Monro, of Boise’s Public Works Department, in an email.
Since many coronavirus cases are asymptomatic, wastewater can also be a good way to test a community all at once, Kirby added.
“No mailing, right? You don’t have to phone in your results, you just flush. And the results are sent to the city,” said Greg Hampikian, a DNA expert at Boise State University.
Beginning in late May 2020, the city of Boise reported the number of copies of SARS-CoV-2, the virus that causes COVID-19, in a liter of wastewater. After a two and a half month hiatus, the dashboard is up again.
More regular reports are set to restart in the next couple months, as the city completes a switch from testing at the University of Missouri to Boise State. The most recent results are still from Missouri, Monro wrote. Once the city validates the two universities’ results against one another, Boise State will completely take over the testing.
The switch to Boise State testing is because of “cost and timeliness,” Monro wrote.
Since Boise State receives grants, testing occurs “at no cost to the city,” according to Monro. Boise State also can analyze the samples immediately. Sending samples to the University of Missouri cost about $340 per day, and testing took an additional day due to shipping, Monro wrote.
Speed is the main advantage of wastewater surveillance. Most other community testing methods take about two weeks after infection to detect an outbreak, Kirby said.
Wastewater can predict community peaks about a week or 10 days after infections, said Hampikian, whose lab took over Boise’s wastewater testing.
In Boise, “wastewater data was the first to detect the wave of cases that occurred last summer,” Monro wrote.
COVID-19 variants in wastewater
This widespread testing also can identify variants spreading in a community. Earlier this year, Boise detected COVID-19 variants from the UK and California in wastewater before seeing them in clinical tests.
Though the delta variant was detected in Texas and Missouri wastewater, Boise hasn’t sampled its wastewater for variants in several months. A delta variant case was, however, confirmed in lab tests last week in Twin Falls, according to the South Central Public Health District.
The delta variant is more contagious than even the UK one, according to the World Health Organization. This could be because of changes to genes that affect its outer spikes, said Joan Rose, an environmental virologist at Michigan State University, by phone.
Boise has plans to test its wastewater for variants again at some point.
“When they change that little spiky protein, (the virus) is more efficient at attaching to the cell, getting into the cell and causing the disease,” she said.
The delta variant, the CDC estimated, is now the dominant strain in the U.S. and responsible for more than 40% of the cases circulating in the region that includes Idaho.
Wastewater surveillance a new field
Since the 1980s, the virus that causes polio has been tested for in wastewater, Kirby said. Though, she added, wastewater “surveillance is still a young field, especially for COVID.”
Since it is so new, scientists are still figuring out problems inherent in sample collection and analysis.
Every two days, Boise State receives wastewater samples from two treatment centers serving Boise, Garden City and Eagle. Once the Boise State lab receives them, workers filter out the solids in the samples and purify them, lab researcher Ernie Ogden said. Then they measure the amount of virus in the sample.
While researchers have matched changes in wastewater data with reports from other types of COVID-19 tests, scientists can’t directly report how many people have COVID-19 from wastewater tests.
“Wastewater fluctuates. All we can do is say ‘detected,’ ” Hampikian said. “We know it’s there. We know there’s more there than there was yesterday that is detectable. And just that is enough for Health department officials to start planning.”
From day to day, changes in wastewater test results may not always relate to differences in infections. If there’s a lot of agricultural runoff that gets into a city’s sewer system or something similar, the samples will be diluted before they get into the lab.
While Boise State is not yet doing this correction, one way to account for dilution is to also test for another prevalent virus and compare its signal to that of the virus that causes COVID-19. The pepper mild mottle virus, which might replicate in humans’ guts, is one common virus that labs use to figure out how diluted wastewater may be.
Even if researchers can account for wastewater dilution, the analysis step where they multiply the virus segments is prone to interference.
Rose said detergents, shampoos or other materials in wastewater can inhibit the detection process.
The combination of unknown inhibitors and dilution sources makes wastewater testing less useful for determining exactly how many community members have COVID-19. But it can still be helpful for understanding spikes in infections.
As for the future of testing, Monro wrote, “we expect to continue testing in the coming months and for as long as the data continue to add significant value to COVID-19 monitoring.”
Though Boise doesn’t yet have any specific plans, wastewater surveillance can also monitor drug use and non-coronavirus diseases in the population.
“Transitioning testing to Boise State provides an opportunity to expand our testing in the future,” Monro wrote.
This story was originally published July 21, 2021 at 4:00 AM.
