Like a lot of the rural West, Yosemite National Park stood as a safe haven from the coronavirus. No park employees or residents tested positive. No visitors reported being sick. The fresh air and open space seemed immune.
That’s until local health officials started looking for the coronavirus in the park’s raw sewage — that’s right, the poop. This week, lab analysis of feces at two wastewater treatment plants serving Yosemite revealed the presence of the virus that causes COVID-19. Dozens of people in Yosemite Valley are believed to have been infected.
“It’s one thing to live in denial: We live in the mountains, no one’s sick,” said Eric Sergienko, the health officer for Mariposa County, who is overseeing coronavirus testing in the Yosemite area. “But we can now confirm it’s here.”
With the pandemic surging across the country, more and more communities are keeping watch for the virus in wastewater. As foul as it may be, untreated sewage has long been used to track some of society’s most persistent ails, from illicit drugs to pollutants to disease. In 2013, a polio flare-up was famously identified through wastewater in northern Israel, helping authorities get a jump on containing the outbreak.
Scientists hope that human excrement can similarly help guide health policy today, telling them where the novel coronavirus emerges, what areas should receive medical supplies or be locked down, and when it may be safe to reopen communities, their schools, stores and businesses.
Wastewater testing is seen as a complement to clinical testing, which has been hampered by test shortages, long waits for results and false negatives. With sewage, scientists can identify the presence of the coronavirus a week before a person tests positive with nasal swabbing, and the testing covers potentially tens of thousands of people, not just one.
“It allows us to do surveillance, knowing we couldn’t test all the visitors to Yosemite or any visitors from other parts of California,” Sergienko said.
Working with the National Park Service, Mariposa County health officials started collecting untreated wastewater last month. They’re taking samples weekly from the communities of El Portal, where sewage from Yosemite Valley is piped and treated, and Wawona, where sewage from the park’s southern end and several private residences is managed. The samples are sent to Cambridge, Mass., lab Biobot Analytics for analysis.
While swab testing at the park’s health clinic has yet to yield a case of the coronavirus, the lab testing this week detected the virus in the sewage collections from June 30 to July 6 at both El Portal and Wawona. Biobot officials told the county that, based on how much of the virus they counted, they think about 170 people were infected in Yosemite Valley and just one or very few in Wawona.
Sergienko, who provides guidance to the park on public health issues, said it’s not surprising that the coronavirus finally emerged in Yosemite, and attributed it to the region’s many visitors. Its presence, he said, is not likely to trigger significant policy changes because the park is already adhering to local and state safety directives. However, he said he believes the positive test results will make people more vigilant.
“It heightens awareness,” he said. “We know the problem is here. We know the challenge is here. Now we have to be serious about facing it.”
More than 4 million people visit Yosemite each year, from all over the world, making it ripe for the spread of the coronavirus. Park administrators referred questions about the newly detected virus to county health officials.
The park has so far been cautious, more so than many other national parks, in its operations during the pandemic. Yosemite was closed for nearly three months when the outbreak began, then reopened with restrictions that allow in only half the number of people who normally visit. Visitor centers remain shut down, and campgrounds, gift shops and hotels are limiting services to allow for physical distancing.
Following Gov. Gavin Newsom’s statewide order Monday to shutter indoor dining and a handful of other activities, additional park facilities, such as restaurants, have scaled back operations.
Carolyn Coder, an environmental health specialist for Mariposa County, said the wastewater testing would help determine whether more restrictions would be recommended in the weeks and months to come.
“It’s part of the overall decision-making,” Coder said. “Do we need to go back to shelter-in-place? Do we need to go back to stage one?”
Sewage testing works by identifying genetic material, or RNA, from SARS-CoV-2, the coronavirus that causes COVID-19. The virus is not believed to be infectious in the waste, but plenty of it is there so scientists can see the RNA. Over the past few months, several private labs and universities have gotten into the business of hunting for it.
What these researchers haven’t been able to do well, though, is use the genetic material to figure out definitively how widespread a viral infection is, though some like Biobot have begun to provide estimates. The fact that not everybody with the virus ejects it through their stool and that some expel it even after they recover are some of the complicating factors.
Ali Boehm, a professor of civil and environmental engineering at Stanford University who has been studying the virus in wastewater since February, says concentrations of the genetic material can show trends, such as whether infections are going up or down. But getting more precise information from the testing, she said, is still an imperfect exercise.
Boehm and others are working to improve the science. They’d like to be able to unravel such unknowns as the true scale of infections and how the virus is mutating, and do it all in real-time.
“We hope by the end of this summer we’re going to have data that is actionable and complete,” she said.
Her team at Stanford is analyzing wastewater samples from about 50 utilities, including many in the Bay Area. These participating agencies stand to better grasp the spread of the virus in their backyards and customize containment measures from whatever breakthroughs the researchers make.
Biobot, which is doing sewage testing for about 400 communities in the United States, says the modeling it has developed for RNA concentrations gives a pretty good idea of how many people might be infected with the virus, though the company acknowledges its methods aren’t perfect.
“At this time, our prevalence estimates are a back-of-the-envelope exercise, and there’s much work to be done to improve accuracy,” the company wrote in a blog shared with The Chronicle.
Biobot was in position to get into coronavirus testing because its prior business was tracking opioids in wastewater and analyzing patterns of drug use. It quickly transitioned at the start of the pandemic.
In the Bay Area, the East Bay Municipal Utility District, which treats the sewage of 685,000 residents, was one of the nation’s first utilities to send off wastewater samples for analysis — to Stanford as well as UC Berkeley and other labs — and now it’s gearing up to do its own coronavirus testing.
The goal, says agency Director of Wastewater Eileen White, is nothing short of being able to pinpoint outbreaks by ZIP code. Also, the district wants to know when such areas may be virus-free.
“If we’re really going to stop the spread, we need good data,” she said.
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