Bay Area scientists are searching for the COVID-19 virus not only in our noses, but somewhere more private: our poop.
When we flush our toilets, the waste vanishes, never to be seen, smelled or considered again.
But the sludge, a precious resource for public health officials, is captured downstream in sewage pipes and wastewater treatment plants – and then sent off for analysis by virus hunters at UC Berkeley and Stanford.
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These poop reports, planned or already underway in every Bay Area county, can reveal hidden outbreaks of disease. They also provide an efficient way to track the pandemic’s ebbs and flows over time – especially in communities without easy access to routine testing, where some infected residents may never feel sick.
“It’s designed to give us an early warning,” said Sasha Harris-Lovett, an urban water expert with the UC Berkeley team that is working with officials in Alameda, Contra Costa, San Francisco and Marin counties.
“It’s like fighting fire on a mountain top – if we see the smoke, we can marshal our resources before it becomes an inferno,” she said.
The new strategy, which has not yet been used to make public health decisions, relies on this important fact: After someone is infected with the COVID-19 virus, the pathogen’s genetic material is released through feces for weeks.
Wastewater testing can detect infections in as few as a handful of individuals in a building or town. But it’s highly unlikely that the pathogen in wastewater is still alive and transmissible, so is believed to pose little threat.
So far, the Berkeley and Stanford analyses have proven accurate, with sewage reports consistent with trends seen in more conventional clinical testing. Concentrations of floating virus seem to rise and fall along with known outbreaks of disease.
Genetic sequencing of the captured virus also helps scientists track any changes, over time, that might make the pathogen more dangerous. The Berkeley sleuths recently reported that they identified the same viral strains in wastewater that have been found through nasal testing — but, intriguingly, they also found strains that had not yet been observed in California. The researchers believe those new strains pose no practical significance.
The scientific strategies enlisted by the UC Berkeley and Stanford teams are similar. Their work is the basis of a regional Bay Area-wide wastewater monitoring project called COVID-Web.
The Berkeley team focuses its work in so-called “sewersheds,” where many sewers flow to a single pipe or collection station. This approach can detect outbreaks in crowded settings like dorms, nursing homes and prisons.
On city streets, they stop traffic, pry off manhole covers and suspend a large gray plastic barrel in a sewer hole. Several times an hour, a hose draws up a small sample of wastewater from the sewer pipe and empties it into the barrel. Samples are then sent to a new ‘’pop-up’’ lab — a temporary, 1,200-square-foot facility set up in the campus’s chemistry building, Hildebrand Hall.
“Every time we do this, it’s a little bit of a crapshoot, pun intended,” environmental protection specialist Tim Pine told scientists earlier this month while sampling a pipe at UCB’s University Village, according to a university news release. He pointed at a piece of toilet paper, stuck on a ladder rail in the drain, which could have botched the collection by plugging a hose.
At Stanford, civil and environmental engineering professor Alexandria Boehm and her team are working with 50 wastewater treatment plants that serve entire cities or counties around the nation.
Soon it will add a more focused project, providing faster feedback – testing wastewater daily, and processing it within 24 hours of collection — from eight different treatment plants. One site is Palo Alto’s Regional Water Quality Control Plant; another is the San Jose Santa Clara Regional Wastewater Facility. Stanford is also analyzing samples from specific sewers in San Jose’s sanitary system.
“It’s an opportunity to look for virus in a more broad population,” said Michael Balliet, director of Environmental Health for the County of Santa Clara. “It provides a potential resource for getting samples from individuals who might not otherwise be tested.”
Sewage sampling – called “wastewater-based epidemiology” — is an increasingly valuable tool around the world. It is used to monitor deadly pathogens such as the salmonella bacteria and polio and hepatitis A viruses. It can even detect the presence of illicit drugs.
Until recently, the daily or weekly tracking of the COVID-19 virus has proved challenging, because testing labs lack capacity. But testing of wastewater doesn’t require detection of the whole virus particle. Instead, the new technique can simply hunt for bits of viral genetic material, called RNA, that floats around the sewer system.
This approach can’t tell scientists exactly how many people are infected. That’s because It’s unknown how many viral particles are shed in the feces.
There are other challenges. For example, wastewater contains bleach and other chemicals that can destroy the virus. It also carries a plethora of other pathogens, complicating the search for the COVID-19 virus.
But the new strategy presents a unique opportunity to monitor and manage infections within communities.
“We are getting an unbiased look at what is happening in the whole population,” said Harris-Lovett, so in the future “we can direct our resources where they are most needed.”
