When people think of the words “COVID-19” and “testing,” the images that come to mind are usually long nasal swabs, wielded by people in full personal protective equipment. Testing individuals has been the main path forward to track the spread of the disease across San Francisco, but it’s not the only available method. Testing sewage — the natural waste we flush down our toilets, as well as shower or sink water — is another tactic, one that can often pinpoint the spread of the disease more quickly than the painstaking testing of individual city residents.
Since April, UC Berkeley has been studying wastewater samples from 11 districts around the Bay Area — including San Francisco. It’s a project that’s picking up speed; while 30 samples a week can be tested currently, the team expects to ramp that up to 200 samples a week by the end of the year.
In San Francisco, samples are being collected from wastewater treatment plants, several neighborhoods, and a residential care facility. The data UC Berkeley detects could be vital for local health departments to track a sudden increase in spread.
“From the very beginning of the pandemic, it was clear that there were major limitations to the ability to test every individual in a population frequently enough to find out whether they were infected or not,” says Kara Nelson, professor of civil and environmental engineering at UC Berkeley. “Wastewater naturally pools the waste from hundreds to even millions of people in a single sample, so if you can collect a representative sample of wastewater and analyze it, you can gain a tremendous amount of information that you likely couldn’t gain through testing people individually.”
But determining COVID-19 traces is tricky: Detecting the virus in wastewater samples is decidedly more troublesome than finding in it a nasal swab. For one thing, wastewater contains more than just sewage. Bleach is added as a disinfectant, and to control odor, which can break down and kill the COVID-19 virus as it travels through the sewers.
“The research community has yet to find evidence of survival of COVID-19 virus in wastewater systems,” explains Will Reismann, spokesperson for the San Francisco Public Utilities Commission. “Essentially, the virus dies, but RNA remnants (the gene copies) remain in the wastewater samples.”
Wastewater also contains many other viruses, making it trickier to isolate COVID-19 molecules in samples. Also, people excrete different amounts of COVID-19 particles in their poop, which can complicate studies on how prevalent the virus is in certain areas.
UC Berkeley has figured out some workarounds for the above issues. The answer lies in something we all have at home: table salt. Nelson’s team partnered with UC Berkeley’s Department of Molecular and Cell Biology and found that salt can slice open the outer layer of the virus, which causes it to spill all of its genetic material into a single, collectible sample. The salt has the added benefit of catching bits of virus particles that may be partially disintegrated and preserving them for testing.
It’s proven to be a highly successful system. Not only is it fast (results can be determined in eight hours), it’s also highly sensitive. It’s possible to detect if a small number of people shed the virus in a wastewater sample that contains material from thousands of people.
This isn’t the first time San Francisco’s poop has been studied.
“The SFPUC is constantly testing our wastewater to ensure public health for chemical and biological parameters,” Reismann says. “We collaborate with the research community regularly to help advance the science of wastewater treatment.“
But this is the first time the stakes may be this high. Down the line, this model could be used to test specific areas — such as a nursing home, or a neighborhood where individual testing numbers are low — to catch an outbreak early.
“One of the huge bottlenecks in wastewater testing has just been testing capacity,” Nelson says. “This pop-up lab is the first high-throughput lab in the Bay Area that has the capacity to bring in a large number of samples and provide results quickly to public health officials.”
UC Berkeley has been providing data from its study to San Francisco’s Department of Public Health, but so far The City has not made use of it or released it to the public.
“While wastewater testing is not currently part of our infectious disease surveillance, it could be in the future,” the department says. “We look forward to collaborating with researchers and other City agencies as we determine how best to collect and use this data.”
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