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Since the University of California San Diego campus reopened last summer, university officials have relied on proven public health testing and contact tracing strategies. But they also added a new tool to their arsenal: excrement.
This tool alerted researchers to about 85% of cases in dormitories before they were diagnosed, according to a soon-to-be-released study, said Rob Knight, professor of pediatrics and computer science and engineering who helped to create the campus wastewater analysis program.
When covid is detected in sewage, students, staff and faculty are tested, which has enabled the school to identify and isolate those infected who do not yet have symptoms, which could stop epidemics in their tracks.
The UC-San Diego testing program is one of hundreds of efforts in California and the country to turn waste into valuable health data. From Fresno, Calif. To Portland, Maine, universities, communities, and businesses monitor human feces for signs of covid.
Researchers have high hopes for this muddy new data stream, which they say can alert public health officials to infection trends and is not dependent on those tested. And because people excrete the virus in their stool before they show symptoms, it can serve as an early warning system for outbreaks.
The Centers for Disease Control and Prevention find the practice so promising that they have created a federal database of wastewater samples, turning raw data into valuable information for local health departments. Experts say the program essentially creates a real-time public health tool, which could have a range of uses beyond the current global pandemic, including tracking other infectious diseases and germ resistance to antibiotics.
“We think this can really provide valuable data, not only for covid, but for many diseases,” said Amy Kirby, the microbiologist leading the CDC efforts.
The virus that causes covid infects many types of cells in the body, including those in the respiratory tract and intestines. The virus’s genetic signature, viral RNA, enters the stool and usually appears on poop days before symptoms start.
At UC-San Diego and other campuses, researchers are taking samples from individual buildings, capturing data so granular that they can often infer the number of infected people who live or work there. But in most other settings, due to privacy concerns and resource constraints, testing is done on a much larger scale, with the goal of tracking trends over time.
Samples are taken from wastewater, which is what comes out of our sewer lines, or sludge, the solids that have settled in wastewater. They are usually extracted mechanically or by a human with a ladle at the end of a rod.
When researchers in Davis, Calif., Saw the viral load increase in several neighborhood sewer streams in July, they sent SMS alerts and hung signs on the doors of 3,000 homes recommending that people get tested. .
Before the pandemic, testing of sewage to identify and prevent disease in the United States was largely limited to academic use. Israel used it to ward off a polio epidemic in 2013, and some communities in the United States were taking wastewater samples before the pandemic to determine what types of opioids people in their community were using, a service offered by the United States. Biobot company.
But when covid hit the United States amid political chaos and a shortage of tests, local governments rushed to get all the information they could get about the virus.
In rural Lake County, California, health officials had identified a handful of cases by sending nurses to search for infected people. They were sure there was more but couldn’t get their hands on any tests to prove it, so in the spring of 2020 they signed up for a free wastewater testing program run by Biobot, which pivoted to covid testing as the pandemic took off and now is in charge to be tested in K-12 schools, office buildings and nursing homes, in addition to local governments and universities, said Mariana Matus, CEO and co-founder of the company.
The covid virus appeared in samples from four Lake County wastewater treatment facilities.
“It’s a way to just get more information because we can’t do tests,” Gary Pace, then county health officer, told KHN.
As wastewater sampling gained momentum around the world, the US Department of Health and Human Services began providing grants in fall 2020 to wastewater treatment plants. Biobot has won a bid to run a second cycle of this program, currently running until the end of August, testing the wastewater of up to 30% of the US population.
At least 25 California wastewater treatment plants participate in the program, and many more receive money from the CDC, work with local universities, or pay for their own tests. While states like Ohio and Missouri have created public dashboards to display their data, California’s efforts remain scattered.
Test data alone doesn’t add much value to health officials – it needs to be translated to be useful. Scientists are still learning to read data, a complicated process that involves understanding the relationships between the amount of virus shed by people, the number of people using a sanitation system, and the amount of rainwater flowing out. in the system, potentially diluting the wastewater, among many others. other factors. Since the use of wastewater to track disease was not widespread before the pandemic, there has been a steep and continuing learning curve.
Besieged public health officials have struggled to fit the new data into their already overwhelming workloads, but the CDC hopes it can fix these issues with its new national system that tracks and translates wastewater data for governments. local.
Throughout 2020, CDC microbiologist Kirby and engineer Mia Mattioli formed a two-person wastewater team within the agency’s largest 7,000-person covid response. Meanwhile, fellow academics generously shared what they knew about the epidemiology of wastewater, Kirby said. In September 2020, the couple launched the National Wastewater Monitoring System, which interprets sampling data for state and local governments. Today, they lead a team of six and have a permanent place in one of the departments of the CDC.
“Every part of this system has had to be built largely from scratch,” Kirby said. “When I look at this, it really surprises me where we are now.”
In the months after the system launched, it was able to detect an increase in the number of cases four to six days before diagnostic tests showed an increase, Kirby said.
She hopes that by the end of next year, the federal surveillance program will be used to detect a range of diseases, including E. coli, salmonella, norovirus and a deadly drug-resistant fungus called Candida auris, which has become a global threat and has wreaked havoc on hospitals and nursing homes.
The more operational these programs are, the more useful they become, said Colleen Naughton, professor and civil engineer at the University of California-Merced who leads COVIDPoops19, which tracks wastewater monitoring efforts around the world. Naughton is working with colleagues at the University of California-Davis to launch surveillance programs near his workplace in the Central Valley, but finds some small communities lack the resources to conduct tests or have enough staff. to analyze or use the data.
It is in those small communities with limited access to testing and doctors that the practice may hold the most promise, Naughton said. Covid has exposed long-standing inequalities between communities which it says will be perpetuated by the use of this new public health tool.
Privacy concerns also need to be addressed, the experts said. Wastewater data has traditionally not been viewed as protected personal health information like diagnostic tests. Health officials have handled previous concerns about wastewater tracking of illicit drug use by sampling wastewater streams large enough to ensure anonymity. But testing for certain health issues requires looking at DNA. “I think it will be a challenge for public communication,” Knight said, “to ensure that this is not seen as essentially spying on the genetic secrets of each individual.”
Public health and wastewater officials said they are excited about the potential of this new tool and are working on ways to address privacy concerns while leveraging it. Greg Kester, director of renewable resource programs at the California Association of Sanitation Agencies, wrote to CDC officials in June 2020 to request a federal monitoring network. He finds it hard to believe how quickly this call has come true. And he hopes he’s here to stay, both for the ongoing pandemic and for the inevitable next outbreak.
“As vaccination rates increase and we get variants, this will remain important as clinical testing decreases,” Kester said. “We really want to make that part of the infrastructure.”
This story was produced by KHN, which publishes California Healthline, an independent editorial service of the California Health Care Foundation.
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