COLUMBIA, Mo. — University of Missouri researchers have turned to an unusual way to track the spread of COVID-19: by looking at feces.
While nasal swab tests continue to be plagued by scarcity, slow turnaround and inaccuracy, Mizzou scientists and state officials hope that testing wastewater for the coronavirus’ genetic signature could give communities a faster way to spot a flare-up in cases.
“Everybody poops, no one can hide it,†said Marc Johnson, a Mizzou professor of molecular microbiology and immunology and one of the lead scientists on the project. “It’s an unbiased measure that doesn’t rely on how many tests you perform. It’s a reality check of where things actually are at.â€
Johnson and Chung-ho Lin, a Mizzou research associate professor of forestry, have joined forces with the Department of Natural Resources and the Department of Health and Senior Services to test wastewater from 64 sites across the state. They hope the stool test data will help health officials and the public make informed decisions about the virus.
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SSM Chief Medical Officer Dr. Alexander Garza said the method is important because it continues to be difficult to understand COVID-19’s true prevalence in the community.
“If you’re testing only a subset of the population, you’re missing a large chunk of the population,†said Garza, who heads the St. Louis Metropolitan Pandemic Task Force. “That’s where wastewater data could be beneficial.â€
More importantly, evidence suggests that people start shedding the virus in their stool up to five days before they develop symptoms. Garza said this data can serve as an early warning system to public health officials.
“We could use that info to prepare the health care system for a potential surge in cases or ramping up testing to identify those cases,†he said. “On the public policy side, it would trigger some kind of action such as ratcheting back capacity in restaurants or bars or rolling back some business reopening guidelines.â€
The team is testing all seven of St. Louis County’s wastewater facilities as part of the project.
While other states also are screening wastewater for COVID-19, Johnson said that the number of samples his lab processes makes it the biggest statewide effort across the country. Third-party companies like BioBot have to run tests, but Lin said his team is charging the state much less — just enough to cover the cost of the chemicals and labor.
Working day and night
The testing process starts at wastewater facilities, where small pipes suck hourly samples from the river of sewage. Collecting a composite sample helps create a more complete picture of the virus’ spread in the community.
Gloved, masked and goggled workers load the samples with ice packs and hand them over to the state’s dedicated courier system, which takes them to Jefferson City. The courier system has been handling water samples since the 1970s to test drinking water in compliance with the Safe Drinking Water Act.
“The fact that we have this centralized system of getting samples to one lab for 64 sites is significant,†said Chris Wieberg, Water Protection Program director for the state’s Department of Natural Resources, or DNR. “I don’t know any state that has this much wastewater testing coverage of a single state.â€
Next, a DNR team brings the samples to Johnson’s lab in Columbia. His team prepares the samples for analysis by concentrating them and extracting genetic information.
Johnson, who studied HIV before the pandemic, adds a known amount of an engineered virus that he uses for his usual research. This step allows him to ensure that he properly and efficiently extracted the genetic information from the sample.
The samples then head to Lin’s lab, a few buildings over. There, his team prepares the concentrated samples for qPCR, or quantitative polymerase chain reaction, analysis. The method allows researchers to understand exactly how much of this coronavirus’ RNA, or genetic information, is in each sample.
Lin is meticulous about avoiding contamination in his lab: No one outside his team is allowed inside, and he asks his researchers to strictly limit their social activities.
From start to finish, Lin said, a single sample requires 11 hours to process and analyze. The teams work upward of 10 hours a day, with day and night shifts, to meet the high demand.
The end result is a number that represents the concentration of coronavirus genetic material in the samples. The logic goes: the higher the concentration, the more COVID-19 cases in the community. But it is not so easy, according to Jeff Wenzel, chief of the state health department’s Bureau of Environmental Epidemiology.
While Johnson and Lin have refined their methods to detect the indications of the virus in wastewater to a high level of certainty, that does not yet mean the data will be useful to public health officials. A team of 10 epidemiologists at Missouri’s Department of Health and Senior Services has been working to better connect the wastewater data to clinical data from nasal swab tests.
Wenzel, who heads the team of epidemiologists, said they have to control for many factors before the data can be released. For example, they have to account for “superspreaders,†or people who shed abnormally high amounts of the virus.
Wenzel said he would also expect a superspreader to shed more virus through their stool, meaning that a higher concentration of virus particles in the wastewater may have come from one person.
His team is also looking into how to factor in heavy rainfall, which could dilute the waste flowing through the sewer system.
‘Holy crap’
Though researchers are still trying to make sense of the wastewater data, Johnson said they have seen a noticeable spike in wastewater virus particles across the state in recent weeks, coinciding with clinical testing results.
Eventually, Johnson hopes the data will be available on a public dashboard.
“It’s another piece of information that lets people know how they might go about spending their week,†he said.
The team is prioritizing testing municipalities that have higher populations, a higher COVID-19 positive rate, and known vulnerable populations such as correctional facilities, college campuses and large factories.
“We’re hoping to avoid the surprise of what’s happened at meatpacking plants across the country,†said Johnson, referring to large COVID-19 outbreaks that have forced some factories to shut down.
When Mizzou is back in session, the team plans to collect wastewater from four places across campus, combine them, and run analyses to try to detect any COVID-19 surge on campus.
In addition to the Missouri sites, the team has also been testing wastewater from Boise, Idaho. In the last few weeks, Idaho’s number of cases has spiked. The amount of virus the researchers saw in Boise’s samples went up nearly a thousandfold.
“When we first saw the data, we thought, ‘holy crap,’†Johnson said. Lin said they repeated their analysis three times because they could not believe how high the numbers were. Now, Boise serves as a good indicator that their methods work.
Scientists have long been testing wastewater to detect polio in countries where the disease persists and, more recently, to estimate the prevalence of opioid abuse in some U.S. communities.
Johnson said the CDC eventually hopes to standardize wastewater testing across the country. “This kind of testing will be like Zoom,†he said. “It’s one of those tools we didn’t know we had until the pandemic hit.â€
Even though their buildings are right next to each other, Johnson and Lin had never worked together prior to this project. Lin had never even worked with a human pathogen — his expertise is in bioremediation.
It took Johnson and Lin two weeks to refine their method of extracting the viral particles. Johnson said he slept much better after they worked out the system’s kinks.
“It’s crazy, this is stuff that has gone through our digestive system,†he said. “I really didn’t think the particles would survive.â€
Johnson also said his family has gotten a kick out of his new project.
“I have two sons — 8 and 13 years old — and they get no shortage of giggles about this,†he said.
