Old sewers are becoming a modern Covid-19 watchdog

Dirty work.
Dirty work.
Image: Louisville/Jefferson County Metropolitan Sewer District
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When Britney Carson drove into a rural neighborhood in northern Kentucky in July, she had to double check her maps to make sure she had the right place. A wastewater pretreatment specialist, Carson was looking for a manhole that could give her access to the intricate sewage pipes below, but she couldn’t find it. She got out of her van and walked around until she finally spied the cover, obscured in someone’s yard. “It was half buried,” she says, and lifting the roughly 60 lb cover up took a pickaxe for leverage—plus a conversation with the yard’s owner, who was fine with her work there.

Carson’s job that day was to set up one of eight wastewater monitoring sites across Campbell, Boone, and Kenton counties along Kentucky’s northern border. Today, those sites are monitoring Covid-19 activity, searching for viral signals in several hundred thousand people’s waste.

Early in the pandemic, scientists discovered that fecal matter contains bits of the genetic material from SARS-CoV-2, the virus that causes Covid-19, up to a week before a person tests positive. Sewage couldn’t tell you exactly who is infected, but it could reveal if there were infections afoot in a region—potentially, even before people started feeling sick.

A manhole equipped with an autosampler.
A manhole equipped with an autosampler.
Image: Britney Carson

So a few months ago, Carson and her team in northern Kentucky’s Sanitation District No. 1 (SD1) teamed up with the local public health department and researchers at the University of Louisville to start a wastewater-based epidemiology program. They cranked open manholes, gazed down into the rusty sludge, and snaked down tubing that sucks up about a half cup of flowing waste. An autosampler—which Carson says looks a bit like R2D2 from Star Wars—sits near the manhole, slurping up a sample every half hour for 24 hours and storing the waste on ice until Carson or one of her team members picks it up to take it to a lab.

It’s too early for the Kentucky program to inform public health decisions just yet. There are no standards or procedures here; the methods are younger than the pandemic itself. So far, SD1 has collected two months’ worth of samples; they’re watching for the amount of SARS-CoV-2 genetic material to go up or down, and comparing that data with metrics like active cases and hospitalizations. They’ll make adjustments as they learn, all while the pandemic rages on. “It’s a bit like working on the engine while we’re driving the car,” says Ted Smith, an environmental medicine researcher at the University of Louisville also working on the project.

Wastewater monitoring is a bit of a long shot—but given the failure of other strategies to contain the pandemic, it’s an intriguing option. This month, more than 25 states broke records for new daily coronavirus cases as total cases in the country approached 9 million. Individual clinical testing has proven too expensive and logistically complex to slow the spread. Contact tracing is useful, but equally difficult to execute as cases soar. By providing a canary-in-the-coalmine metric, wastewater-based epidemiology could sharpen testing efforts to increase their impact; instead of testing everyone, the method could indicate which populations to test and proactively isolate.

“It’s extremely cost effective,” David Larson, an environmental epidemiologist at Syracuse University who’s been working with his local health department in Syracuse, New York to monitor wastewater, told Quartz earlier this year. “You get a population-level understanding of transmission in a single sample.” Networked collection could capture the majority of the population: Sewers serve over 80% of US residents. And its impact could last beyond the current pandemic: Similar systems could be used to track drug use, antibiotic resistance, toxic pollutants, and outbreaks of other infectious diseases.

It’s not surprising, then, that Louisville isn’t alone in trying to monitor its sewage. Hundreds of cities across the country are trying to get their own wastewater monitoring systems off the ground. The US Centers for Disease Control and Prevention (CDC) launched a National Wastewater Surveillance System (NWSS, pronounced “news”) in August that is so far working with eight states. The goal is to organize a national project that turns sewers—one of the oldest public health tools—into a modern public health watchdog.

Getting there will require major investment, though. Sewers weren’t built to be monitoring systems. Not all public health departments have a large enough staff to take on extra roles, or nearby labs to analyze samples. And even those that do have the right resources have no idea what to look for: There’s no standardized way to measure the components of wastewater, which for now makes it impossible to compare data from region to region.

That’s the biggest obstacle facing the Kentucky group. An alphabet soup of federal agencies is brainstorming to get standards in place to make the NWSS a fully-operational public health tool, inciting a sewage turf war among the Environmental Protection Agency (EPA), CDC, and even the Department of Homeland Security. “There’s a fair amount of confusion between federal agencies about whose purview it is,” says Smith.

That could spell disaster for the effort in the long run. “It’s really expensive to do this in an uncoordinated way,” he says. Without a clear national plan, the meager funding municipalities have scraped together will run dry before sewers have their chance to shine.

The secret’s in the sewage

In late April, the head of SD1, Adam Chaney, was on the lookout for ways to apply his knowledge of Kentucky’s sewersheds. He was worried about the economic effects of lockdown orders—and wastewater, he saw in the early research, could help tell his community if such measures were warranted. Scientists don’t believe the coronavirus is infectious in fecal matter; instead, it seems that our bodies break down the virus in our digestive tracts, and little bits of its genetic material show up in stool. And it seems that everyone with SARS-CoV-2 in their systems excretes it—regardless of if they show symptoms.

If northern Kentucky’s sewage showed low levels of SARS-CoV-2, Chaney thought, they could avoid unnecessary economic hardship while keeping people safe. “I just am a community resident,” he says. “I want the best, most unbiased data and the best decisions made for my community.”

Chaney eventually got in touch with Smith at the University of Louisville, who had been working with the local health department since June. This time last year, Smith had launched a wastewater-based epidemiology study in the greater Louisville area—except instead of tracking an infectious disease, he was looking for signs of air pollution. He wanted to see if extra trees planted in urban areas could reduce the fecal biomarkers associated with air pollution and improve cardiovascular health. “It’s the only drug trial in the US where if you look at the drug intervention [on clinicaltrials.gov], it says ‘trees,’” Smith says. (It actually says “greenness.”)

Smith and Chaney thought they could pivot that work. They could set up sites similar to the ones Smith had for his air pollution work and hunt for SARS-CoV-2’s genetic material. The best news, then just emerging, was that sewage could be an early indicator: Studies have shown that bits of viral genetic material appears in wastewater two to four days before people get sick, which means theoretically, it could act as an early warning system to help keep outbreaks small.

It wasn’t as straightforward as they hoped.

Not that the concept wasn’t good. Wastewater monitoring for public health has worked before: In the US, it’s been used to combat the opioid epidemic, revealing patterns of substance abuse in the metabolites of opium-based drugs. In 2013, scientists in Israel found evidence of poliovirus in the country’s wastewater, despite the fact that public health officials thought they had eradicated the virus; their investigational work led the Israeli government to require polio vaccines for all children under 10.

But while our excretions can tell all kinds of truths about where we’ve been and what we’ve consumed, they lose some of that value once they’re flushed down the toilet. “There’s a lot of data turned over to [public health departments] that we don’t know what to do with,” says Chuck Gerba, a microbiologist at the University of Arizona.

For one thing, scientists haven’t agreed on the best way to extract genetic material from wastewater. Broadly, they’re using a lab-based polymerase chain reaction (PCR), which copies signature snippets of SARS-CoV-2’s RNA and replicates them until they’re easily detectable. But there are disagreements over how to isolate that genetic material to begin with.

Some groups are using a solution that works best when the waste collected is solid; others prefer liquid processing, which requires the autosamplers used by the folks at SD1. Others are using a form of digital PCR, which is cheaper on a per-test basis, but requires expensive lab equipment typically found in state-of-the-art university labs—not local public health departments.

Scientists may yet agree on some best practices: A Colorado-based nonprofit called the Water Research Foundation has conducted a study with 33 laboratories across the country to compare methods. But their results (pdf) don’t agree on a set of standards; they just explain some of the differences. And once data collection becomes standardized, public health researchers will have to figure out how to interpret their results: It’s hard to tell if high levels of SARS-CoV-2 RNA are the result of many cases clustered together, or just one super-shedder who excretes more viral genetic material than others.

In the meantime, the Louisville and northern Kentucky group is working with the systems they know best. They isolate the RNA using polyethylene glycol and magnetic beads, and replicate it using a quantitative form of PCR. That’s okay for now, since the goal of their study is to see how trends in viral genetic material in sewers relate to the positive test results and hospitalizations they see above ground.

But if they want to turn their sewer systems into a machine for infection prevention, they’re going to have to figure out exactly where to look.

Mapping a community underground

When Ray Yaeger looks at maps of the sewer system serving the greater area, the University of Louisville health geographer sees veins in a body. “It’s kind of like, ‘What vein would I sample from if I wanted to determine how much of an infection exists in your hand?’” he says. If he skipped a body part, he could miss an isolated infection that could swell into a more serious condition. Instead of body parts, though, he wants to make sure he can catch pockets of Covid-19 in different neighborhoods.

A single sewershed can serve tens of thousands or hundreds of thousands of people. So Yaeger, who has been working with Chaney and Smith, has been determining which sites in the Jefferson county and northern Kentucky sewershed serve which populations. It was important to him not to only find sites that reflect the greatest number of people, but the most diverse populations.

Once he figured out how to capture representative samples of waste, he had to pick sites that were physically appropriate to sample from; some were inaccessibly deep, for example. Others served industries that degraded the quality of their samples, like a distillery that dumped its warm water down the drain; those wastewater samples came in a full 40°F (about 20°C) warmer than others, and the high temperatures denatured the genetic material they were looking for. Wastewater that contained hospital discharge contained a mix of disinfectants and high levels of SARS-CoV-2.

Image for article titled Old sewers are becoming a modern Covid-19 watchdog
Image: Louisville/Jefferson County Metropolitan Sewer District

Now, the team is monitoring about 24 different sites across northern Kentucky and the greater Louisville area. Some are wastewater treatment plants, some are smaller sewersheds, and two are prisons. At first, they collected samples once or twice a week and analyzed them in a virology lab at University of Louisville, but they’ve since switched over to a lab called EuroFins to allow the university scientists to get back to work.

This labor-intensive process will look different from town to town, because sewers are so diverse. When US civil engineers started building the first modern sewer systems in the 1800s, they were only thinking of a blossoming city’s immediate public health needs: to keep poop out of the drinking water. A secondary goal was to keep stormwater from flooding the streets; most sewers, therefore, also functioned as storm drains (they figured stormwater could even serve as a helpful cleaning for the sewers when the waters surged a few times a year.)

Even once that hard surveying work is done, that doesn’t mean you have a foolproof infection detection system—unless you install sensors for every household. There’s just one type of community where that’s happening right now: universities.

At the University of Arizona, where microbiologist Gerba works, the campus invested in sensors for each of its dorms, which it could install because it manages its own central sewage system. “I know where all the party dorms are and where all the nerd dorms are,” says Gerba. When they detect a spike in viral material, the college can test the entire dorm and isolate the students who turn up positive.

Gerba says they’ve done just that several times already; they’ve been able to pick out just two to three cases in a dorm of 500 and stop the outbreak from growing—keeping the party from getting out of hand, in other words. Other schools, like Utah State University and Syracuse University, are following suit.

The real world, though, is a lot bigger than just a few dorms. And few local governments have the resources to scale up a university-style preventative monitoring program. Even the 24-site Kentucky survey is only possible with funding from a handful of private grants. The Louisville area also got around $3 million through the Coronavirus Aid, Relief, and Economic Security (CARES) Act; the wastewater monitoring has spent hundreds of thousands of that budget.

To make it work, cities will need a crap ton of cash. And that’s not going to come until there’s a consolidated national network of pooper scoopers.

Waste(d) resources

It’s 2020, and in a year full of seemingly improbable scenarios, the US Department of Homeland Security (DHS) is deeply concerned with its citizens’ excretions.

“Our job is to ask what is the best available research and development that we can bring to homeland security challenges, and where we can leverage that,” says David Alexander, a senior science advisor for resilience at DHS. The work of countering pandemics is built into its DNA.

Along with Phillp Mattson, standards executive and director at DHS, Alexander has been working closely with Smith and the rest of the northern Kentucky group to develop standards for wastewater-based epidemiology so that one day, a national program can get off the ground. They’ve looped in scientists at the National Institute of Standards and Technology and the EPA to do some of the science, and the CDC for public health monitoring expertise. Representatives from each of these agencies meet once a month on a National Sewage Surveillance Interagency Committee.

The goal is to regulate wastewater monitoring so the science can get the federal funding it needs to continue. “Generally in the US, we only know the things we make money knowing or things that there are regulations saying that we have to know,” says Smith. It’s a catch-22: Without investing up front in scientific and methodological standards, it’ll never exist as the cheap public health tool it could be. And without proof that it actually works as a cheap public health tool, it’s less likely to get the necessary funding. That’s why it’s vital that localities collect as much data as they can while they have the cash.

The desire is there. At the beginning of the pandemic, Boston-based biotech company Biobot pivoted to testing wastewater for SARS-CoV-2. It decided to launch a pro-bono campaign for the first 100 cities willing to test their capabilities. These slots filled up within a week, and the company realized it had underestimated the demand for wastewater analysis. “We quickly scaled our operations,” says president and CEO Newsha Ghaeli. “We ultimately ended up onboarding about 400 communities in the US.”

Biobot’s distributed services are cheaper than Louisville’s approach: The company sends a testing kit with tubes for wastewater; people at the treatment plan fill them up and ship them back overnight with a prepaid FedEx return label; and Biobot’s labs analyze the sample and get results back in two or three days. “A community can sample once a week for $5,000 per month, or just over $50,000 annually,” says Ghaeli. But while they’re cheaper, they’re also less specific: They test single samples from wastewater plants that reflect the sewage of hundreds of thousands of people. It’s not a scalable solution.

At the moment, extra funding for wastewater monitoring is scarce and scattered; the funding for Kentucky from the CARES Act is set to dry up at the end of the year. And although the CDC just provided $2.5 million in funding to an initial list of eight states (California, North Carolina, Ohio, South Carolina, Utah, Virginia, Washington, and Wisconsin) to kickstart their own statewide wastewater monitoring programs, that’s not nearly enough to bring others on board, or keep those programs going.

That’s why the work to develop standards is so important. Without shared guidelines, Covid-19 activity in wastewater can only be interpreted in binary: It’s either there, or it isn’t. Until national efforts establish standard methods—a single extraction technique, and a unified analytic approach that accounts for the population served by a sewershed—wastewater’s potential as a public health tool will be limited.

“Standards feel so bureaucratic, but for me the scientific issue is without some kind of harmonized process, I can’t make any progress,” Smith says. Right now, the hodgepodge wastewater-based epidemiology team of northern Kentucky is still looking for any way to make their data useful for their counties. If they can pull it off, their work could serve as the model for programs across the country.