Nasa Sinnott-Armstrong, a graduate student at Stanford, does not have much experience as a sewage courier—normally, they’re busy studying genetics. But as with many of us, the pandemic is upending routines. Since early March, Sinnott-Armstrong has been making the rounds of the Bay Area’s wastewater treatment plants, collecting samples that may offer clues to Covid-19’s spread around the region.
Sinnott-Armstrong (who uses the pronoun they) does their work with care because: sewage. But also for the protection of the utility workers, who keep the sewers safely swirling while everyone shelters in place. That means wearing protective gear and filling out a medical questionnaire on arrival. In return, they receive a plastic bottle filled with untreated sewage, an extra sample set aside by the workers during routine quality checks. “They seem excited to help,” Sinnott-Armstrong says. “But we’re trying to ask them to do as little extra work as possible, especially right now.”
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Back at Stanford, the samples are filed away in the lab freezer of Alexandria Boehm, an engineering professor who studies microbes in the environment. Soon, their team will begin analyzing those samples for traces of genetic material from SARS-CoV-2, the virus that causes Covid-19. That freezer is becoming a library of what the Bay Area’s bowels have revealed as the pandemic has progressed, and if all goes according to plan, it will become a blueprint for how studying sewage might provide a way for cities to detect flare-ups of Covid-19.
Right now, health experts are focusing on efforts to flatten the curve, urging people to shelter in place and keep their distance to get the spiraling rate of infection under control. But what comes next? As safety measures relax, life won’t go back to normal, exactly. Without a vaccine, which is a year off (at least), and without herd immunity to stymie the virus’s spread, public health officials will next face a long game of whack-a-mole, requiring constant vigilance to contain infection hot spots. Part of that will involve large-scale testing—likely a mix of blood tests and swab tests—to identify individual cases, plus getting those people into quarantine and tracing who they’ve had contact with. But Boehm’s team wants to know whether passive forms of disease surveillance, like monitoring our sewers, could get us that information sooner.
The approach holds promise because a number of studies have shown high levels of viral shedding in fecal samples from Covid-19 patients. Since that shedding happens early in the disease’s progression, well before patients show any symptoms, there’s reason to suspect evidence of the virus might show up in a city’s wastewater, even before the residents of that city have been tested. (By the way, don’t worry about catching the virus from sewer water; contaminated water is an unlikely route of infection. Plus, in the US, at least, wastewater treatment should destroy the virus just fine.)
A number of groups are racing to figure out how to make such monitoring work. Last week, researchers at the KWR Water Research Institute in the Netherlands were the first to publicly report they had detected SARS-CoV-2 in wastewater samples. The group started testing in early February in cities across the country, before the Netherlands had identified any Covid-19 cases. As the first cases emerged and then spread in early March, the researchers found the viral concentration in sewer water went up in tandem. Other groups, including researchers at the University of Arizona and an MIT startup called Biobot, have begun collecting samples from towns and cities across the US, but neither has released data yet.
At Stanford, the retooling began in early February, when Boehm and her colleagues applied for an emergency grant from the National Science Foundation. The US, at the time, had just two cases. (“My program manager thought I was crazy,” Boehm says.)
Coronaviruses like SARS-CoV-2, however, are not Boehm’s specialty. She studies different pathogens, mostly those that infect via the fecal-oral route, usually when someone ingests contaminated water. Some of those diseases have been subject to sewage surveillance efforts in the past—to eradicate polio in Israel, for example, and to track salmonella outbreaks in Hawaii.
She says the Dutch results offered validation, even though that data has not yet been peer-reviewed. “It’s encouraging as a proof of concept,” Boehm says. Demonstrating that the virus’s RNA is actually detectable in sewage samples is an important first step. But the bigger challenge is making that value predictive—to correlate RNA concentrations in a sewage sample to the actual number of cases in a community.
“The ability to back calculate from the sewer to the number of people could be difficult,” says says Dan Burgard, a professor of chemistry at the University of Puget Sound who specializes in wastewater epidemiology. “We don’t have a Star Trek tricorder where you hold up a device and it tells you exactly how much material is present.”
Burgard’s research largely focuses on detecting traces of illicit drugs, such as opioids, as part of strategies to inform public policies. But like others in his relatively small field, he’s considering a pivot to help with Covid-19 detection. “We’ve been talking about this as the direction our field is going. I just don’t know if we were ever planning to scale it up so fast,” he says.
Coronaviruses haven’t been well studied in watery environments. They’re structurally different too. Viruses that spread via wastewater, such as poliovirus and norovirus, are “non-enveloped” viruses, encased in a protein shell. SARS-CoV-2 is different. It’s an “enveloped” virus, with bits of protein and genetic material enclosed by a lipid membrane. That’s part of the reason why disinfectants like soap work so well on the virus—they tear right through the weak fatty structure. But it also means that many well-honed lab techniques for handling viruses are largely moot.
In the Stanford lab (where it’s currently one researcher per aisle; social distancing doesn’t stop for research) the first step is to concentrate the sample—to filter out the rest of the muck so that the virus’s genetic material can be detected. “It’s the boring part of this research, but it’s critical,” Boehm says. Usually, she would do that with a precipitation method, called PEG. But for enveloped viruses, the technique doesn’t work as handily.
Luckily, one of Boehm’s collaborators, Krista Wigginton at the University of Michigan, has spent years pushing for the better study of pandemic diseases, including flus and coronaviruses, in the water supply. The lab is currently validating her coronavirus-specific techniques, which involve a different set of membranes and filters.
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From there, the process is similar to testing for viral RNA in a patient, using PCR, or polymerase chain reaction. That’s helpful, because there are by now plenty of assays that detect various parts of the virus’s genome. But it also means Boehm has to be cautious about not using up too many supplies. “We have to be very careful that we don’t take away reagents needed to save lives,” she says. So far, she’s been monitoring calls from her colleagues at Stanford Medical School for urgent supply needs and found little overlap. In any case, she has more flexibility than her medical counterparts, because she can swap out reagents without needing to heed clinical regulations.
Validating those methods will be critical. To start making predictions about the number of Covid-19 cases out in the community, the researchers need to know how much RNA from the sample is lost in the lab procedures. They will also need to consider local conditions, Sinnott-Armstrong notes: The make-up of sewage in one city, or even neighborhood, is not necessarily the same as the sewage in another. It also changes over time. Did it rain one weekend, flushing the system with extra water? What is the catchment area for a particular testing site—in other words, how many people does the sample of wastewater reflect?
The researchers say the best results will likely come from collaborating with the other groups gathering similarly detailed local data around the world. That will allow them all to calibrate the sensitivity of their lab methods and to agree upon epidemiological models that map the concentrations of virus RNA found in the sewer water to the likely number of local cases.
In the end, Boehm believes those scientific barriers are surmountable. The next step will be getting sewage surveillance to be used by public health officials as part of their overall response, an effort that still has many unknowns. In the past, local governments have been wary of wastewater surveillance, citing concerns about privacy, says Burgard. (Unlike a blood test or swab, there’s no asking people for permission to rummage through their sewer system.) And municipalities are rarely eager to reveal what’s going on in their turbid waters. “Nobody wants to be the hot spot,” he says.
But that was before the pandemic struck. Perceptions change in a crisis, Burgard notes. As the opioid crisis became more widely acknowledged, city officials became far more likely to accept wastewater surveillance as a public health tracking mechanism. “Once you hit the crisis level, people start to ask, ‘What are the other tools I can use?’” he says. “There’s this sense of, ‘Let’s get this done.’” Add it to the list of ways the world may change once the pandemic has run its course.
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