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Poop may tell us when the coronavirus lockdown will end

The novel coronavirus under a microscope
The coronavirus known as SARS-CoV-2, shown in purple, infects a cell, colored in green.
(National Institute of Allergy and Infectious Diseases)

Every day, millions of Americans could be flushing critical coronavirus data down the toilet.

With the nation growing ever more weary of sweeping stay-at-home orders and a worsening economy, some scientists say our poop could be the key to determining when a community might consider easing health restrictions.

From Stanford to the University of Arizona, from Australia to Paris, teams of researchers have been ramping up wastewater analyses to track the spread of SARS-CoV-2, the virus that causes COVID-19. Initial studies show that sewage monitoring, or “wastewater-based-epidemiology,” could not only tell us how much the virus might actually be spreading in a community — but also when the virus has finally gone away.

Understanding the true scale of COVID-19 has been a major stumbling block across the country, as officials struggle with testing shortages, false negatives, and people who are infected but have no symptoms. Sewage data could potentially help fill these gaps by capturing critical information in the aggregate.

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“With wastewater, you can very quickly get a snapshot of an entire population,” said Mariana Matus, who co-founded Biobot Analytics, a wastewater epidemiology start-up inspired by her PhD at the Massachusetts Institute of Technology. “The closest approach to replicating the data from wastewater would be to literally test every single person in a community and then take the average of that. It is very powerful.”

The amount of virus detected in the sewage can, in essence, mirror the timing and scale of an outbreak in ways that more delayed (and more expensive) in-person testing cannot, experts say. All this information, when pieced together, is critical to informing and validating public health decisions — such as where to allocate medical supplies and when to reopen schools, restaurants and other public gathering spaces.

And as cities start loosening stay-at-home orders in the coming weeks and months, some say monitoring sewage could also provide early warnings if the virus suddenly makes a comeback.

The latest maps and charts on the spread of COVID-19 in California.

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Americans might find the idea gross, but wastewater early warning systems have helped catch norovirus, Hepatitis A and other diseases around the world for decades.

In Israel in 2013, a polio epidemic was detected in the sewage before any clinics had reported cases. This heads-up gave the government enough time to launch a vaccination campaign and contain the virus. Not a single case of paralysis was ultimately reported.

The monitoring program, set up in 1989 by the Israeli health department, had previously detected at least four other “silent” episodes of poliovirus before clinical cases were reported. Similarly, in Mumbai, India, researchers were able to detect poliovirus in sewage three months before any cases were observed.

In Australia, sewage monitoring is already in place to better understand patterns of illicit drug use — cocaine, methamphetamine and other substances that would otherwise be difficult to test and track. Researchers are now looking into this approach to monitor for SARS-CoV-2.

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Similar work is happening in France, where public utility officials sampled sewage across greater Paris and confirmed a rise and fall in SARS-CoV-2 concentrations that corresponded to the shape of the outbreak. In the Netherlands, a research team was able to detect the virus in one city’s sewage before local officials had even reported any cases of COVID-19.

As for the United States, using wastewater data to inform public health remains relatively uncharted. A research team at Stanford University just recently received a rapid grant from the National Science Foundation to analyze wastewater samples in the Bay Area and study whether monitoring for coronavirus in treatment facilities can be used to spot early outbreaks in a community.

Back at Biobot Analytics, which spun out of MIT with the goal of scaling this approach to every city in the country, researchers started out by tracking and tracing the opioid crisis — but recently pivoted to the coronavirus.

During a one-week period in March, Matus and her team carefully identified and quantified virus particles in sewage samples from a wastewater treatment plant in Massachusetts. (Evidence so far suggests that the virus is fairly inactive by the time it’s in fecal matter, but as an extra precaution, the scientists boiled each sewage sample at 140 degrees Fahrenheit for 60 minutes.)

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In a study released this month and awaiting peer review, Matus — along with researchers from MIT, Harvard University’s T. H. Chan School of Public Health and Brigham and Women’s Hospital in Boston — reported their wastewater analysis showed a much higher number of infected people in the region than what individual clinical confirmations had shown.

Compared to the 446 reported cases in the area, the sewage samples revealed that even by conservative estimates, at least 2,300 — and as many as 115,000 — people could have actually been infected and shedding the virus during that period in March.

There are still some kinks to work out — how much virus does each person actually shed per trip to the toilet, for example, and how do you account for rain and snow and other factors that might impact sample dilution? But so far, Matus said, the study shows that a more routine wastewater monitoring system across the country could help cities and states be more proactive in preventing future outbreaks.

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Since this pilot study in Massachusetts, hundreds of wastewater treatment facilities across the country — including more than a dozen in California — have asked Biobot to analyze their sewage. The researchers, doing the weekly (sometimes biweekly) analysis pro bono, hope to work with as many as 10,000 facilities to create a more comprehensive picture of how the virus is spreading or “flattening” in different parts of the United States.

To preserve the natural anonymity of sewage data, Matus said that her team has only been sampling areas that represent at least several thousand people.

They’ve started sharing their findings with local public health officials and other scientists to fine-tune these methods. Combined with clinical tests and the random antibody tests that cities have increasingly been conducting, routine wastewater analysis could help piece together a puzzle that everyone is still trying to figure out, Matus said.

Charles Gerba, a professor of microbiology at the University of Arizona who has been doing similar research in his lab, said the COVID-19 pandemic has highlighted the potential for this largely untapped — but critical — form of epidemiology in the United States.

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“Everything ends up in the sewer,” he said. “Even herpes virus you can detect by molecular methods.”

Gerba, who has been studying coronaviruses in wastewater since the SARS outbreak, said that molecular technology today has made sewage testing much faster and relatively inexpensive — compared to traditional cell cultures from decades past that could take weeks to process.

Now with SARS-CoV-2, Gerba noticed that viral concentrations started dropping in sewage samples taken from a community that embraced stay-at-home orders. Analyzing the sewage right now is helping officials and scientists better understand the true level of outbreak and how successfully the virus is being contained, he said. In the coming weeks, perhaps it could help inform when social distancing measures can be relaxed.

Ultimately, any fine-tuning now could help alert cities in the future if the virus returns for round two. Working groups, he said, are starting to form with wastewater researchers and the Centers for Disease Control and Prevention.

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“We’re having discussions on how to best do this in the future, how to organize it, how do we look at our preserved samples,” Gerba said. “Everything we learn from this will probably benefit us in the future — maybe in the fall … everyone is worried about the virus coming back in the fall.”


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