For virus tracking, wastewater is liquid gold. Scientists hope that work isn't flushed away
Scientists want to scale up global sewage surveillance, as others fear funding may be insecure post-pandemic
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One night in March 2020, as wastewater researcher Robert Delatolla was making dinner at his Ottawa home, his wife wondered out loud: Was it possible to spot the novel coronavirus in the city's sewage system?
Delatolla had spent years of his environmental engineering career exploring wastewater treatment technologies — not tracking viruses. He scoffed at the idea.
"I obnoxiously said, 'It won't work,'" the University of Ottawa professor recalled.
A few days later, Delatolla realized his wife was right. In late March, Dutch researchers announced wastewater surveillance efforts in the Netherlands were successfully identifying the virus behind COVID-19, even before official cases were reported.
Delatolla and his laboratory team raced to get a similar system up and running. "By April 8th, 2020, we were able to get our first detection," he said. "That was our first detection of SARS-CoV-2 in wastewater in Canada."
The first but not the last.
For more than two years, research teams across the country — and around the world — have been using human waste to monitor rising and falling coronavirus levels. The approach can also be used to track the viruses behind monkeypox and polio. It's capable of spotting antimicrobial resistant bacteria or toxic drugs. And researchers say the public health possibilities are boundless.
Still, the future of wastewater testing remains uncertain.
Some Canadian scientists are concerned about insecure funding. Others believe scaling up surveillance on a global level is essential for tracking emerging pathogens — but that it's also fraught with challenges.
What's clear is this type of surveillance system works. And it starts with something we all just flush away.
From the wastewater treatment site...
On a hot August morning, you can smell the pungent brown sludge flowing through a concrete channel at a wastewater treatment facility in the east end of London, Ont. It's one of the dozens of Canadian sites participating in wastewater research projects in collaboration with various universities and public health agencies.
Roughly 20,000 cubic meters of wastewater — an amount that could fill eight Olympic-sized swimming pools — arrives at this facility each day. It's filled with all the random junk people flush down their toilets; human waste, of course, but also cereal, tampons, needles and masks.
"We get T-shirts, clothing, wet wipes," said Andrew Nimetz, a shift operator at the site.
And, he adds, a lot of different pathogens that are invisible to the naked eye. But it wasn't until the COVID-19 pandemic hit that his team realized how useful wastewater data could be once researchers from nearby Western University began requesting sewage samples to start tracking SARS-CoV-2.
Now, gathering samples for scientific research is a regular part of the team's weekly routine.
The process goes like this: First, filters remove all the debris, then the sewage enters an automatic sampler. The machine takes small, 200-millilitre samples once every 15 minutes over a 24-hour period, which flow into a refrigerated 19-litre jug.
A few times a week, Nimetz pours out portions into jars that he hands off to the Western research team, as its members travel around to the city's various wastewater sites to fill a cooler with their liquid gold.
…To the laboratory
After the jars of wastewater are delivered to the researchers, located inside a containment lab on campus, team members split the liquid into 40-millimetre test tubes.
Those test tubes are spun in a centrifuge at a speed of up to 12,000 rotations per minute, concentrating all of the solid waste and any pathogens it contains.
Clad in personal protective equipment, microbiologist Eric Arts describes what happens next: The solid material is condensed into a tiny pellet, which is then suspended in a solution that's capable of breaking open any bacteria cells or viruses, spewing out their hidden genetic code.
"It preserves the virus RNA — so, the virus genetic material that exists in the wastewater — and that viral RNA, we can pull out in an extraction process," Arts said.
To track SARS-CoV-2, the team analyzes that genetic code in two different ways.
The first is polymerase chain reaction (PCR) testing, a term now familiar to many. It's a form of testing that involves making millions of copies of the genetic material found inside a particular sample until it's detectable by a PCR machine, whether that's from one single nasal swab, or a wastewater sample containing pathogens secreted by hundreds of thousands of people. The goal is simple: Determining whether a particular type of virus — in this case, SARS-CoV-2 — is present.
The second type of analysis that's done on the viral RNA is sequencing, to determine the order of the nucleotides — the basic building blocks of RNA and DNA, which create a blueprint providing the instructions for building a specific virus or other organism.
SARS-CoV-2, for instance, contains more than 30,000 nucleotide sequences, which can be slightly different depending on the variant of the virus.
"We then do a calculation of the percentages of each variant of concern in the wastewater sample," Arts said.
Wastewater testing exploded during pandemic
Similar systems are now in place around the world, mainly to track SARS-CoV-2.
The aptly-named CovidPoops19 project — a roundup of coronavirus wastewater surveillance efforts from University of California Merced researchers — shows the number of global monitoring sites has exploded to roughly 3,600, involving more than 280 universities and spread across 70 countries.
And now researchers are using similar techniques to monitor other pathogens.
The University of Ottawa's Delatolla started publishing monkeypox wastewater signals on his personal Twitter account, from Ontario cities like Ottawa and Hamilton. South of the border, New York State officials picked up poliovirus in sewage in multiple counties, after one person suffered paralysis from a polio infection.
Another new program, which includes researchers at Stanford University and Emory University in the U.S., is monitoring monkeypox by analyzing wastewater samples from dozens of communities across 10 different states. The team has already picked up viral signals from nearly two dozen locations.
The technology, to be clear, is nothing new. In his research into wastewater testing in early 2020, Delatolla realized teams had been trying to use it for years to detect drug levels in city sewage, from illegal drugs to pharmaceuticals.
"I was amazed going through the history and seeing that in 1974, they were doing this in Canada, and following polio," he said.
Everything old is new again, it seems. In part, Delatolla noted, because it's so simple.
"It's very economical. It's insane," he said. "You're talking about one sample, and a PCR test, to get a bearing on the health of a million people."
WATCH | Here's how scientists use wastewater to detect COVID levels:
The future of sewage in science
But the future of wastewater testing seems hazy. Will it continue expanding, alerting the world to the spread of viruses and possibly detecting new pathogens before they explode globally? Or will interest — and funding — fizzle out as the threat of COVID-19 dies down?
Those questions concern the more than a dozen Ontario labs whose funding is in place until March 2023, Delatolla said. Right now, he says, it's not clear if more cash is coming after that.
In Quebec, officials restarted wastewater testing efforts last spring after funding for a pilot project initially ran out in December. And not all provinces have been swift to implement it in the first place.
"It just comes down to: Is there enough of an appetite for this to continue to be funded?" Delatolla said.
At a federal level, officials seem eager to keep exploring the possibilities.
"It doesn't inconvenience anyone, no one has to come forward for testing, it doesn't rely on a significant amount of infrastructure, and it really gives us a pulse check about what is happening," said Dr. Guillaume Poliquin, vice-president of the Winnipeg-based National Microbiology Laboratory, run by the Public Health Agency of Canada.
"There's a lot of potential there — not only for SARS-CoV-2, but for other pathogens."
Right now, that national team is monitoring wastewater at 25 sites in 13 Canadian cities, largely for the coronavirus, but more recently for monkeypox as well. And efforts to track polio are also underway.
Poliquin said public health teams are also interested in exploring how to gauge levels of antimicrobial resistance or monitor for tuberculosis or influenza.
WATCH | Canada's goals for wastewater testing:
So far, only COVID-19 data is publicly reported on the federal online wastewater surveillance dashboard, but Poliquin hopes to eventually expand into a service that's almost like a weather forecast, providing Canadians with public health trends.
"How do we leverage that dashboard and that visualization of data for other pathogens as those programs come online, both to make them accessible to Canadians, to understand what's happening in their communities — but also to decision-makers, to help with policy decisions?" he said.
Even more critical, according to multiple scientists, is getting this kind of surveillance network built up between countries, in order to catch early viral signals — something that might prevent global outbreaks.
"We shouldn't be limiting it to just SARS-CoV-2 or monkeypox or polio," said virologist Angela Rasmussen, from the Vaccine and Infectious Disease Organization at the University of Saskatoon.
"We should be sequencing some of this wastewater, so we can potentially identify new pathogens that are emerging."
She added it's not a "perfect solution" for global surveillance, and collecting samples can be more challenging outside of cities where people may be using septic tanks or other means of disposing waste that don't involve public sewage systems.
But Arts, from Western, is hopeful the world can make it happen.
He's already working with teams on the ground in Uganda to collect wastewater through open drainage systems and latrines, and he says colleagues in India are striving to do the same.
Meanwhile other countries — including Venezuela, Colombia, Uganda, New Zealand and Fiji — are collecting and sharing samples from their regions and sending them abroad for analysis at Western's lab.
"What we want to see is that data coming out before we identify [a future] pandemic in the population, so we can predict what might be coming through," Arts said.
"Not only in Canada, but around the world in a co-ordinated fashion."
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