The Secret Weapon in Canada’s Sewers

As a virologist, I spend my days thinking about how to detect outbreaks of coronaviruses, mpox, West Nile and other pathogens early enough to stop them. Right now, I’m concerned about Canada’s awful flu season and the fact that we recently lost our measles-elimination status. But mostly, I’m terrified of what’s unfolding south of the border.

The consequences of the Trump administration’s cuts to the CDC and NIH will extend far beyond America. Those agencies form the backbone of North America’s infectious-disease surveillance. They track variants, monitor cross-border spread and feed data into global systems coordinated by the World Health Organization, helping everyone on Earth prepare. When those programs are dismantled, Canada loses key warning signs of influenza, RSV, measles and whatever diseases are coming next.

It’s a grim picture: we’ll detect and respond to devastating outbreaks slower than we should. Canada’s intensely overcrowded ERs will bear the brunt of this delay, making wait times even longer. (As of last summer, the shortest were in Newfoundland and Labrador, at roughly three hours.) The country’s research capacity will erode, because surveillance data is what we use to spot new, unknown viruses and build out public-health policy. As the U.S. becomes a less reliable teammate in data-gathering, we should strengthen our own independent methods. The fastest, cheapest and most effective way to do that is through wastewater.

Related: Can Canada Survive Trump’s Attack on Science?

This approach isn’t new. Wastewater surveillance was used to trace polio after the vaccine was introduced in 1955. Decades later, Canada became a global leader in this technique during the pandemic. In Ontario, where I work, wastewater data told us when COVID cases were rising. (Remember those unsettling charts that seemed to spike ever higher every day?) By 2022, we expanded tracking to influenza, RSV and other infectious microbes. For a brief moment, Canada’s public-health officials had a real-time dashboard of population health. 

Wastewater offers a window into what’s happening in our bodies. When we’re infected with a virus, most pathogens pass through our intestinal tracts and get excreted. Those viral fragments flow through sewer systems, arriving at wastewater-treatment plants within hours. The sampling process is simpler than it sounds: automated valves open and close to suck wastewater into sealed containers, collecting small amounts over a 24-hour period. 

Once in the lab, researchers chemically extract DNA and RNA, the genetic material all viruses use to replicate. Using these “fingerprints,” we can identify if a virus is present, how much of it is circulating and whether new variants are emerging. They’re anonymized snapshots of the diseases carried by entire communities. With consistent, daily collection, we can track whether infection rates are rising, falling or holding steady—often before those shifts show up at clinics or hospitals.

Unfortunately, we seem to have forgotten our pandemic-era successes. As COVID faded and funding dried up, the provinces scaled back and centralized surveillance programs within the Public Health Agency of Canada. Critical data became sporadic and decoupled from specific cities and regions. COVID testing in doctors’ offices is now so rare that it’s statistically useless. What little surveillance we still conduct is publicly available, but more challenging for the average Google sleuth to find. 

Related: Canada Needs a National Vaccination Registry

Part of the story is simple budget reallocation; the other part is politics. When surveillance data reveals an outbreak, governments are forced to explain what they’re doing about it. This can invite bad press—especially during election cycles. Then there are the economic pressures: many of Canada’s agricultural industries have pushed back against increased waste surveillance out of fear that reporting outbreaks in livestock could hurt sales, even when the risks to humans are low.

But pulling back is profoundly short-sighted. Ontario’s entire wastewater program costs between $10 and $15 million a year, a rounding error compared to the pandemic’s trillion-dollar toll on the province’s health-care system and broader economy. If surveillance helps us prevent even one major outbreak, it pays for itself many times over. It also helps Canadians make informed choices: when to avoid crowds, when to get vaccinated, where to travel. When you keep people in the dark, they assume everything is fine—until the microscopic barbarians are at the gates.

Going forward, we should expand surveillance, not shrink it. Ontario, for example, has roughly 340 wastewater-treatment plants to cover the needs of roughly 16 million people. Pulling samples two or three times a week from even half of those sites would give the province comprehensive coverage. We should roll out similar sampling schedules in other provinces as well. The initial water analysis could happen on-site, with concerning samples sent to centralized labs for deeper sequencing. This is entirely doable with existing infrastructure across the country. In fact, Canada is behind: in India, researchers at the Indian Institute of Technology Madras are now working with AI models to isolate emerging outbreaks in precise neighbourhoods and hospitals by analyzing wastewater flow patterns in real time. Canada could do this too, provided we put protections in place to maintain individual privacy.

Beyond viruses, wastewater can tell us where in the country vaccine uptake is low, allowing public-health units to target outreach campaigns that encourage people to get their shots—an especially vital service given Canada’s lack of a national vaccine registry. Broad sampling can alert health-care providers to the presence of antibiotic-resistant bacteria, like MRSA. And it could even reveal crisis-level increases in toxic drugs within communities, giving harm-reduction teams early warnings before overdoses surge.

Related: Confessions of an Ex-Anti-Vaxxer

One of the biggest upsides of watching our wastewater is wide access to credible health information. Thanks to a climate of vaccine hesitancy—fuelled by years of social-media misinformation, some from prominent American politicians—the country is blanketed in measles. People read online that the flu shot wasn’t a one-to-one match for this year’s dominant strain and decided it wasn’t worth taking at all, not realizing that even a partial match still reduces transmission and severity. Canadians should be able to access viral forecasts by region the same way they do with weather. We know from the pandemic that data-sharing didn’t cause panic; it created co-operation.

Canada can’t fully rely on the U.S. or the WHO to warn us about which pandemic is heading our way. When it hits, we’ll be wishing we maintained and improved our wastewater surveillance. It’s not just a nice-to-have; it’s a matter of life and death.

Eric Arts is the Canada Research Chair in HIV pathogenesis and viral control and a professor of microbiology and immunology at Western University.