For the past three years, Alexandra Johnston has started her work day by reaching for the pickaxe in the trunk of her car.

It is her tool of choice for prying open manhole covers – a task she demonstrated with practised ease last week while on a tour of her wastewater sampling regimen in Toronto.

Wearing a surgical mask and gloves, Ms. Johnston dragged the heavy cover aside, then grabbed hold of the fishing line secured underneath. After hauling up a few metres of line, she displayed her catch: a dripping wet tampon she had placed there the day before.

Her teammate, Claire Gibbs, quickly moved in with a prelabelled plastic bag to capture the sewage-laden sample. Using scissors, Ms. Gibbs deftly snipped the line, sealed the bag and stowed it away in the trunk as part of that day’s delivery.

On the city’s busy streets and sidewalks, where it’s not feasible to set up more sophisticated sampling gear, tampons have proved ideal for capturing traces of whatever is passing through the sewer pipes below, including disease-causing viruses.

“They’re cheap and they come pretty sterile, so it’s kind of an easy solution,” said Ms. Johnston, a wastewater technician with Toronto Metropolitan University (TMU), where the samples she and Ms. Gibbs collected would be analyzed later that day.

Cheap and easy are the operative words for a provincial program that began as a grassroots effort by university researchers to detect COVID-19 in their communities and has since matured into a powerful data-gathering tool for tracking a range of health threats. Supporters of the effort, which has cost $10- to $15-million a year since it was launched in 2020, say it functions as an early warning system that can reduce infections and hospital visits, saving money that would otherwise be spent on patient care.

Unpersuaded by such arguments, Ontario is putting an abrupt end to its Wastewater Surveillance Initiative this week, much to the dismay of investigators at 13 universities and research institutions who helped to build the program, and many others who use the data it provides.

“We’ve been relying on it for the past few years,” said Sharon Straus, a specialist in geriatric medicine and physician-in-chief at St. Michael’s Hospital in Toronto. “It’s really distressing to know that it’s about to stop.”

The sentiment is echoed by several health experts and participants who told The Globe and Mail they were stunned when news broke last month that the program was being dismantled at the end of July, two months before its current budget runs out.

Their reaction reflects disappointment that the province is abandoning a public-health strategy that it helped to pioneer and is now being adopted globally as an essential pillar of pandemic preparedness.

The scientific case for wastewater surveillance is straightforward: While most people who get sick don’t go to the doctor, they do go to the bathroom. In doing so they release genetic debris from viruses and other infectious agents that reveal what strains are in circulation.

Compared with clinical testing, the method is non-invasive and unbiased, offering timely data on disease dynamics that would be impossible to obtain from reported cases alone. And while the Ontario-wide program continues to function as a COVID-19 surveillance measure, it has also been used to track mpox, RSV and flu, with the capacity to quickly pivot to other pathogens as needed.

If there is a scientific case for cancelling the initiative, the province has not made it.

Gary Wheeler, a spokesperson for Ontario’s Ministry of Environment, Parks and Conservation, said the program was “winding down” to avoid duplicating wastewater surveillance conducted by the federal government.

This overlooks the large difference in scale between provincial and federal sampling in Ontario.

At present, the Public Health Agency of Canada tests wastewater samples shipped from four Ontario locations, all of which are located in Toronto. After the province’s decision, Anna Maddison, a spokesperson for the federal agency, told The Globe that it plans to establish federal testing in “four additional cities” ahead of the upcoming flu season.

In contrast, Ontario’s program samples at 58 locations all across the province multiple times a week. (Prior to a previous scaling down of the initiative in April, 2023, there were 107 sites covering nearly three-quarters of Ontario’s population.) The provincial program is also closely interlinked with regional health units so results can be acted on promptly. In a follow-up statement to The Globe, Mr. Wheeler did not address these differences.

Given the lack of overlap with federal sampling, the end of the provincial program seems certain to disproportionally affect northern and rural communities already challenged by deficits in health care resources. For example, Health Sciences North in Sudbury, which conducts sampling and testing for five regional health units in Northern Ontario, from Sault Ste. Marie to the Quebec border, is among the centres losing its provincial funding for wastewater sampling this week.

Others who are affected include residents of city shelters and long-term care facilities in Toronto, where provincial funding has supported sampling at individual sites to catch COVID-19 outbreaks as recently as last month.

“There is no alternative,” to the current program said Stefan Baral, a family and population health physician with Inner City Health Associates, which specializes in delivering health care to residents in Toronto’s shelter system. He added that wastewater surveillance “gives us notice before people are overly symptomatic or everybody in a residence is already affected.”

More broadly, participants say the province’s decision amounts to giving up near real-time information about disease prevalence in most provincial locations as communication lines between research labs and public-health units fall silent. That includes pulling the plug on an online dashboard, not publicly accessible, that local health officials use to get a detailed view of what is happening beyond their jurisdictions in order to co-ordinate responses.

“You need that collaboration between public-health units and the people doing the analysis because it is tricky data to interpret,” said Claire Oswald, who co-leads TMU’s role in the initiative. “A lot of that is going to get lost.”

REALITY CHECK

Robert Delatolla still remembers getting a phone call from a fellow scientist during the first lockdown who told him: “I’ve got an empty mayonnaise jar. Where is the wastewater treatment plant?”

Dr. Delatolla, an environmental engineer who specializes in wastewater surveillance and epidemiology, explained to his colleague why it would not be possible to walk into a treatment plant unannounced and take away a sample. But soon after, his lab at the University of Ottawa became the first in Canada to detect the virus that causes COVID-19 in wastewater. It was April 8, 2020.

At such an early stage in the pandemic, when the focus was still on identifying and isolating individual cases, the importance of wastewater for disease detection was not widely appreciated. But an influential Dutch study had already demonstrated that fragments of the virus had turned up in sewage samples weeks before the Netherlands had its first reported case of COVID-19.

Later that summer, Dr. Delatolla’s group showed that wastewater data had successfully anticipated a COVID-19 outbreak in Ottawa. This helped to persuade Ontario’s newly created Science Advisory Table to recommend provincewide wastewater surveillance.

The importance of the program became more apparent to the public in early 2022, when the province was closing down testing centres at clinics and hospitals just as the highly transmissible Omicron variant was sweeping through the population. People switched to rapid test kits to check for infections and fewer mild cases were reported to health authorities. At that point, wastewater offered the best window on the virus.

What that window revealed was a complicated evolutionary battle as new variants of Omicron exhibited and shared their genetic diversity. Instead of screening for particular variants, scientists shifted to looking for trends in mutations of the viral genome to discern when one lineage was gaining ground over others. In total, at least 10 major waves of Omicron have left their mark in Ontario’s wastewater, a story that media coverage has largely lost track of, but that has helped public-health officials understand the ebb and flow of the virus and anticipate its continuing impact.

It has also served as a reality check on public-health measures.

As one example, when the World Health Organization made its first announcement of the existence of Omicron as a variant of concern, the federal government reacted with a travel ban blocking entry from seven African countries to delay the variant’s arrival in Canada.

Yet, in a retrospective study published last month by the Royal Society of Chemistry, researchers at Dalhousie University in Halifax demonstrate that Omicron was already present in wastewater sampled from a university residence a full three weeks ahead of the WHO announcement.

For Graham Gagnon, a professor and specialist in water quality and treatment who led the Dalhousie study, the result demonstrates that the power of wastewater as a disease surveillance tool was underappreciated at the time and has not been exploited to its fullest even now.

“How can a public-health expert use this information? That to me is a more interesting question,” Dr. Gagnon said.

By now, the combined impact of vaccines and exposure has reduced the virulence of COVID-19. But it remains a drain on public health that is currently responsible for about 26 deaths a week in Canada, with Ontario’s latest wastewater sampling data showing a rising trend.

“It doesn’t make a lot of sense that you cancel the program at this stage,” said Eric Arts, a virologist at Western University in London, Ont., whose lab conducts genetic sequencing for samples gathered as part of the Ontario initiative. “It’s not warning you before the cases occur, but it’s warning you before hospitalizations occur, which is when it really matters.”

Others have sought to quantify the benefit that the province would derive from maintaining a robust surveillance program. In a modelling study published in January, Dr. Delatolla and colleagues found that wastewater data can offer a 12-day lead time in advance of a future surge of pediatric cases of RSV. The study concluded that using the data to guide the distribution of a preventive drug to vulnerable infants under six months old would prevent 249 hospitalizations and 950 clinical visits a year, with annual savings of up to $3.5-million for RSV alone.

In a separate effort to reduce health care costs, researchers at the University of Windsor and the University of Guelph last month received $15-million in federal funding in part to explore how wastewater can be better used to anticipate demand for biomedical supplies and help avert supply chain problems ranging from vaccines to PPE.

But infectious disease experts say it is the risk and potentially catastrophic impact of emerging viruses that underscore the need for continued surveillance.

One of the ironies of Ontario’s decision is that it comes just as public-health agencies are on alert for H5N1 avian flu, which has jumped from birds into dairy cattle in a number of U.S. states. While no such cases have been observed in Canada, the possibility that the flu strain could acquire the capacity for human-to-human spread makes wastewater surveillance look more prudent than ever.

If H5N1 turned up in Canadian wastewater, there would be ambiguity about whether it originated with animals or people. But the timing and precise genetic signature of the strain would provide epidemiologists with critical clues about an emerging risk.

“Wastewater surveillance is all about monitoring for multiple pathogens at once, cost-effectively, and rapidly,” said Fiona Brinkman, a professor of bioinformatics at Simon Fraser University in British Columbia. “This is really one of the few positive things that came out of the pandemic.”

NEVER AGAIN

Natalie Prystajecky, a microbiologist with the British Columbia Centre for Disease Control, said she was initially skeptical that wastewater offered a practical way to track a respiratory disease.

“I was not convinced we would be able to detect it,” particularly in mildly infected individuals, she said.

She has long since changed her view, and is now looking to develop wastewater surveillance into a more sophisticated form of disease monitoring. Together with environmental health physician David McVea, Dr. Prystajecky won $41-million in funding last December from Genome Canada to develop project SAFEGUARD.

The project employs a method known as target enrichment to rapidly isolate and genetically sequence the versions of different respiratory diseases that show up in wastewater sites across B.C. The point is not only to determine if flu, COVID or RSV are on the rise but to understand how the different viruses are changing at the genetic level.

Dr. Prystajecky said a key advantage of their approach is that it can identify versions of a virus that may be lurking in the background but not predominant in clinical cases. It can also reflect how pathogens respond to public-health interventions. Significantly, the B.C. project relies on exactly what Ontario is giving up: a wastewater surveillance system that is already in place.

Elsewhere, community advocates are demonstrating how wastewater can be used to address longer-term health issues.

During the pandemic, First Nations groups in Yukon were among those who acquired the training and technology to monitor wastewater for COVID-19 and have since expanded testing to include other pathogens of interest such as tuberculosis, measles and H. pylori – a bacteria associated with stomach cancer that has elevated prevalence in northern Indigenous populations.

This spring, the First Nations-led health advocacy group One Yukon Coalition launched a campaign to detect signs of drug use in communities through wastewater. As with disease monitoring, the approach can reduce preventable deaths, for example by improving access to naloxone kits for treating overdoses. But a side effect has been to boost the communities’ self-determination in matters previously regarded as the exclusive domain of outside authorities.

“It’s confirmatory, science-backed evidence,” said Math’ieya Alatini, the coalition’s board chair and a former chief of Kluane First Nation. “People are seeing wastewater as a tool for making pro-active decisions around public health.”

Compared with other measures that were deployed during the pandemic, wastewater has a track record of public trust, in part “because everybody intuitively understands how it works,” said Bernd Manfred Gawlik, a co-leader at GLOWACON, a global consortium for wastewater and environmental surveillance launched in March by the European Union.

The coalition, which includes Canada as a participant, aims to create an international sentinel system for early detection of emerging diseases and antimicrobial resistance based on wastewater sampling in communities and at key transportation hubs.

Dr. Gawlik said Ontario should be credited for the “extraordinary work” it has done developing wastewater surveillance during the pandemic. While he did not speak on the record about the province’s decision, he said he is familiar with questions that officials in many jurisdictions have raised about the cost of having such a program in place now that COVID-19 is no longer a global health emergency.

“To which I reply, what’s the cost of having to go through that again?” he said.

SO MUCH KNOWLEDGE

Across Ontario, groups that have been contributing to the provincial program have been looking for ways to carry on in the absence of provincial support.

Last week, there was some good news for Dr. Delatolla when Ottawa Public Health said it would continue to fund his team to test wastewater on a short-term basis. But the longer-term future remains in doubt, and there is no indication that the federal government will attempt to replace what Ontario is shutting down.

Kim Gilbride, a molecular microbiologist and co-leader of TMU’s participation in the effort, said she can’t understand why Ontario never worked out how to build its initiative and all the work it represents into a sustainable program, despite having had four years to do so.

“I think that it is time to have a division of public health that could do wastewater sampling and testing,” Dr. Gilbride said. Otherwise, the province’s decision means that “so much knowledge no longer has a home.”

Meanwhile, in her laboratory, researchers are shutting down their operations ahead of losing their jobs as the program comes to an end this week. Ms. Johnston and Ms. Gibbs, the wastewater technicians who have supplied them with samples gathered from all across the city day in and day out, will also soon be looking for work.

Toward the end of their tour with The Globe, the pair reflected on the fact that, at some point, the province may have to reinvent the operation it is about to cancel. Given the inevitability of future pandemics, it seems a likely scenario.

Asked what advice they would give to a future team charged with opening manhole covers all over Canada’s largest city, Ms. Gibbs had a ready answer: “Don’t be scared of what you see down there.”