A novel method of sampling sewage for is showing an “alarming” surge in viral transmission in Ottawa, researchers say — a detection process that belies flattening case counts registered by the province’s strained testing system.

Toronto is set to get its own poop report within weeks.

Because people with COVID-19 shed the virus in their stool, the presence of viral fragments in municipal wastewater has been successfully used as an . In Ontario, scientists at the Children’s Hospital of Eastern Ontario (CHEO) and the University of Ottawa have been at the forefront of this technique.

After remaining low all summer, the virus levels in Ottawa’s wastewater doubled over the month of September, the researchers say. Then, in the first half of October, it doubled again. Tuesday’s measurements were particularly concerning.

“This morning, we can see rather alarmingly that it’s three to six times higher than it was back on Oct. 8. So it seems to be tracking up,” says Dr. Alex MacKenzie, a pediatrician and senior scientist at CHEO Research Institute.

“It’s going up, and it’s going up faster, which is something to take note of,” said Rob Delatolla, a professor of civil engineering at the University of Ottawa.

Epidemiologists that upheaval in the province’s testing system — difficulty accessing assessment centres, backlogs of swabs, and changes to testing criteria — mean that any apparent flattening in Ontario’s case curve should be considered suspect.

Ottawa’s seven-day average of new cases dropped from 117 on Sunday to 98 on Tuesday, according to the public health unit’s monitoring dashboard. Both Premier Doug Ford and Chief Medical Officer of Health Dr. David Williams have recently referenced signs the Ontario curve is flattening.

But testing in Ottawa has also dropped since the switch to appointment-based booking, according to data from the Ottawa COVID-19 Testing Taskforce. Across the city’s five assessment centres, the weekday swab average fell from 2,686 in the week before the change to 2,184 the week afterwards, a drop of 19 per cent.

“What is innovative and important is that this is an indicator that is not based on the effectiveness of the testing system at any given point in time,” says Alex Munter, CHEO’s president and CEO.

“I do think it is really useful information … that can help guide policy-making and help the community understand where things are at. And so from our perspective here in Ottawa, where we have the highest rate per hundred thousand people of COVID at the moment, this is a really important measure of the effectiveness of our public health regulation.”

Across the province and country, researchers are already providing sewage samples to municipalities to use as part of their COVID-19 monitoring arsenal.

At Ryerson University in Toronto, Kimberley Gilbride, a professor of chemistry and biology, and Claire J. Oswald, an associate professor in the department of geography and environmental studies, are part of a national COVID-19 Wastewater Coalition through the non-profit Canadian Water Network.

It’s taking them a little longer than their counterparts in Ottawa, given the size of Toronto. But they hope to have results within the next weeks to month, Oswald said, which they will first share with Toronto Public Health.

“This could be an additional source of information that’s made public,” she said, perhaps even on , alongside other indicators such as hospitalizations and new daily cases.

Oswald said they are looking at the west side of the city and have “initial results” from the wastewater treatment plant that serves that area.

As it’s so “time and money intensive” to get the samples and analyze them, they decided to keep the scope tight, but this includes the hard- hit northwest corner of the city.

They’re using early results to “refine the method right now,” in collaboration with groups like the one working in Ottawa, and doing quality assurance.

They are also working to get sampling sites set up “upstream” of the wastewater treatment plant, so they can see different branches of the sewage system at the community level.

has been used in cities across the world, from to New Haven, to track trends in COVID-19 cases, and

The virus has a relatively long incubation period of up to two weeks. Some people don’t show symptoms at all, others don’t for a while, and not everyone will get tested.

But they shed virus in feces, and everyone’s goes down the drain whether they know they have COVID-19 or not.

The RNA fragments of the SARS-CoV-2 virus, like a fingerprint, can tell scientists that the virus was there.

It’s known as an “envelope virus” because it has a layer of fat around it that doesn’t make it into sewage, so it’s not infectious at that point.

Sewage epidemiology can’t replace classic outbreak tools of testing, and isolation. But it can be a complement to those tools and serve as an early warning system for spikes in cases, regardless of limitations on testing.

Toronto Water is also participating in two other “independent research initiatives” on the virus in wastewater, according to a spokesperson: with Statistics Canada/Public Health Agency of Canada (National Microbiology Laboratory), and with the Ministry of Environment, Conservation and Parks/University of Guelph.

“Toronto Water’s contribution is limited to the collection and supply of wastewater samples to the researchers. Timelines and research results may be available through the respective research teams,” the spokesperson said in an email.

Toronto’s Public Health head Dr. Eileen de Villa was asked about the status of these projects at the daily COVID press conference, Wednesday. She said the agency is “actively participating in those research endeavours and engaging with the researchers on their findings.”

Similar projects are also underway at campuses, including and the and an official with Peel Region said they plan to publish findings from sewage tracking there online, on Friday.

Dr. Barbara Yaffe, Ontario’s associate chief medical officer of health, said at the province’s daily news briefing that this kind of surveillance can be “an alarm bell,” as research has shown it’s possible to “identify an increase in the sewage probably two-to-four days earlier than you start to see an increase in cases.”

This kind of data is being collected “sort of on a pilot basis” across the province, she said.

CHEO Research Institute’s MacKenzie warned that Ottawa’s wastewater surge this week came from infections that occurred before the long weekend, “so let’s hope everyone behaved over Thanksgiving.”

Kate Allen is a Toronto-based reporter covering science and technology for the Star. Follow her on Twitter:

May Warren is a Toronto-based breaking news reporter for the Star. Follow her on Twitter: