Canada is flying blind with Omicron as COVID-19 testing drops off a cliff

Canada is flying blind with Omicron as COVID-19 testing drops off a cliff-Milenio Stadium-Canada
People wait in line for a walk-in COVID-19 test site in Toronto on Dec. 22, 2021. The highly infectious Omicron variant has completely overwhelmed testing capacity across Canada. (Chris Young/The Canadian Press)

Canada has lost sight of the true size of its pandemic, with the number of people infected with COVID-19 now a mystery, as the highly infectious Omicron variant overwhelms testing capacity across the country.

Omicron is causing a never-before-seen surge in COVID-19 that has prompted provinces to reinstate curfews and gathering restrictions, shutter bars and restaurants and move schooling back online in a desperate attempt to mitigate the impact on hospitals.

Yet those case levels are about to drop off a cliff — not because of the flood of new public health restrictions across the country that haven’t yet taken effect, but because health officials have simply stopped testing the majority of Canadians for COVID-19.

So how do we track the impact Omicron is having across Canada? And how will we know whether public health restrictions are working if officials aren’t collecting accurate data?

“Omicron is moving so quickly that it has become pretty much impossible to pin down the full extent of spread in real time,” said Dr. David Naylor, who led the federal inquiry into the 2003 SARS epidemic and co-chairs the federal government’s COVID-19 immunity task force.

“PCR testing capacity is overwhelmed,” Naylor said. “Rapid antigen tests [RAT] are inconsistently available. Those with positive RAT results often have no way to register them let alone confirm them.”

Covid-19 test at North York Hospital-Milenio Stadium-Canada
A doctor administers a COVID-19 test at North York General Hospital in May 2020. Case levels are about to drop off a cliff because the majority of Canadians aren’t being tested for COVID-19 due capacity issues. (Evan Mitsui/CBC)

Watch hospital admissions closely

Public health experts and epidemiologists agree COVID-19 hospitalizations and intensive care unit (ICU) admissions have replaced case numbers as some of the most important metrics for understanding Omicron’s impact on the health-care system and severity of illness it causes.

“It was always what was going to happen,” said Dr. Allison McGeer, a medical microbiologist and infectious disease specialist at Toronto’s Mount Sinai Hospital who worked on the front lines of the SARS epidemic in 2003.

“We were always going to switch from cases to hospitalizations as a measure of how well we were doing.”

But even those numbers can be skewed with Omicron. Data shows while the variant is highly contagious, vaccines still offer protection against serious illness and those infected are less likely to wind up in hospital than people with the Delta variant.

That may lead to a shift in focus to hospitalizations, because the biggest concern with Omicron is that it’s spreading like wildfire and leaving more people exposed to potentially serious outcomes that could strain the health-care system.

A recent report from Public Health Ontario found that while the risk of hospitalization and death was 54 per cent lower for Omicron than Delta — the fact that it is infecting so many more people may actually lead to an overall increase in hospitalizations.

Omicron is also better at dodging immune protection from vaccines and prior infection than previous variants, dealing a massive blow to the effectiveness of COVID-19 vaccines against infection — but not necessarily against severe illness.

A new preprint study from the Institute for Clinical Evaluative Sciences (ICES) in Toronto, which has not yet been peer reviewed, found two doses does not provide adequate prevention against Omicron infection and three doses was just 37 per cent effective — but the vaccines still protected well against hospitalizations.

And as case counts creep into the tens of thousands, many provinces have scaled back testing and reimposed restrictions while officials estimate the true number of people infected could be in the hundreds of thousands per day in the coming weeks.

“It’s going to be a mess. We have, once again, waited too long,” said McGeer.

“It’s really looking like the sheer numbers are going to stress, honestly, not just the hospitals but the ICU … and in the next two or three weeks from now, the hospital system is going to be really, really stressed again.”

Monitor test positivity rate

Another useful metric for examining the burden of COVID-19 across Canada is the test positivity rate — which doesn’t measure the number of individual cases but the percentage of tests that come back with a positive result.

Canada’s national test positivity rate has sat at an astonishingly high 25 per cent over the past week, meaning one in four Canadians who have been tested are positive.

“Test positivity is going to probably be the only thing that matters,” said Dr. Alexander Wong, an infectious diseases physician at Regina General Hospital and associate professor of infectious diseases at Saskatoon’s University of Saskatchewan.

“It’s going to be really key to get an understanding of where provinces and territories are at with regards to their peaks.”

When that rate starts to come down, we’ll get a better understanding of whether our Omicron-driven wave has peaked, but Wong said it’s important to keep in mind that even that number can be affected by access to testing.

“In Saskatchewan, which is probably the least advanced relative to all other Canadian jurisdictions with regards to Omicron, even our testing capacity is pretty much overrun at this point,” he said. “And that’s just going to continue to worsen in the coming days.”

Naylor said the test positivity rate is also affected by changes in test-seeking behaviour, meaning the number of people testing positive and the total number of cases are now both compromised due to a lack of access and a desire to even get tested.

Walk in PCR test-Milenio Stadium-Canada
People wait in line for a walk in PCR COVID-19 test site in Toronto on Dec. 22, 2021. Canada’s national test positivity rate sits at an astonishingly high 25 per cent over the past week, meaning one in four Canadians who have been tested are positive. (Chris Young/The Canadian Press)

“We aren’t able to test the majority of people anymore who are symptomatic. We stopped testing those who have been exposed. We have significantly reduced any type of asymptomatic testing,” said Dr. Dominik Mertz, an infectious diseases physician and associate professor of medicine at Hamilton’s McMaster University.

“The case numbers become even more meaningless.”

Look to sewage for virus presence

One other tool for understanding the extent of COVID-19 levels in the community is through wastewater testing, which examines sewage for the presence of the virus to determine how much is circulating within the population at a given time.

While not a perfect assessment of the specific number of cases or the severity of disease, wastewater testing can help specific regions understand when the risk of exposure is high.

“It can really show trends quite well,” said Sarah Dorner, a water quality expert and  professor at Polytechnique Montréal. “So if you’re really seeing rising numbers, it’s very much associated with rising cases.

“And that’s really what’s important in the current context because right now whatever’s in the wastewater is what’s happening in your community.”

Dorner said such trends allow policymakers to determine when to act and to alert the population on where to protect themselves most from transmission.

“It’s low-cost, high-impact and high-accuracy,” said Raywat Deonandan, a global health epidemiologist and associate professor at the University of Ottawa.

“It won’t be as timely and won’t be as personal but in many ways it gives a better sense of the true impact of a disease on the community because it’s getting everyone — not just those who got tested.”

Wastewater-Milenio Stadium-Canada
A researcher tests wastewater in a sewer outside Risley Hall, a residence at Halifax’s Dalhousie University, as part of the wastewater testing project in Nova Scotia. (Submitted by Graham Gagnon)

Wastewater surveillance has been used sporadically in countries around the world to monitor COVID-19 levels throughout the pandemic, but has been slow to gain mainstream global acceptance because of its limitations compared to case numbers.

“It’s not perfect,” said Eric Arts, a professor of microbiology and immunology at Western University’s Schulich School of Medicine and Dentistry in London. “But it’s better than saying ‘13,000 cases today,’ when it’s probably three times more.”

Dorner said Montreal’s wastewater provided a “very clear signal” that Omicron was heavily circulating in the population in December — before testing would have picked it up.

Because the data is so readily available, with many public health labs across the country doing the testing, Dorner said she hopes Canadians will soon be able to use it to assess their personal risk level.

But public health units across Canada have been slow to release wastewater data to the public to determine the level of virus being picked up in sewage, despite using the data to inform their own decision making.

“We’re expected to kind of move on to managing all of our risks on a personal basis, because the health care system isn’t doing testing and tracing,” said Dorner, who had been helping run a wastewater pilot program in Quebec until funding ended last month.

“So how does the individual access the information they need?”


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