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A worker hands out COVID-19 antigen test kits at Yorkdale Mall in Toronto on Dec. 22.STRINGER/Reuters

For much of the pandemic, daily case counts have offered a steady, if imperfect, means of taking the virus’s measure.

But a surge in cases of the Omicron variant is now swamping COVID-19 testing sites and forcing people to rely on at-home rapid tests, the results of which are generally not added to official tallies. This has caused those daily counts to become so unreliable that health officials are looking to other metrics for pandemic surveillance.

The scientific director of Ontario’s COVID-19 science advisory table, Peter Juni, estimates that the province’s daily count is now capturing just one case out of every five to eight cases in the province.

“It’s absolutely impossible to understand the numbers we’re seeing right now compared with the numbers two weeks ago,” said Dr. Juni, who is also an epidemiologist at St. Michael’s Hospital in Toronto.

The daily measurement has always had flaws. For one, it almost exclusively records cases that have been confirmed during lab-based polymerase chain reaction (or PCR) testing. In the past, when the demand for tests outstripped the capacity of labs, such as during the virus’s deadly first wave, many people who suspected they were infected couldn’t get tested, causing government tallies to undercount the spread of the virus.

Now, with labs overwhelmed by Omicron, the gap between confirmed cases and probable cases is particularly pronounced. In many regions of the country this week, sudden demand for PCR tests has forced medical officers to implement new restrictions on who can get one.

Nova Scotia’s Medical Officer of Health, Robert Strang, said on Tuesday that PCR testing would be reserved for “those who have COVID-like symptoms and are at high risk for severe disease.” Everyone else will need to use at-home rapid test kits.

Manitoba’s Chief Public Health Officer, Brent Roussin, said unvaccinated people with symptoms would be prioritized for PCR testing because they are at higher risk than others for severe disease. Lower-risk Manitobans seeking tests will receive at-home rapid tests.

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And on Wednesday, British Columbia’s Medical Officer of Health, Bonnie Henry, advised fully vaccinated people with mild illness to avoid getting tested.

Such advice may further skew daily case numbers. In Ontario, even before Omicron came along, case counts only captured about two out of every five COVID-19 infections, according to Dr. Juni – a ratio verified by mortality data and serological testing.

“A lot of people who are symptomatic and a lot of people who have tested positive on rapid tests will not be able to get a PCR any more, and they won’t end up in any of our case counts,” Dr. Juni said.

He added that the province can overcome the new data gap by focusing on other surveillance methods, such as testing municipal sewage for the presence of the virus.

Ontario currently monitors wastewater at more than 200 sites. The advantage of the approach is that it allows officials to track infection levels across entire populations, regardless of whether individual people seek COVID-19 tests.

Alberta’s Chief Medical Officer of Health, Deena Hinshaw, also acknowledged a shift away from case counts and toward wastewater for COVID-19 monitoring, saying the Omicron surge would outpace lab capacity across the country.

“With the shift to making rapid tests available, I would anticipate the PCR tests that we’re currently reporting as positive are just the tip of the iceberg, and it would be expected that the total number of people who actually have Omicron would be much greater than is currently captured in our numbers,” she said this week.

Dr. Juni said the data gap could be overcome if there was a standardized way for people to self-report rapid test results. Right now, reporting obligations vary across the country.

Nova Scotia is urging people to e-mail public health if they test positive on rapid tests, but Dr. Strang said the results will not be included in daily case counts.

Ottawa Public Health tweeted on Wednesday that it doesn’t need to be notified of rapid test results.

Ontario’s COVID-19 website says people who test positive on rapid tests must get lab-based PCR tests within 48 hours, even though many testing sites currently show no availability.

In B.C., Dr. Henry said the province has launched an online reporting tool for rapid test results.

But she noted that daily counts from PCR testing will remain an important pandemic metric. “PCR testing is one of a range of surveillance that we’ve used all along,” she said during a briefing on Wednesday. “It is consistent and that is one of the hallmarks of a surveillance tool, that it tells you trends over time.”

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