'Just a sample of what's really happening': increased screening could reveal reality of variant spread in Canada

Here's why variants are still a concern in Canada Toronto's Medical Officer of Health Dr. Eileen de Villa expects Canada's experience with variant infections to mirror other countries.

TORONTO — Even with COVID-19 cases declining in Canada, experts say we could already be headed for a third wave with variant cases on the rise.

As of Feb. 12, Canada has recorded 497 cases of the three new variants of concern of the novel coronavirus. That’s almost double the total of 278 recorded a week earlier on Feb. 5, and more than four times as many as the 109 cases two weeks ago on Jan. 29.

With provinces just beginning to publish variant data, some say this picture could be far from complete.

“My sense is that what was being picked up is still just a sample of what’s really happening,” says Thomas Tenkate, occupational and public health professor at Ryerson University. “From what I’ve understood, up until more recently they haven’t been testing that frequently for it.”

Public Health Ontario says as of Feb. 3, all positive COVID-19 cases are being screened for variants. The Quebec Ministry of Health and Social Services said Thursday it will also be sending all positive cases for variant testing.

But with many provinces having only recently increased their testing for variants, it’s still unclear how many variant cases there actually were prior to having these measures taken.

“They might have been testing a smaller sample to try and judge a proportion of what might be circulating in the community, but what it really means is that the larger number of variants that are actually in the community, the larger proportion of what they make up versus the original strain, actually puts a lot more strain on the whole system,” says Tenkate.

In a Friday briefing, Canada’s Chief Public Health Officer Dr. Theresa Tam called the situation a “really delicate period” that could lead to a third wave if Canadians don’t remain cautious. Prime Minister Justin Trudeau also warned that a third wave with more transmissible variants “can cause real challenges.”

With evidence showing that the new variants can be transmitted more quickly and easily, Tenkate says the potential for a third wave is “very real”.

“We are definitely in quite a steep downward trend since early January, and so it means that the lockdown measures that have been in place, I think it really worked. In a lot of ways, if those are eased off with the combination of a more infectious variant, then I think the potential there is very real for an upsurge in case numbers again.”

There is also a sizeable lag between the time a variant case is identified and when that information gets published.

To identify the new variants of concern, positive COVID-19 tests are screened for the N501Y gene mutation. If the mutation is detected, the samples are sent for genome sequencing to identify the specific variant type. Results are only published when those results come back, up to 14 days later.

In addition to screening all positive cases for variants, provinces are also now committing to sequencing a portion of all COVID-19 cases to identify potentially undiscovered variants of concern beyond the three that have been identified in the country. Quebec, for example is currently sequencing 8.5 per cent of all cases, and has announced funding to later sequence 10 per cent of all cases.

But with many provinces only recently starting to screen widely for variants of concern, Dr. Samir Patel, deputy chief of microbiology and laboratory science at Public Health Ontario, says we will likely see a rise in variant numbers.

“We’re reporting out to the local public health unit as well as the submitters and we are prioritizing them for whole genome sequencing, so you may see more samples have been confirmed in coming days.”

A Feb. 11 report from the Ontario COVID-19 Science Advisory Table is warning of the same thing. With the B.1.1.7 variant spreading, “Aggressive vaccination and sticking with stay-at-home order will help avoid a third wave and a third lockdown,” the report says.

With this in mind, Dr. Patel says that Canadians should continue to be cautious.

“Follow public health guidance: maintain physical distancing, wearing a mask, washing hands. If you’re sick, please stay home and get tested for COVID, and if you’re positive for COVID, self-isolate yourself to prevent further spread.”