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Why Alberta has identified more variant cases but they’re believed to be more prevalent in Ontario

Alberta has identified more COVID-19 variants of concern to date than any other province, but the variants are actually estimated to have gained a larger foothold in Ontario.

How can that be?

Like with so many things related to COVID-19 in Canada, it’s complicated.

Interprovincial comparisons are especially tricky because every province measures and reports its COVID-19 data a little differently, and this includes data on variants of concern.

These mutated versions of the coronavirus are especially worrisome to public health officials because they can be more transmissible and vaccines may be less effective against them.

The Public Health Agency of Canada (PHAC) publishes a regular update on variants of concern, with data gathered from each province, and as of Monday, Alberta was at the top of the list with 1,711 variant cases.

Ontario — with more than triple Alberta’s population — had the second-highest total, with 1,424 variant cases identified. But there is an important asterisk attached to that number.

The total number of variant cases in Ontario has been described as a drastic undercount of the real situation, due to the time it takes the province to complete genetic analysis of virus samples — a process that can take up to three weeks.

Alberta, by contrast, reports most of its variants of concern (known as VOCs) without waiting for full genetic analysis if the initial screening identifies a telltale mutation in the virus.

“This means that the vast majority of VOCs are reported immediately, with only a small number needing followup testing for confirmation,” Alberta Health spokesperson Sherene Khaw said.

The difference in reporting methods can be seen in the chart below, published this week by Public Health Ontario.

Why Alberta has identified more variant cases but they're believed to be more prevalent in Ontario
A chart showing about 1,400 identified variant-of-concern cases in Ontario (the blue, orange and purple bars) but also about 14,000 cases where a mutation has been identified but genomic analysis has yet to be completed (the green bars). (Public Health Ontario)

The little blue bars in the chart show cases identified as the B117 variant, the most common of the variants in Canada right now. The even smaller orange bars show the B1351 variant cases, and the tiny purple bars show the P1 variant cases.

The massive green bars, meanwhile, show the number of cases where a key mutation has been identified in the virus, indicating it is likely a variant of concern, but the virus’s genetics have yet to be fully analyzed to identify exactly what kind of variant it is.

These yet-to-be-analyzed cases number nearly 14,000 — roughly 10 times more than the current variant count that shows up in the PHAC data for Ontario.

It’s likely that many of these cases will end up being confirmed as variants and eventually end up in the official count. But for the moment, they don’t show up — making Ontario’s variant caseload appear smaller than Alberta’s if the two provinces’ tallies are compared directly.

Meanwhile, Ontario’s science advisory table on COVID-19 now estimates that 55 per cent of new cases in the province are actually variants of concern. That’s nearly 1,000 new variant cases per day, at current rates.

The proportion of new cases that are variants of concern is seen as an indicator of how dominant a particular version of the virus has become in a particular area. 

In Alberta, variants of concern have accounted for increasingly more cases as time goes on, but they have yet to reach a level as high as Ontario’s estimate of 55 per cent.

Back in January, variants represented just one or two per cent of new cases in the province.

That proportion has steadily grown since then but so far has peaked at just over 25 per cent.

How variant screening works

Screening for variants in Ontario has involved a three-step process.

First, a swab taken from a patient’s nose or throat is tested for the virus that causes COVID-19. If it comes back positive, the sample is then analyzed further, which begins with a relatively quick test for a particular mutation that is common to all three variants of most concern (B117, B1351 and P1).

If that mutation is detected, the sample is then sent for further testing. This time, its genetics are analyzed more fully to determine exactly what type of variant it is — a process that takes significantly longer.

This is what’s behind the backlog that has developed in the reporting of Ontario’s variant cases.

Why Alberta has identified more variant cases but they're believed to be more prevalent in Ontario
A nurse uses a swab to perform a test on a patient at a drive-in COVID-19 clinic. Ontario has changed its screening process for variants after a backlog developed, bringing the province more in line with how screening is done in Alberta — where all COVID-positive samples are screened for mutations, but not all samples undergo a full genetic analysis. (Paul Chiasson/The Canadian Press)

As of Monday, however, Ontario changed its screening process to help speed things up. Samples found to have the mutation common to all three variants of concern — but not a second mutation that’s common to just the B1351 and P1 variants — will no longer require the full genetic analysis. They will simply be presumed to be a variant of concern, most likely B117.

This brings Ontario more in line with how screening is done in Alberta, where all COVID-positive samples are screened for mutations, but not all samples undergo a full genetic analysis.

It takes an average of 44 hours to complete variant screening by this method, according to Alberta Health Services, and the tests are considered valid for confirming cases of the B117 variant, which was first identified in the U.K. and represents the vast majority of variant cases in the province to date.

In addition, Alberta Health Services says it also conducts full genetic sequencing on hundreds of variant samples each week to monitor for other variant strains.

The net result is that, to date, Alberta’s reporting of most variant cases has taken about two days, compared with up to three weeks in Ontario.

Some positive samples aren’t screened

Another complicating factor is that not all samples that test positive for COVID-19 end up being screened for variants of concern, for one of two reasons.

The first reason, especially earlier in the pandemic, is that the screening capacity wasn’t in place.

Alberta only screened a select number of positive samples from December and January for variants of concern. By February, it had ramped up its screening to include all positive samples.

“Alberta started screening every positive case of COVID-19 for variants before any other part of Canada did, so we’re a little ahead regarding the number of samples that have been screened,” said Khaw of Alberta Health.

The pace of screening has varied from province to province over time, but by now it’s become more consistent, if not perfectly consistent.

“Most provinces and territories aim to screen 100 per cent of their COVID-19 cases for mutations associated with variants of concern,” PHAC told CBC News in an email this week.

The second problem is that not all positive samples can be successfully screened for variants.

In some cases, there isn’t enough viral material left in the sample to do a proper screening. Degradation of the virus’s RNA or other technical issues with the genetic sequencing can also cause failures in the screening process.

Alberta Health Services says about 80 to 85 per cent of all positive samples are successfully screened for the variants of concern.

What’s not in doubt: Variants are taking over

All of this paints a complicated picture of the variant situation, but public health experts say one thing is clear: Variants of concern are becoming increasingly dominant.

Canada’s chief public health officer, Dr. Theresa Tam, said on Tuesday that this is being observed not just in Alberta and Ontario, but all across the country when it comes to these mutated versions of the virus.

“They account for a greater proportion of COVID-19 cases across Canada, reminding us of how tight the vaccines-versus-variants race continues to be.”

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