Rapid screening test will help track coronavirus variants in Alberta

Alberta is ramping up its surveillance for two coronavirus variants — which have now been reported in the province — as a team of scientists at the provincial laboratory develop a quicker and easier test to identify cases and determine if and when the strains take root.

Provincial lab team developing test that will screen for specific mutations in sampling of COVID-19 cases

Kara Gill, with Alberta Precision Laboratories’ specialized diagnostics team, loads samples on a sequencer to determine the genetic sequence of the SARS-CoV-2 virus. (Alberta Precision Laboratories)

Alberta is ramping up its surveillance for two coronavirus variants — which have now been reported in the province — as a team of scientists at the provincial laboratory develop a quicker and easier test to identify cases and determine if and when the strains take root.

Five cases of the variant first identified in the U.K. have been confirmed in Alberta, along with one case of the variant first discovered in South Africa.

All of the cases are travel-related, according to Alberta Health, but there is a small amount of transmission in one case where a traveller spread COVID-19 to two household contacts. Health officials say there is no evidence there was further spread beyond that household.

"The fact that these are present in the province is obviously a concern," said Dr. Lynora Saxinger, infectious disease specialist at the University of Alberta.

"If one of these variants becomes established in a population it can be responsible for worsening the epidemic quite significantly over a short period. So, the question really is, has there been some spread in the background of these variants that we have not yet detected? And ... the other good question is, how would we know?"

Dr. Lynora Saxinger, a University of Alberta infectious diseases specialist, says vigilance is key now that coronavirus variants are being identified in Alberta. (Martin Weaver/CBC)

Alberta doesn't test all of its COVID-19 samples for the variants.

So, the province's chief medical officer of health, Dr. Deena Hinshaw, says there is no guarantee the variants aren't circulating in the community.

But, according to Hinshaw, the provincial lab has been doing full genetic sequencing on up to 150 samples a week to detect mutations.

"What we can say with certainty that the variant is not widespread at this time, because we have been doing that sampling and sequencing over the last many months," she said Tuesday.

1st variant detected overnight on Christmas

A team of scientists at the provincial lab has been conducting that full genome sequencing on a proportion of COVID-19 cases since the start of the pandemic. To date, they've completed roughly 4,000 of those sequences.

And it was through that painstaking process that Alberta's first case of the coronavirus variant that was initially identified in the United Kingdom was discovered.

Over the holidays a technologist at the provincial lab first spotted the variant — working through the night Christmas Eve and into the morning.

Dr. Graham Tipples, medical-scientific director with Alberta's provincial public health lab, says the provincial lab can conduct full genome sequencing on between 800 and 1,000 cases per week. (AHSChannel/YouTube)

"I phoned Dr. Hinshaw on Christmas morning with that news of the first U.K. variant," said Graham Tipples, medical scientific director for the provincial public health lab.

Once identified, it took a few days to confirm and then the work began to develop a test that could more quickly and easily identify the specific mutations found in that variant.

According to Tipples, reagents have been ordered and are expected to arrive "imminently." Once here, the lab will proceed with the specific testing for both of the variants now confirmed in Alberta.

"It's going to be easier once we get this rapid screening test up and running. Then we can do more," he said.

Hinshaw said Tuesday the provincial lab aims to run 100 of these variant tests per day by the end of January. Tipples says once they get going they could do significantly more than that.

Paul Dieu and Kara Gill, with Alberta Precision Laboratories’ specialized diagnostics team, analyze sequencing data to determine the lineage of the SARS-CoV-2 virus. (Alberta Precision Laboratories)

It is unlikely — unless overall daily testing numbers are low — that all COVID-19 samples could be screened.

So, health officials are relying on focused surveillance to try and find cases early.

"It's not about doing everything. It's about doing it smart and doing it targeted so that you're detecting whether that strain is established in Alberta or not," said Tipples.

The surveillance program is targeting travellers, outbreaks or clusters and severe cases with its surveillance program. It will also keep an eye on whether specific age groups are susceptible as well as watching for for cases in a variety of geographical areas.

"The big question is, is it being imported into Canada? Is it establishing itself in Canada? And, is it in fact truly associated with enhanced spread or did that just happen to be the strain that was around in the U.K. when they found a surge in tests? So those are the kinds of questions that we need to keep an eye on things to understand a little bit better," he said.

According to Tipples, there is no sign right now that the variants are established or widespread in the province.

"Which way it's going to go, honestly I don't know. My job is not to predict that. But my job is … that we have the system that we're capable of detecting it," he said.

Tipples points out Alberta is doing this work alongside other provinces and sharing information through the Canadian COVID-19 Genomics Network (CanCOGeN), as the group works to track the emergence of these new variants.

Vigilance is key, doctors say

Meanwhile, doctors say the appearance of these variants in Alberta comes as no surprise.

"This is not unexpected," said Dr. Vanessa Meier-Stephenson, an infectious disease physician and virology researcher at the University of Calgary's Cumming School of Medicine. "The virus will evolve and mutate over time just as part of its natural process."

According to Meier-Stephenson, the key now that cases showing up here is for Albertans to stay vigilant and follow public health guidelines.

"It would only take one person with that variant strain to spread it to a larger group and to a larger group. It doesn't take much to result in a cascade of infections from one individual."


Jennifer Lee


Jennifer Lee is a CBC News reporter based in Calgary. She worked at CBC Toronto, Saskatoon and Regina, before landing in Calgary in 2002. If you have a health or human interest story to share, let her know.


To encourage thoughtful and respectful conversations, first and last names will appear with each submission to CBC/Radio-Canada's online communities (except in children and youth-oriented communities). Pseudonyms will no longer be permitted.

By submitting a comment, you accept that CBC has the right to reproduce and publish that comment in whole or in part, in any manner CBC chooses. Please note that CBC does not endorse the opinions expressed in comments. Comments on this story are moderated according to our Submission Guidelines. Comments are welcome while open. We reserve the right to close comments at any time.

Become a CBC Member

Join the conversation  Create account

Already have an account?