Canada is on the hunt for coronavirus variants — but may not be able to keep up with outbreaks

Only five per cent of virus samples in Canada are tested for coronavirus variants, including those first identified in South Africa, Brazil and the U.K. — with the latter estimated to be at least 56 per cent more transmissible than the main coronavirus and potentially more deadly as well.

There have been at least 34 cases of variants confirmed in Canada in recent weeks, but several have no known link to travel and have prompted concerns the variants could be already driving outbreaks undetected.

“To ensure that virus variants that can spread more easily do not take hold, there is even greater urgency to suppress COVID-19 activity in Canada,” Chief Public Health Officer Dr. Theresa Tam said Wednesday.

First variant outbreak in Canada a ‘wake-up call’

Canada’s first outbreak due to a coronavirus variant was identified this week at the Roberta Place long-term care home in Barrie, Ont., where at least 81 staff and almost all 130 residents have been infected with COVID-19 since the outbreak was declared on Jan. 8, including 27 who have died.

Local public health officials suspected the outbreak was caused by the variant first identified in the U.K., also known as B117, and sent samples to public health laboratories for further testing earlier this week.

Six preliminary samples have since tested positive for a variant, but it will take days to determine whether the outbreak was caused by B117 or a different strain. 

“Barrie has become ground zero for what is likely a [coronavirus] variant of concern, which has spread rapidly throughout Roberta Place and we are concerned that it will spread into our community and into other long-term and retirement homes,” said Dr. Charles Gardner, Simcoe Muskoka District Health Unit’s medical officer of health.

“This is a race against time and we need to use the COVID-19 vaccine as our most effective means to protect these residents. We have to do what we can to prevent other outbreaks.”

Local public health officials said Friday night they were accelerating the vaccine rollout in light of the outbreak and will begin vaccinating residents and staff at the long-term care home this weekend.

Prof. Robyn Lee, a genomic epidemiologist at the University of Toronto’s Dalla Lana School of Public Health, said the situation at Roberta Place should be “another wake-up call that we really need to be doing something to stop transmission in the community and to test people to make sure that this doesn’t come into long-term care facilities.” 

Lee is awaiting the full results from the Public Health Ontario laboratory to see which variant specifically was spreading at Roberta Place, but says it’s likely we’ll see more outbreaks across Canada in the near future. 

“These variants appear to be more transmissible, which means we’re going to see more cases — especially if they do kind of kick off,” she said.

Lee says Canada needs to “very seriously crack down” with public health measures and speed up vaccination rollouts across the country in response to the threat posed by variants.

“What we’re seeing in Roberta Place is what happens when these get in and how aggressive they can be,” said Dr. Zain Chagla, an infectious diseases physician at St. Joseph’s Healthcare Hamilton and an associate professor at McMaster University.

“The whole concern about this variant is it getting into care facilities and places with vulnerable people — and it did exactly that.” 

Chagla said the Roberta Place outbreak has also raised concerns that variants could be the driving factor behind other recent COVID-19 outbreaks in Canada with unusually high numbers of cases in a short period of time. 

“There certainly is a worry that some of those were actually related to coronavirus variants,” he said.

“There’s probably a bigger burden out there.”

‘Detective work’ identifying variants is slow

Testing for the variants is done through a time-consuming process called genomic sequencing, which requires highly specialized staff and equipment and takes days to return results — precious time when variants could spread more widely. 

“We need to increase our surveillance of the virus in Canada,” said Art Poon, an associate professor in the department of pathology and laboratory medicine at Western University in London, Ont.

“We need the resources to do more sequencing so that we have better capability of tracking the spread of not only variants of concern, but other variants that may be arising in Canada.” 

Catalina Lopez-Correa, executive director of the Canadian COVID Genomics Network (CanCOGen), which was formed in April 2020 to track variants and co-ordinate viral genome sequencing across Canada, said that while the number of samples tested in Canada is low, the testing efforts are focused on very specific samples. 

“It’s not about the numbers, it’s about the strategy,” she said. “It’s about prioritizing the right samples and co-ordinating efforts.” 

Lopez-Correa said CanCOGen’s strategy for testing for variants in Canada includes targeting fast-spreading outbreaks; geographic regions with an unusually high growth in cases; younger patients with very severe disease; reinfections; and those infected after being vaccinated.

There are currently eight labs across Canada testing virus samples for the variants, including the National Microbiology Lab in Winnipeg and seven other provincial labs. 

“Some people are calling us genomic detectives and that’s exactly what we are,” said Lopez-Correa. “It’s detective work trying to figure out where those variants are and how to trace them.” 

But although scientists are working around the clock to test the samples, they can only move as fast as the results will allow — meaning scaling up surveillance in the face of faster spreading variants isn’t easy. 

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“If you have a contained outbreak in a specific geographical region, you don’t need to sequence everybody that’s infected in that outbreak, because most of them will have the same variant of the virus,” Lopez-Correa said. “But, of course, it’s a challenge to increase the amount of samples we’re doing.” 

CanCOGen was created with initial federal funding of $40 million, half of which was allocated specifically for sequencing the virus, but Lopez-Correa said Canada could divert more money to staff and resources to test for the variants faster.

Lee said even with increased funding there is only a certain amount of surveillance Canada can reasonably do, given that the labs work on samples for all kinds of different viruses across the country. 

“Ideally, we would be sequencing more, and I know there are efforts to do this, but there are some limitations,” she said, including the time it takes to collect samples, transport them to specific labs, sequence them and analyze the results. 

“That involves a lot of different people and a lot of different resources. So, while it would be great to keep scaling up, there are going to be limits on what can be done.” 

Canada ‘way behind’ on sharing data on variants

The World Health Organization called on countries around the world to increase their capacity to test for variants earlier this month, but also underscored the need to share the data internationally. 

Poon said Canada is “way behind” in sharing data on variants around the world, partly because our public health system is understaffed and doesn’t currently have the resources to keep up with genomic surveillance.

“We are conservative about data sharing … I think that concerns about privacy have overridden calls to share data with other countries,” he said.

“Since this is a global pandemic, getting a clear picture of what’s going on requires open sharing of data between countries. But that’s not something that’s been happening with Canada.” 

Lopez-Correa said Canada could improve its capacity to share data across the country and internationally. She said data is first shared domestically before being sent overseas.

“We could do better, but we’re submitting the data,” she said. “If you look at regions like Africa, Latin America, they’re not generating that data. They don’t have the capacity.” 

Without effective international sharing of data, Canada could continue to see new variants arise in the future that are only identified after they’ve spread around the world. 

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In the meantime, Lee said, the emergence of variants in Canada further underscores the need to vaccinate those most at risk of severe illness and death as soon as possible.

“Vaccination is going to play a critical role in this. We need to get everyone vaccinated who is in those long-term care facilities and all of the staff as well as their primary caregivers,” she said.

“I think that has to be the No. 1 priority at the moment.” 

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