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Tracking omicron: Canadian scientists race to understand new variant

Canadian scientists are racing to understand more about the threat of the omicron variant — how fast it spreads, whether it causes more or less severe illness, and if it can escape previous immunity to COVID-19 — but it could take weeks before a full picture emerges.

There have been dozens of suspected and confirmed cases of omicron reported throughout Canada in recent days, but several have no known link to international travel and have prompted concerns the variant could already be driving outbreaks here.

Health officials in London, Ont., confirmed omicron is now linked to a cluster of at least 40 COVID-19 cases in the city associated with schools, child care centres and a church, with 171 high-risk close contacts identified. 

And countries such as South Africa, Denmark and England are already reporting widespread community transmission of the variant, with growing evidence that omicron was already spreading in Europe before it was identified by researchers in southern Africa. 

Tracking omicron: Canadian scientists race to understand new variant
Dozens of suspected and confirmed cases of omicron have been reported throughout Canada in recent days, but several have no known link to international travel and have prompted concerns the variant could already be driving outbreaks here. (Evan Mitsui/CBC)

Canadian labs better prepared for omicron 

But the capacity to analyze this new variant and quickly share information about it both in Canada and globally has grown dramatically from a year ago, when the alpha and beta variants of concern first emerged.

“The most important thing for Canadians to know is that we have spent more than a year building the capacity for genomic surveillance,” said Catalina Lopez-Correa, executive director of The Canadian COVID Genomics Network (CanCOGeN). 

“But it’s really early days for us to predict the clinical outcomes, the transmissibility, also we don’t know if this variant will be as fast taking over like delta … all this we can only see with time.”

Marc-André Langlois, a molecular virologist at the University of Ottawa who heads the Coronavirus Variants Rapid Response Network (CoVaRR-Net), says labs across the country are working tirelessly to conduct experiments on omicron. 

“What’s changed is the fact that we’ve managed to bring our academic laboratory assets together,” Langlois said. “We have epidemiologists, we have modellers, we have immunologists, virologists and they’ve all come together.” 

Guillaume Bourque, director of bioinformatics at the McGill Genome Centre in Montreal, says Canada is also now able to act on the data more quickly.

“Now we have the system in place,” Bourque said. “We want to make it available to public health and to the scientific community as fast as possible, so that people can really start working on trying to understand the variant and then give advice to public health in terms of the best approach to try to contain it.”

Langlois says that the early data coming out of southern Africa on omicron is useful — but limited in scope.

“That snapshot is very, very different to the Canadian landscape. So the information we have now is indicative, but it’s not a true reflection of what’s going to happen when this variant spreads in Canada,” he said. “This is why we need a Canadian network to look at the Canadian situation.”

WATCH | Spike in COVID-19 levels in South Africa as omicron variant spreads:

Tracking omicron: Canadian scientists race to understand new variant

South Africa sees spike in COVID-19 cases as omicron variant spreads

4 days ago

Duration 2:02

The omicron variant is driving a sharp increase in COVID-19 cases across South Africa. Scientists believe the variant is more transmissible, and may even bypass acquired immunity in some people who have recovered from COVID-19. 2:02

Langlois said the first tests will look at whether antibodies from COVID-19 vaccines will still neutralize the virus compared to other variants, but figuring out how much of an impact omicron could have on vaccine effectiveness at a population level will take time. 

“We’re talking about maybe two, three more weeks to get some neutralizing data from the blood of Canadians,” he said. 

Not enough data to ‘speculate’ on omicron impact yet

But Canadian scientists aren’t just looking on Canadian soil for answers — they’re also poring over hints from around the world about the impact omicron could have here. 

Angela Rasmussen, a virologist at the Vaccine and Infectious Disease Organization (VIDO) at the University of Saskatchewan, says epidemiologic data from documented omicron cases in Canada and globally will be key.

“We’re looking at the number of breakthrough infections that occur, looking at the number of people who’ve been vaccinated, who end up not only with infection with the omicron variant but also in the hospital,” she said. 

“We are reliant on these studies to determine really whether the vaccines will remain effective — including protecting against severe disease caused by omicron.” 

Another way scientists are understanding more about how omicron spreads is by experimenting with the virus in other species using challenge studies, where animal models are vaccinated and then infected with the variant to determine how severe their illness is. 

“We’re looking to see what type of clinical manifestations this variant causes in laboratory animals and if in laboratory animals this particular variant can transmit easily,” said Alyson Kelvin, a virologist at the Canadian Center for Vaccinology and VIDO in Saskatoon.

“Those are key evaluations that need to occur before we can really speculate anything about this variant.” 

Tracking omicron: Canadian scientists race to understand new variant
People travel at Pearson International Airport during the COVID-19 pandemic in Toronto on Friday. New travel testing and restrictions have been put in place due to the omicron variant. (Nathan Denette/The Canadian Press)

Could omicron overtake delta in Canada?  

Delta remains the dominant variant in Canada, but if early speculation about omicron being more transmissible and causing less severe disease holds true, experts say we could be looking at a very different epidemic picture in Canada in the coming weeks and months. 

“To be honest, I wouldn’t be surprised if it does take off because if it’s like delta, the main thing we can do is slow down progression,” said Bourque. 

“We need to learn as much as we can from experiments that we’ll be doing here on those samples, but also from other colleagues from all over the world.” 

Bourque says Canadian scientists can piece together a better picture of omicron in the coming days, which will help  “buy ourselves a few weeks” to make the most educated decision possible going forward on how best to mitigate potential spread.

“What concerns I think a lot of scientists, including myself, is that we’re seeing omicron slowly overtaking delta in southern parts of Africa. So at least over there, it looks like it is more transmissible than delta,” Langlois said. 

“Will that hold true for Canada and the northern hemisphere? We don’t know. But it is likely to be more transmissible.” 

Tracking omicron: Canadian scientists race to understand new variant
Delta remains the dominant variant in Canada, but if premature speculation about omicron being more transmissible and causing less severe disease holds true, experts say we could be looking at a very different epidemic picture in Canada soon. (Ben Nelms/CBC)

‘Concerning’ mutations don’t tell whole story

Omicron contains more than 30 mutations in the spike protein alone, the part of the coronavirus which helps it enter human cells, some of which are associated with resistance to neutralization from antibodies. 

But scientists are urging caution before drawing too much from the limited data on the real world impact of omicron to date.

“Those mutations are concerning, but we had several different variants across this pandemic that had mutations in very concerning sites and they didn’t end up being highly transmissible or more pathogenic,” said Lopez-Correa. 

Kelvin says just because a variant has concerning mutations, does not mean it will necessarily take off — especially in the face of other variants like delta.

“The beta variant, which was first identified in South Africa, had probably the lowest amount of neutralization from either vaccine antibodies or antibodies from people who’ve recovered from COVID-19,” she said. 

“But that’s not the variant that we saw that spread around the world.” 

Until we know more from laboratory tests and real world data in highly vaccinated populations, speculation about the impact omicron could have in Canada and around the world should be weighed carefully. 

“Yes, this variant is concerning. Yes it will likely be more resistant to neutralization. But is this variant a monster? Probably not. ​​The vaccines will work against this variant,” said Langlois. 

“To what extent? That’s the question.” 

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