Labs across Canada tracking COVID-19 mutations to understand which are circulating and compare internationally

A network of laboratories across Canada is studying mutations in the genetic footprint of COVID-19 to track patterns of transmission across the country and internationally. 

Led by the Public Health Agency of Canada's National Microbiology Laboratory, along with Genome Canada, the research is working to identify as many genetic sequences as possible. 

The goal is to understand which sequences are circulating in Canada and compare those to others around the world. 

"Monitoring interprovincial or international spread of the virus will become increasingly important as public health measures are slowly lifted and cross-border travel resumes," said Natalie Mohamed, a spokesperson for the Public Health Agency of Canada, in a written response to questions.

"Genetic variants may also impact the sensitivity and performance of the current COVID-19 diagnostic methods. By comparing viral genome sequences, we will be able to monitor the spread of these established lineages in Canada."

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The agency said most genetic mutations in the virus are "silent," meaning they do not modify the virus's function or make it more dangerous. However, these genetic differences can be used to identify different variations that form a lineage, with a common ancestor and descendents.

Identifying source of new cases

Understanding the variations circulating in Canada will help to identify the source of new cases as travel restrictions are lifted.  

It can also help identify links between cases when investigating outbreaks, which is particularly useful when contact tracing is not available or inconclusive.

The agency said it is too early to tell whether Canada has distinct virus lineages. 

It said monitoring of viral and genetic variants will be key to ensuring the effectiveness of any vaccines and treatments, and can help make sure testing for the virus is accurate. 

"We need to continuously monitor their effectiveness, otherwise we risk missing positive cases," Mohamed said in reference to testing methods.

The research is being carried out through the Canadian COVID-19 Genomics Network (CanCOGen), a consortium of public health and academic institutions, hospitals and large Canadian sequencing centres. 

The project has been funded for two years with $40 million from the federal government, announced in April. 

"We are already submitting our virus sequence data to the public domain databases and will make study findings available to the public as they become available," said Mohamed. 

Individual virus sequences submitted to open source databases

Although the findings will be released at a later date, the data itself is being shared to open-source databases, like the NextStrain website, as it is generated. 

A spokesperson from the Roy Romanow Lab in Saskatchewan said mutations shown on NextStrain, such as one identified in that province, are "extremely small." 

"The majority of these changes happen randomly and do not affect the virus in any way," it said. 

"It's important to note that currently none of the mutations have been shown to increase infectivity." 

It said coronaviruses mutate very slowly compared to viruses like influenza or HIV.

Vaccine researchers monitoring changes

Darryl Falzarano is a research scientist at the VIDO-InterVac laboratory at the University of Saskatchewan in Saskatoon. 

His team is a front-runner in the race to develop a vaccine in Canada, having recently reported success with a candidate it said proved "highly effective" in pre-clinical trials in ferrets. 

Falzarano said his team keeps a close eye on mutations in the genetic footprint of COVID-19 because dramatic changes could affect the vaccine response. 

At this point he said the virus has not shown signs of significant change.

"Of course if all of a sudden there's some big jump or shift in viruses that are being seen in the region that your vaccine is likely to target, then you need to be concerned," said Falzarano. 

"That's why we pay attention. But at the moment there's no data indicating that it's a big concern — that we would need multiple different antigens, or that we're going to need to make one vaccine this year and need a new vaccine next year."

He said COVID-19 is better at replicating its own genome without making errors — compared with some other coronaviruses — so the mutations are not as dramatic as those in influenza. 

The National Microbiology Lab has centres in Winnipeg, Man., Guelph, Ont., St. Hyacinthe, Que., and Lethbridge, Alta.