Specimens to be tested for COVID-19 are seen in Surrey, B.C., on Thursday, March 26, 2020. For the last four months, Canada’s public health experts have been racing to stop the spread of COVID-19 by trying to figure out how everyone is getting it, and who they may have given it to. THE CANADIAN PRESS/Darryl Dyck

Specimens to be tested for COVID-19 are seen in Surrey, B.C., on Thursday, March 26, 2020. For the last four months, Canada’s public health experts have been racing to stop the spread of COVID-19 by trying to figure out how everyone is getting it, and who they may have given it to. THE CANADIAN PRESS/Darryl Dyck

Genetic detectives begin work to trace spread of COVID-19 in Canada

The kinds of genetic technology being used for this project did not exist when SARS hit Canada in 2003

For the last four months, Canada’s public health experts have been racing to stop the spread of COVID-19 by trying to figure out how everyone is getting it, and whom they may have given it to.

But even the best efforts have left doctors stymied about the source of more than one-third of this country’s known COVID-19 infections. Not knowing where cases come from makes outbreaks that much harder to stamp out.

Now medical researchers and supercomputers are turning genetics labs into virus detective agencies, looking first to find the novel coronavirus itself within blood samples from thousands of infected patients, and then comparing all of those isolated viruses to each other looking for places they differ.

Every close match will draw a line from patient to patient, ultimately painting a picture of how the virus spread.

“This is the big effort over the next four weeks,” said Andrew McArthur, director of the biomedical discovery and commercialization program at McMaster University.

“What’s going to come out of there pretty soon is a glimpse of what just happened, how did it move around the province, how did it move between provinces or how big was Pearson (airport) in the early days of the airport being open.”

Knowing how the virus spread will show where there were weaknesses in public health measures early on, said McArthur. Being able to keep divining genetic codes from samples will mean when there are flare-ups of cases, they can be quickly compared to each other to see if they’re all related or are coming from multiple sources.

It means, for example, a long-term care centre should be able to quickly know if its 10 new cases are because one case spread widely or arose from multiple carriers coming into the facility.

“That’s a very different infection-control problem,” said McArthur.

It also means that maybe, just maybe, the second COVID-19 wave most think is coming won’t be as bad, or as hard to control, as the first, because the sources can be isolated very quickly.

“A second wave is likely,” McArthur said. “But we’ve never spent this kind of money and effort before, either, so maybe we’ll beat it.”

The kinds of genetic technology being used for this project did not exist when SARS hit Canada in 2003.

READ MORE: Provincial COVID-19 data can now be used for B.C. to prepare for a second wave

This genetic mapping is constantly on the look-out for mutations. Thus far, SARS-CoV-2, the official name for the virus that causes COVID-19, has not mutated as quickly as many others do. Influenza, for instance, changes so much over a year the vaccine has to be retooled every summer to keep up.

But there are enough subtle changes still happening among the 28,000 individual markers that make up a genome for SARS-CoV-2 that cases can be traced backward and linked to the ones that came before. McArthur said it takes a lot of data storage, a lot of high-capacity computer analysis, and a lot of money, to run the comparisons among them all.

The federal government put $40 million on the table in April for genetic research on COVID-19. Half is to keep tabs on the virus as it spreads, look for any changes it undergoes, and map its pathway across the country. The other half is to look at the genetic structures of the patients who get infected, trying to answer the puzzling question of why some people die and others have symptoms so mild they never even know they are sick.

Genome Canada is administering the project, with six regional genomics agencies overseeing the work locally and labs like McArthur’s doing the testing and analysis. The funding is intended to create genetic maps from 150,000 patients. Canada thus far has had about 108,000 positive cases, and the expectation is that almost every one of them will be gene-mapped.

The results will be loaded into a global site comparing all known infections of COVID-19, but also be analyzed for national and regional reports.

In New York, genetic sequencing was used to figure out that COVID-19 in Manhattan wasn’t coming from China and Iran as imagined, but from Europe. In Canada, it is suspected that much of the virus came into this country from travellers returning from the United States in early March. But the work is only now beginning to confirm that belief.

McArthur estimates the first data will be available for Ontario in about four weeks, but warns it will take many more months to complete all of the tests. His lab sequenced 600 samples on Wednesday alone.

Overall, McArthur expects the genetics project to last for two years.

Mia Rabson, The Canadian Press


Like us on Facebook and follow us on Twitter.

CanadaCoronavirus

Get local stories you won't find anywhere else right to your inbox.
Sign up here

Just Posted

Williams Lake musicians Evan Jensen and LeRae Haynes continue to share songs through social media, something they started when the COVID-19 pandemic first began. (Photo submitted)
OUR HOMETOWN: Musical generosity abounds

A Williams Lake couple continue to share music through social media

Luke Lavigne of Clearwater is the 2020 recipient of the North Thompson Communities Foundation’s Donnie Nicholson Memorial Trades Bursary, and is shown here on Jan. 23 receiving the $1,500 cheque from NTCF treasurer Cheryl Thomas. (NTCF Facebook photo)
Clearwater’s Luke Lavigne awarded Donnie Nicholson Memorial Trades Bursary

Congratulations to Luke Lavigne of Clearwater, B.C., on the successful completion of… Continue reading

Dr. Bonnie Henry, provincial health officer, updates British Columbians about COVID-19 at a press conference earlier this week. (B.C. Government image)
B.C.’s 1st case of COVID-19 confirmed a year ago today

Here’s a look at some of the key dates in the province’s fight against the novel coronavirus

The Canadian Cancer Society Office located inside the Williams Lake Seniors Activity Centre closed its doors this month after being notified the CCS would be moving to regional offices located across Canada. (Angie Mindus photo - Williams Lake Tribune)
Canadian Cancer Society closes office in Williams Lake

“I didn’t realize how hard it would hit me when it actually closed down,” Allan said.

Toronto’s Mass Vaccination Clinic is shown on Sunday January 17, 2021. THE CANADIAN PRESS/Frank Gunn
Interior Health reports 2 more deaths, 83 new COVID-19 cases

Health authority also identifies new virus cluster in Fernie

British Columbia Health Minister Adrian Dix looks on as Provincial Health Officer Dr. Bonnie Henry addresses the media during a news conference at the BC Centre of Disease Control in Vancouver B.C. (THE CANADIAN PRESS/Jonathan Hayward)
B.C. announces 485 new COVID-19 cases, fewest deaths in months

‘The actions we take may seem small, but will have a big impact to stop the virus,” urges Dr. Henry

Sooke’s Amy McLaughlin holds Theodore, a bunny who will be going to a new owner in Nanaimo within the coming days if all goes will at an upcoming bunny play-date. (Aaron Guillen/News Staff)
Vancouver Island woman looking to hop into bigger space for bunny rescue operation

Amy McLaughlin has rescued more than 400 bunnies, pushing for the capacity to help more

Cannabis bought in British Columbia (Ashley Wadhwani/Black Press Media)
Is it time to start thinking about greener ways to package cannabis?

Packaging suppliers are still figuring eco-friendly and affordable packaging options that fit the mandates of Cannabis Regulations

Grad student Marisa Harrington and her supervisor Lynneth Stuart-Hill say preliminary results from a study into the affects of stress on hospital nurses show an impact on sleep and heart variability. (Courtesy of Marisa Harrington)
University of Victoria study shows stress impact on B.C. nurses

Stress may be impacting sleep, heart health of hospital nurses in Victoria region

Keith Thorpe/Peninsula Daily News
Search called off for small plane that went down in rough water south of Victoria

Plane bound for Port Angeles from Alaska believed to have one occupant, an Alaskan pilot

Royal B.C. Museum conservator Megan Doxsey-Whitfield kneels next to a carved stone pillar believed to have significance as a First Nations cultural marker by local Indigenous people. The pillar was discovered on the beach at Dallas Road last summer. Museum curatorial staff have been working with Songhees and Esquimalt Nation representatives to gain a clearer picture of its use. (Photo courtesy Royal BC Museum)
Stone carving found on Victoria beach confirmed Indigenous ritual pillar

Discussion underway with the Esquimalt and Songhees about suitable final home for the artifact

Former Vancouver Giants forward Evander Kane is seen here in Game 7 of the second round of the 2009 WHL playoffs against the Spokane Chiefs (Sam Chan under Wikipedia Commons licence)
Gambling debts revealed in details of bankruptcy filing by hockey star Evander Kane

Sharks left winger and former Vancouver Giants player owes close to $30 million total

Othman “Adam” Hamdan, pictured in front of Christina Lake’s Welcome Centre, was acquitted of terrorism related charges in 2017. He has been living in Christina Lake since November 2020. Photo: Laurie Tritschler
Man acquitted on terrorism charges awaits deportation trial while living in Kootenays

Othman Ayed Hamdan said he wants to lead a normal life while he works on his upcoming book

B.C. Premier John Horgan wears a protective face mask to help prevent the spread of COVID-19 prior to being sworn in by The Honourable Janet Austin, Lieutenant Governor of British Columbia during a virtual swearing in ceremony in Victoria, Thursday, November 26, 2020. THE CANADIAN PRESS/Jonathan Hayward
Premier Horgan calls jumping COVID vaccine queue ‘un-Canadian’

Horgan says most people in B.C. are doing their best to follow current public health guidelines

Most Read