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

OTTAWA — 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.

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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.

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.

This report by The Canadian Press was first published July 12, 2020.

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