Genomics researchers working to track the COVID-19 pathway across Canada

Ottawa-Over the past four months, Canadian public health professionals have stopped the epidemic of COVID-19 by figuring out who gets it, how it is given, and who is given it Have been competing for.

However, even the best efforts have confounded physicians with more than one-third of the known COVID-19 infections in this country. Without knowing where the case came from, it would be much more difficult to counter an outbreak.

Today, medical researchers and supercomputers are turning genetic laboratories into virus-detection agencies, first finding new coronaviruses themselves in blood samples of thousands of infected patients, and then those isolated viruses. Looking for different places, comparing everything to each other.

Every close match draws a line from patient to patient and ultimately depicts how the virus spread.

“This is a big effort,” over the next four weeks, said Andrew MacArthur, Head of Biomedical Discovery and Commercialization Programs at McMaster University.

“Just out there is what happened, how we moved between states, how we moved between states, the size of the original Pearson (airport) when the airport opened. did. “

By knowing how the virus spreads, MacArthur said he would be able to see where the weaknesses in public health measures were. Being able to derive the genetic code from a sample allows us to quickly compare them when case flare-ups occur to see if they are all related or from multiple sources. I will.

For example, a long-term care center should be able to quickly see if 10 new cases are due to one case being widespread or coming from multiple carriers entering the facility.

“It’s a very different infection control problem,” MacArthur said.

Also, perhaps the second COVID-19 wave means it’s not as bad as the first wave or less controllable than the first because the sources can separate very quickly.

“There is likely a second wave,” said MacArthur. “But I’ve never spent such money and effort before, so I’ll probably beat it.”

When SARS hit Canada in 2003, the type of genetic technology used for this project did not exist.

This genetic mapping is always looking for mutations. So far, the official name of the virus responsible for COVID-19, SARS-CoV-2, is not mutating as rapidly as many other viruses. For example, influenza changes drastically over the course of a year, requiring the vaccine to be modified every summer to maintain the vaccine.

However, among the 28,000 individual markers that make up the SARS-CoV-2 genome, there are still sufficient subtle changes that can correlate the case with what came before. According to MacArthur, performing all of those comparisons requires a lot of data storage, a lot of high-volume computer analysis, and a lot of money.

The federal government invested $40 million in April for genetic research on COVID-19. Half is to monitor the virus as it spreads, look for changes that the virus undergoes, and map virus routes across the country. The other half is to look at the genetic makeup of infected patients and answer the mysterious question why some people die and others don’t even know why they are ill because their symptoms are mild.

Genome Canada administers the project, with six regional genomics agencies overseeing local work and McArthur overseeing labs and other testing and analysis sites. The funding is aimed at creating a genetic map from 150,000 patients. There are approximately 108,000 positive cases in Canada so far, and it is expected that almost all of them will be gene mapped.

The results are loaded into a global site that compares all known infections of COVID-19, but is also analyzed for country and region reports.

In New York, using gene sequencing, we found that Manhattan’s COVID-19 was from Europe, not from China or Iran. In Canada, many of the viruses are believed to have entered the country from travelers returning from the United States in early March. But work has just begun to confirm that belief.

Macarthur predicts that the first Ontario data will be available in about four weeks, but warns that it will take several more months to complete all tests. In his lab, we sequenced 600 samples on Wednesday alone.

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