The coronavirus is mutating — and that can help us track it

Sequencing the coronavirus's RNA is providing researchers with valuable information about the strains of the virus in Canada and how to stop its spread.

Inayat Singh CBC News • May 15, 2020

The novel coronavirus has very simple personal goals. Its main purpose in life is to replicate, something it has done with alarming efficiency, causing havoc around the world.

And in this process of replicating itself, it is leaving behind tiny genetic markers of its spread that are being picked up by researchers hot on its trail.

These small mutations don't change the virus or the illness it causes, COVID-19, but they do carry clues on how to fight its spread.

This is a visualization of what the coronavirus that causes COVID-19 looks like. It's named after the crown-like spikes on its surface.

When the virus enters a human body and infects a cell, it releases a piece of genetic material called RNA.

As the virus multiplies, the RNA multiplies as well — but with some copying errors.

These tiny mutations can lead to new strains of the virus, which can be used to track where in the world it originated.

The new strains don't fundamentally change the virus — its RNA contains over 29,000 genetic bases or letters, with the mutations only representing about 40 differences in them.

But they help researchers map the family tree of the virus and track where it comes from.

Labs around the world are sequencing — or analyzing — the RNA of the virus and sharing the data to track its spread. Public Health Ontario is one such lab sharing data.

"It's thinking about how we can get insights through these new tools, not just for research but for decision making," said Vanessa Allen, the chief of medical microbiology at the Public Health Ontario Laboratory in Toronto.

A few samples of the virus have been sequenced in Canada, sent mainly by public health labs in Ontario and B.C.

Allen's lab has sequenced 64 samples of the virus, with a special focus on early cases of the virus, to form a picture of its spread.

The Canadian data shows the virus coming in through travel from various parts of the world and how easily the virus spread before travel restrictions were invoked. It's still too early to draw definite conclusions, but as more sequencing results come in, researchers will have a clearer understanding of how the virus spread through Canada.

The Canadian sequencing data is submitted to Nextstrain, an open-source database that has now collected information on more than 4,500 samples of the virus. Data is submitted by labs from around the world.

The Nextstrain database contains 110 sequences sampled in Canada. By linking the genetic information to strains of the virus sequenced in other countries, researchers can track how the virus travelled through the world and its multiple points of entry into Canada.

The first sample on the Nexstrain database was collected in Ontario and shows the virus arriving in Canada through travel from China, which was the epicentre of the outbreak.

The purple lines, representing how the virus spread from China, show the virus spreading to Europe, the U.S. and Iran.

Subsequent samples collected in B.C. were linked to travel to Iran, which has also suffered a major outbreak.

The virus is recorded mutating and spreading across Europe, with this strain travelling to Canada and the U.S.

A new strain of the virus later appears in the U.S. where regional transmission is also recorded.

Sequences collected in Canada are linked to mutations of the virus found south of the border.

There are also sequences from a second mutation linked to Europe found in Canada.

The virus is a global problem, and the sequencing data reflects this intermingling.

As cases spike in Europe and North America, the Nextstrain database shows the outbreak coming full circle as the virus is reintroduced into Asia with infections that originated in North America and Europe.

"We can learn how those different infections are related, whether they're local transmissions or whether they were imported from a country, and that can be really helpful for knowing what implementations you should put in place," said Emma Hodcroft, a researcher at the University of Basel in Switzerland and co-developer of Nexstrain.

Going forward, the sequencing data can be used to ferret out local outbreaks in small communities or health care facilities.

It can also be used to make sure that the coronavirus tests are still working as the virus mutates and changes.

"Sometimes, you don't know if the health-care worker acquired [the virus] at home or some health-care setting or other scenarios," Allen said. "So, we can use this typing to actually understand transmission patterns a little bit better."

"When you're trying to determine how to stop the outbreak it's important to understand how it might have been brought in. "The information can help add to other interventions, like physical distancing, to contain an outbreak," Allen said.

There are about 12 other labs in Ontario doing sequencing work to help drive decision making around the outbreak. The Ontario Institute for Cancer Research is one such institution joining sequencing efforts that will help track outbreaks in near real time as test samples come in.

"If you sequence the genomes and you compare them to each other, they might be identical. In that case, that might give you information that they had a common origin, [that] there is someone in common they're both infected from,” explained Jared Simpson, a researcher with the OICR.

"But if they are very different, then that might give you indication that they are completely separate transmission events, and you need to spread your contact tracing wider."

The province is now working on collating the research coming in from the other labs doing sequencing work.

"For it to be of real value is actually matching it to some of these risk factors," Allen said. "Not personal health information but just risk factor data and geography data so that we can actually interpret it in a meaningful way."

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