How tracking variants of the novel coronavirus is like building a family tree

Scientists around the world are digging into a family tree — but they’re not out to prepare for a family reunion. Virologists, epidemiologists, doctors and microbiologists are trying to track down the numerous variants and mutations of the virus behind the global pandemic.

Variants of the novel coronavirus are much in the news. Ontario has already found cases of the highly contagious U.K. variant. British Columbia and Alberta have reported cases of a South African variant. Meanwhile, British health officials are concerned that the vaccines currently being rolled out might not protect against future generations of the virus.

This talk of variant or mutated strains of SARS-CoV-2 may seem alarming, but for scientists, it’s not a new phenomenon. Thousands of genomic sequences have been identified that vary from the original strain of the virus.

Depending on the rate of transmission and efforts to curb infections, the variant can either die out or dominate. That’s why researchers are building what they call “evolutionary trees” to track changes in the virus as it evolves.

“By evolutionary tree, I mean something that’s very similar to looking at a family tree,” says Rowland Kao, professor of epidemiology at the University of Edinburgh.

“We think of family trees in humans — who are my parents or their parents, etc. You can do exactly the same thing for the virus.”

This evolution has been underway since the outbreak began in China. A recent paper released by the World Health Organization describes how the original strain of SARS-CoV2 from China had developed into something called the D614G mutation by late January or early February of 2020. By June, this became the dominant form of the virus that was circulating the globe.

“Our wave was a little bit later than the wave in Asia and Europe. So, by the time the virus landed here in Canada, it’s been dominated by what we call the D614 gene mutation,” says Dr. Samira Mubareka, infectious diseases physician and virologist at Sunnybrook Health Sciences Centre in Toronto.

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Such viral changes are a normal part of the life cycle.

When it comes to coronaviruses, a normal rate would be two mutations per genome per month. Changes outside of the typical rate catch the eye of researchers and scientists because depending on where on the genetic sequence the changes have occurred, they could play a role in how the virus operates.

“Every time they replicate, there’s a chance that they’ll change and they’ll change in a way that makes it more fit, more able to survive in the existing type and the amount of pressure that you put on that virus,” Kao explains.

As scientists detect these variants, they report them to the WHO. Researchers from around the world tap into that information and study whether those changes should ring any alarm bells — or as the WHO puts it, whether the “variants of SARS-CoV-2 result in changes in transmissibility, clinical presentation and severity, or if they impact on countermeasures including diagnostics, therapeutics and vaccines.”

And scientists are watching closely.

On Dec. 14, 2020, the U.K., which is a world leader in genetic sequencing, first reported the variant officially known as SARS-CoV-2 VOC 202012/01. (The VOC stands for “Variant of Concern” and the number refers to the year 2020, the month 12 or December, and the number after the slash means variant 01.)

Around the same time, officials in South Africa shared information about a new variant, N501Y.V2, that was circulating widely in the Eastern Cape, Western Cape and KwaZulu-Natal provinces and that was rapidly replacing other strains of the virus.

Researchers soon found that even though these two variants arose independently and in different parts of the world, they have something in common in how they invade our bodies.

“One thing that these two variants have in common is that they both have a mutation at position 501 in the spike protein,” explains Emma Hodcroft, a molecular epidemiologist at the University of Bern. She is co-developer of Nextstrain, an open-source project that helps teams around the world track pathogens in real-time.

“Spike protein is the part of the virus that sticks out the most. And it’s of increasing interest to scientists because it’s what lets the virus actually get into your cells,” Hodcroft says.

In addition to the change at the 501 position, there are two other notable changes in the spike protein, at K417N and E484K, in the strain first seen in South Africa. Both strains have been identified in Canada as well as numerous other countries around the world.

Scientific information is being gathered on the strains but at this point, it’s believed they do transmit more easily but do not appear to result in increased mortality or severe illnesses.

Researchers are running experiments to see how or if the changes in the genetic structure of the virus will affect the therapies or vaccines currently being used to battle COVID-19.

For example, the U.K. has seen 23 different changes in the virus, says Ravi Gupta, professor of clinical microbiology at the University of Cambridge.

Of those, 14 have an actual “coding change” that alters their building block amino acids, Gupta says.

“And of those 14, eight are in the spike domain. And people are worried about the spike because we have invested all of our current vaccine strategies in that area. So, we don’t want to see the virus changing in that region.”

For now, researchers like Kao say the current vaccines will be successful long enough to get us out of the current wave.

“If we can make it through the summer into the “next season, if a new variant occurs, then we’ll at least reach the stage where we’ve gone back to low numbers of cases, low burdens on the health services, for example, and the opportunity to develop new vaccines as they come about,” Kao says.

Down the road, scientists anticipate that new SARS-CoV-2 variants of concern will surface and be added to the viral family tree.

“I know this is very big picture — a bird’s eye view — but if we lose sight of that, in five years,10 years, we’ll be having the same discussion and I don’t want that to happen,” says Dr. Mubareka at Sunnybrook in Toronto.