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A highly changed coronavirus variant was found in deer after nearly a year in hiding, researchers suggest

<i>Don Emmert/AFP/Getty Images</i><br/>In many ways
AFP via Getty Images
Don Emmert/AFP/Getty Images
In many ways

by Brenda Goodman

An Omicron-like variant of the virus that causes Covid-19 — one that appears to be highly divergent from circulating strains and sticks out on a long branch of the virus’ family tree — has been discovered in a population of white-tailed deer in Ontario, Canada, according to a new study.

The same strain has also been found in a person from the same area who had confirmed contact with deer.

The researchers who first characterized what they are calling the Ontario WTD clade say it’s difficult to determine how this lineage evolved because it seems to have gone along unnoticed and unsampled in the background of the pandemic for almost a year. They speculate that it spilled over from humans to deer and then back to at least one human.

The new branch of the SARS-CoV-2 family tree has about 79 gene changes that set it apart from the original strain of the virus that was first identified in Wuhan, China. About half of those changes — 37 — have been seen in animals, but 23 of them have never before been identified in deer.

“It’s actually a pretty significant study, I think, because we’re seeing potential evolution of the virus in an animal reservoir,” said J. Scott Weese, a professor at the University of Guelph in Canada who specializes in the study of infections that jump between animals and people.

Weese says that before, we might see the SARS-CoV-2 virus pass between people and animals but then stop. There wasn’t an indication that it was persisting and changing in an animal population after these spillover or spillback events.

The closest viral relatives of the new clade, however, date back 10 to 12 months to humans and mink in Michigan, just over the border from Ontario.

“It went somewhere and changed over the course of months to a year, and it looks like most likely that was within an animal. We just don’t know what species or where,” says Weese, who reviewed the study but was not involved in the research.

The study was posted ahead of peer review on the preprint server BioRxiv.

Signs of a new animal reservoir

In many ways, deer are the ideal hosts for SARS-CoV-2, Weese says. They are highly susceptible to infection, but they don’t get very sick, and they nest in groups, making it easy for the virus to spread.

This new strain was detected during hunting season. Hunters brought the deer they killed to scientists who swabbed and tested them.

The researchers say there’s no evidence that this strain has resulted in sustained deer-to-human or human-to-human transmission. However, hunting season has ended in the region, and the Omicron wave has swept through, complicating further surveillance.

Early lab experiments suggest that the new strain is easily knocked down by antibodies created in response to vaccination, which makes this version of the virus unlikely to pose an immediate threat.

The problem is what might happen in the future.

“I think most people were thinking — and it’s true — that humans are driving the pandemic,” said study author Bradley Pickering, who is the head of special pathogens in Canada’s National Centre for Foreign Animal Disease. “So now, it looks like this is circulating in wildlife.”

If it stays in deer in North America, it could continue to circulate and change.

“You do have that risk, that it’s always there and that it could — at any point — it could kind of come back to people,” he said.

Pickering says the researchers are going to try to restart their surveillance of the deer population to continue to monitor the evolution of the virus.

If deer have become a true animal reservoir, that’s a tricky problem to solve, and it signals a new phase in the pandemic, Weese says.

“We need to get beyond a human-centric approach. Individual means individual; it doesn’t mean people,” Weese said. “It doesn’t matter if it’s circulating in 100 million people in a fully vaccinated area of the world or if it’s circulating in 10 million deer in North America. It’s circulating, and as the virus circulates and replicates, that’s how mutations happen.”

Another way for the virus to survive

When SARS-CoV-2 turns up in a population of farmed animals, like mink, or the hamsters sold at pet stores in Hong Kong, they are often culled to contain the spread of the virus.

That’s not possible when the virus is in a population of wild animals.

There are animal vaccines, but veterinarians use those for the same reason they give them to humans, to prevent disease and keep the animal — a tiger at a zoo, for example — from becoming severely ill or dying.

“Vaccines aren’t highly effective at preventing transmission,” Weese said. “We would have to have an animal vaccine that’s better than a human vaccine, and the animal vaccines are an older technology, so that would be a pretty high bar to set.”

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