Canadian scientists find new coronavirus lineage in deer

Strain might have been evolving from start of pandemic.

Scientists have identified a new, highly mutated version of the coronavirus in whitetailed deer in southwestern Ontario, one that might have been evolving in animals since late 2020.

They also found a similar viral sequence in one person in the area who had close contact with deer, the first evidence of possible deer-to-human transmission of the virus.

“The virus is evolving in deer and diverging in deer away from what we are clearly seeing evolving in humans,” said Samira Mubareka, a virus expert at Sunnybrook Research Institute and the University of Toronto and an author of the new paper.

The report has not yet been published in a peer-reviewed journal, and there is no evidence that the deer lineage is spreading among, or poses any elevated risk to, people. Preliminary laboratory experiments suggest that the lineage is unlikely to evade human antibodies.

But the paper was posted online just days after another team reported that the alpha variant may have continued to spread and evolve in Pennsylvania deer even after it disappeared from human populations.

Together, the two studies suggest that the virus may be circulating among deer for extended periods of time, raising the risk that the animals could become a longterm reservoir of the virus and a source of future variants.

“There’s certainly no need to panic,” said Arinjay Banerjee, a virus expert at the University of Saskatchewan. But, he added, “the more hosts you have, the more opportunities the virus has to evolve.”

Studies have found the virus is widespread in whitetailed deer. Research suggests humans have repeatedly introduced the virus to deer, which then transmit it to one another. How humans are spreading the virus to deer remains a mystery and, until now, no evidence has shown the animals passing it back to humans.

The Canada study was a collaboration of more than two dozen researchers in Ontario who collected nasal swabs and samples of lymph node tissue from 300 white-tailed deer killed by hunters in Ontario from Nov. 1-Dec. 31. Six percent of the animals, all from southwestern Ontario, tested positive for the virus, suggesting they were actively infected when they died.

The researchers sequenced the full viral genomes from five infected deer and found a unique constellation of mutations not previously documented. Overall, 76 mutations — some of which had been found in deer, mink and other infected animals — set the lineage apart from the original version of the virus.

The deer samples were most closely related to viral samples taken from human patients in Michigan, not far from southwestern Ontario, in November and December 2020. They were also similar to samples taken from humans and mink in Michigan earlier that fall.

Those findings, as well as the rate at which the virus accumulates mutations, suggest that the new lineage may have diverged from known versions of the virus, and been evolving undetected, since late 2020.

THE NEW YORK TIMES A researcher swabs a white-tailed deer Feb. 2 at a wildlife center at Texas A&M. Scientists have found a version of the coronavirus in Canadian deer.