Scientists have discovered a highly mutated form of the coronavirus that has been found in white-tailed deer in southwestern Ontario. This virus may have been present in animals since late 2020.
They also discovered a similar virus sequence in a person living in the same area as the deer, which was the first evidence of possible human-to-deer 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 virologist at Sunnybrook Research Institute and the University of Toronto and an author of the new paper.
The peer-reviewed journal has not published the report yet. There is no evidence of deer lineage spreading among people, or that it poses an elevated risk to them. Preliminary laboratory studies suggest that the deer lineage is unlikely not to evade antibodies from humans.
The paper was published online days after another team reported on the possibility that the Alpha variant may still have spread and evolved in Pennsylvania deer, even though it was eliminated from the human population.
These two studies together suggest that the virus could be circulating among deer over extended periods of time. This raises the possibility that the animals could become a long term reservoir of the virus as well as a source for future variants.
“There’s certainly no need to panic,” said Arinjay Banerjee, a virologist at the University of Saskatchewan who was not involved in either study.
But, he added, “The more hosts you have, the more opportunities the virus has to evolve.”
Previous studies have shown that the virus can be found in white-tailed elk. Researchers believe that humans have introduced the virus to deer multiple times, and then they pass it on to each other. It is not clear how humans spread the virus to deer. There has been no evidence to suggest that animals are passing it on to humans.
Canada Study was a collaboration between more than 20 researchers from Ontario institutions. The scientists collected nasal swabs as well as samples of lymph node tissues from 300 white-tailed elk killed by hunters in Ontario, between Nov. 1, 2021, and Dec 31, 2021. Six percent of the animals tested positive for the virus. They were all from southwestern Ontario.
Researchers sequenced the entire viral genomes of five infected Deer and discovered a unique constellation. Overall, 76 mutations — some of which had previously been found in deer, mink and other infected animals — set the lineage apart from the original version of the virus.
The deer samples most closely resembled viral samples from human patients in Michigan, near southwestern Ontario in November and Dec 2020. They also resembled samples taken from mink and humans in Michigan earlier in the fall.
These findings, together with the rate at mutations are accumulating, suggest that the new lineage could have diverged from the known viruses, and been evolving undetected since late 2020.
However, it is not known exactly how the virus spread. One possibility is the possibility that humans may have passed the virus to deer and then the virus accumulated mutations among the cervids. Alternately, the lineage may have evolved at least partly in another, intermediate species — perhaps farmed or wild mink — which then somehow transmitted it to deer.
“We don’t have all the pieces in the puzzle,” Dr. Suresh Kuchipudi, a veterinary microbiologist at Penn State, who was not involved in the research, said in an email. “We cannot rule out the involvement of an intermediate host.”
One human patient in southwestern Ontario had a viral sample that closely matched the deer samples in the fall 2021. That person is known to have had “close contact” with deer, According to the researchers.
(They couldn’t divulge more details about this contact for privacy reasons. Dr. Mubareka said that people shouldn’t be concerned about indirect, incidental encounters like a deer wandering through their yard.
Scientists cautioned that the sample size was small and that there is no conclusive evidence that the person contracted the virus from deer. “We don’t have enough information yet to confirm that transmission back to humans,” said Roderick Gagne, a wildlife disease ecologist at the University of Pennsylvania School of Veterinary Medicine.
At the time the human specimen was collected, Ontario was sequencing virus samples from everyone who had tested positive on a P.C.R. test. Researchers did not find any other people infected with the virus in similar cases, so it is less likely that it has evolved in isolation in humans.
“Had it been circulating widely in humans, even narrowly in humans, I think we would have picked it up,” Dr. Mubareka said.
There is no evidence that the infected person passed the virus to others.
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Early data suggests that vaccines are still capable of protecting against this lineage. Antibodies from vaccinated people were able to neutralize pseudoviruses — harmless, nonreplicating viruses — that had been engineered to resemble the deer lineage, the scientists found.
In the second study, scientists from the University of Pennsylvania’s veterinary and medical schools analyzed nasal swabs from 93 deer that died in Pennsylvania in the fall and winter of 2021. Nineteen percent of the deer were infected with this virus. Researchers sequenced seven samples and found that five deer were infected by the Delta variant. Two were infected by Alpha.
Delta was present among Americans at the time of the collection, but the Alpha wave that struck the country in spring 2021 had long passed.
“Alpha seems to be persisting in the white-tailed deer even during the time when it’s not circulating in humans,” said Eman Anis, a microbiologist at the University of Pennsylvania School of Veterinary Medicine and an author of the study.
The Delta samples from deer were genetically identical to human ones, which suggests that it had crossed species lines fairly recently. However, the Alpha sequences were more different from human lineages. (They were also significantly different from one another, suggesting that the variant was at least twice introduced to the deer population.
“The main implication would be that the deer sustain transmission and infections within their populations,” Dr. Gagne, an author of the Pennsylvania study, said. “So that is not just, you know, a spillover event from humans, deer get infected and then it fizzles out.”
It is not clear if these lineages will continue circulating and evolving in deer.
“Based on current information, I’d say that the risk of wildlife, including deer, spreading the virus to people is low,” said Jeff Bowman, a research scientist at the Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry and an author of the Canada paper.
Scientists agree that it is crucial to monitor the situation. Dr. Mubareka suggested that officials should enhance wastewater screening in Ontario and other nearby regions to look specifically for the deer lineage — and to ensure that it is not becoming more prevalent.
Experts also recommended that people continue to follow the public health agency’s guidelines, which include not feeding deer or other wildlife and wearing gloves when butchering game.
“We should also be reducing the biggest reservoir for this virus, which is us,” Dr. Mubareka said, “to make sure we’re not continuously spilling into deer and creating these new lineages.”
Source: NY Times