It is known that SARS-CoV-2 infects white-tailed deer. Indeed, the findings that infected deer were identified in nine locations in Ohio were published in 2021. The authors of that paper, who have been continuing to monitor deer for infection by more recent variants, now report that SARS-CoV-2 viral variants evolve about three times faster in deer than in humans.
The findings suggest that the white-tailed deer species is a reservoir for SARS-CoV-2 that enables continuing mutation, and that the virus’s circulation in deer could lead to its spread to other wildlife and livestock
This work is published in Nature Communications, in the paper, “Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.”
Scientists collected 1,522 nasal swabs from free-ranging deer in 83 of Ohio’s 88 counties between November 2021 and March 2022. More than 10% of the samples were positive for the SARS-CoV-2 virus, and at least one positive case was found in 59% of the counties in which testing took place.
“We expanded across Ohio to see if [the deer infections were] a localized problem—and we find it in lots of places, so it’s not just a localized event,” said Andrew Bowman, DVM, PhD, associate professor, department of veterinary preventive medicine at the Ohio State University said. “Some of the thought back then was that maybe it’s just in urban deer because they’re in closer contact with people. But in rural parts of the state, we’re finding plenty of positive deer.”
Beyond the detection of active infections, researchers also found through blood samples containing antibodies that an estimated 23.5% of deer in Ohio had been infected at one time or another.
Genomic analysis showed that at least 30 infections in deer had been introduced by humans. “We generally talk about interspecies transmission as a rare event, but this wasn’t a huge sampling, and we’re able to document 30 spillovers. It seems to be moving between people and animals quite easily,” said Bowman. “And the evidence is growing that humans can get it from deer—which isn’t radically surprising. It’s probably not a one-way pipeline.”
The 80 whole-genome sequences represented groups of viral variants: the highly contagious delta variant, the predominant human strain in the United States in the early fall of 2021 that accounted for almost 90% of the sequences, and alpha, the first named variant of concern that had circulated in humans in the spring of 2021.
The analysis revealed that the genetic composition of delta variants in deer matched dominant lineages found in humans at the time, pointing to the spillover events, and that deer-to-deer transmission followed in clusters, some spanning multiple counties.
“There’s probably a timing component to what we found—we were near the end of a delta peak in humans, and then we see a lot of delta in deer,” Bowman said. “But we were well past the last alpha detection in humans. So the idea that deer are holding onto lineages that have since gone extinct in humans is something we were worried about.”
The study did suggest that COVID-19 vaccination is likely to help protect people against severe disease in the event of a spillover back to humans. An analysis of the effects of deer variants on Siberian hamsters, an animal model for SARS-CoV-2 studies, showed that vaccinated hamsters did not get as sick from infection as unvaccinated animals.
That said, the variants circulating in deer are expected to continue to change. An investigation of the mutations found in the samples provided evidence of more rapid evolution of both alpha and delta variants in deer compared to humans.
“Not only are deer getting infected with and maintaining SARS-CoV-2, but the rate of change is accelerated in deer—potentially away from what has infected humans,” Bowman said.
How the virus is transmitted from humans to white-tailed deer remains unanswered. And so far, even with about 30 million free-ranging deer in the United States, no substantial outbreaks of deer-origin strains have occurred in humans.
Circulation among animals, however, remains highly likely. Bowman noted that about 70% of free-ranging deer in Ohio have not been infected or exposed to the virus, “so that’s a large body of naive animals that the virus could spread through rather uninhibited.”
“Having that animal host in play creates things we need to watch out for,” he said. “If this trajectory continues for years and we have a virus that becomes deer-adapted, then does that become the pathway into other animal hosts, wildlife or domestic? We just don’t know.”