Covid-positive deer may be harboring the virus and infecting humans, study says

Aside from saving human lives in the immediate moment, the other fundamental reason that public health officials were pushing mass vaccination to slow the spread of COVID-19 is because the more hosts in which a virus resides, the more likely the virus is to eventually mutate into something more virulent. Obviously, that has happened at least twice so far with SARS-CoV-2: first with the ultra-contagious delta variant, and then later with the even more contagious omicron variant.

This article first appeared on Salon.

Currently, the number of human hosts in the U.S. is waning as the omicron wave falls from its peak. If we are lucky, that may imply that this wave of infections is over, and while the coronavirus will continue to circulate (and mutate) as it becomes endemic, it would have fewer hosts in which to do so.

Or, at least human hosts. As we know, SARS-CoV-2 seems to have circulated in bats and pangolins before crossing over to humans. We also know that the virus spread back into animals, presumably through humans: dogs, cats, a zoo lion, and a large population of deer appear to have been infected by humans.

Ominously, the infection trend may now be going the other way. A recent Canadian study raises the possibility that deer — one of the most ubiquitous large mammals in North America — may have infected humans with COVID-19, the disease caused by SARS-CoV-2. That would imply the virus circulated for a while in deer, reproducing and occasionally mutating on its way, before jumping back into people.

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The new study provides evidence that deer may have infected humans, although it is not definitively proven. Conducted by more than two dozen scientists across Ontario and posted on the database bioRxiv (it has not yet been peer reviewed), the study included 300 samples from white-tailed deer in Canada during the final months of 2021. Seventeen of those deer tested positive for SARS-CoV-2, all of them from southwestern Ontario. The scientists discovered that this same strain of SARS-CoV-2, which is highly divergent from other known strains, was also highly similar to a SARS-CoV-2 virus that had infected a human. (It was also closely related to a strain found among humans in Michigan in late 2020.) While the scientists cannot confirm that the virus had been transmitted to the human by a deer, they know that the human lived in the same geographic area as deer and had been in close contact with deer during the same time when the infected samples were collected.

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That said, the sample size is very small and no one has definitively proved that the deer gave the virus to the human. There is also no evidence that the person with the mutant SARS-CoV-2 virus passed it on to anyone else, and initial experiments suggests the new virus would not be able to evade antibodies. In other words, if it did spread among people, individuals who are vaccinated would likely be safe.

Finally, because the deer-based SARS-CoV-2 virus is such an unknown, there is no reason to believe yet that it presents any kind of increased risk to humans. The bigger concern is that, because viruses can evolve in animals, there is the possibility that it could turn into something more dangerous.

"The virus is evolving in deer and diverging in deer away from what we are clearly seeing evolving in humans," Samira Mubareka, a virologist at Sunnybrook Research Institute and the University of Toronto and an author of the new paper, told The New York Times. After fully sequencing the genomes from five of the infected deer, the scientists discovered many mutations that had not been previously documented. They also found 76 mutations that set the new version of SARS-CoV-2 from the original version of the virus. Some of those mutations had been previously discovered in other infected animals like mink.

Shortly before this study was published, a separate group of scientists announced that Pennsylvania deer may have continued to be infected with the Alpha variant even after it disappeared in humans — and that it evolved within them as they continued to spread it. This further reinforces the concern about deer incubating SARS-CoV-2 viruses.

The SARS-CoV-2 virus is believed to have originated in in a horseshoe bat. At some point, the virus is thought to have been transmitted to another animal through one or many "spillover events," and then eventually found its way to a human host. Bats are notorious for serving as hosts to dangerous coronaviruses because their immune systems are unusually aggressive. This means that viruses which live in bats need to evolve and replicate more quickly in order to survive.

"The bottom line is that bats are potentially special when it comes to hosting viruses," Mike Boots, a disease ecologist and UC Berkeley professor of integrative biology, told Science Daily in 2020. "It is not random that a lot of these viruses are coming from bats. Bats are not even that closely related to us, so we would not expect them to host many human viruses. But this work demonstrates how bat immune systems could drive the virulence that overcomes this."