Omicron has been found in deer – that should worry us

There are over 30 million white-tailed deer in the U.S. That’s a boon for hunters, a headache for gardeners, a danger to drivers – and now it looks like a potential problem in the world’s ongoing efforts to contain the COVID-19 pandemic to hold . According to a new study (not yet peer-reviewed) published on bioRxiv, researchers at Penn State University found that several white-tailed deer captured and tested on New York’s Staten Island were infected with the Omicron variant of SARS-CoV. -2. It is the first such discovery in non-human animals.

COVID-19 has been previously found in deer. In 2020 and 2021, the U.S. Department of Agriculture detected previous versions of the virus in 481 deer sampled in 15 states. But the Omicron variety is more of a concern than those earlier species, simply because of its extreme portability and proximity to which humans and deer often live.
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The study was small; researchers took nasal swabs from 68 deer and found Omicron in five of them. The question that the discovery raises is: how transmissible is the virus from human to deer and back again? For now, the researchers can’t say anything. The study only showed that the animals were carrying the virus, but revealed nothing about how they got it, whether they emitted it, or even whether they can pass it on among themselves.

“As we continue to find these spillovers in animals, such as deer, the complexity of virus evolution and transmission networks becomes much more complicated,” said Suresh Kuchipudi, a Penn State veterinary virologist and co-author of the study. “The potential exists that the virus could circulate among the deer and they could become an important reservoir.”

Worryingly, at least one of the deer in the sample not only harbored the virus, but also had high levels of antibodies against it. That suggests a kind of wildlife equivalent of a breakthrough infection: An animal that had had the virus once before developed a natural immune response to it, but then became infected again.

If deer carry the virus, there’s no reason to assume other animals aren’t either. While it is not practical or even possible to test every species of animal that comes within infectious distance of humans, certain animals are of particular interest to researchers. Kuchipudi is concerned about deer mice, skunks and feral cats, which previous lab studies have shown can be easily infected with COVID-19. Other rodent species are also concerned.

“We cannot rule out the possibility that rodents pick up the virus from humans and spread it to other animals living in the same ecological space,” says Kuchipudi.

The biggest concern right now, the Penn State authors say, isn’t so much whether deer will be a more meaningful vector in the spread of Omicron to humans. We are already doing a great job of spreading it among ourselves. Rather, the deer could become a petri dish for viral mutation and the emergence of even more variants, which could theoretically jump across species and infect humans.

“If left unchecked, the continued circulation of this virus in any animal species could result in the evolution and emergence of completely new variants that could potentially undermine the protection of current vaccines,” Kuchipudi said. “The last thing we want is to be surprised by a completely new variant that can originate from animals.”

Researchers are now trying to figure out how to reduce that risk. There’s a precedent for dealing with animals that harbor COVID-19, but it’s extreme: When it was recently found that 11 hamsters at a pet store in Hong Kong had COVID-19, authorities ordered the killing of 2,000 hamsters, and when the virus was found among 17 million farmed minks in Denmark in November 2020, the minks were slaughtered. Taking such measures against infected deer in the US is obviously not possible.

Instead, Kuchipudi recommends, U.S. conservation experts could begin a program to capture and vaccinate deer in areas where the virus appears to be circulating. Searching for the source of the virus – through wastewater or other environmental pollutants – may also be an option.

Infected deer do not represent the most pressing problems facing health officials in managing the pandemic, but they do serve as a sign of the virus’ ubiquity. SARS-CoV-2 is a decidedly opportunistic pathogen, which discriminates less and less between the hosts it infects and will continue to infect. A virus that seemed to arrive suddenly more than two years ago will not leave us anytime soon.

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