Researcher finds ‘astonishing’ rate of COVID in deer. Here’s what it means for humans

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Between October and December of last year, researchers removed the noses of 93 dead deer across Pennsylvania. Almost a fifth of the animals tested positive for COVID.

This is one of the results of a new pair of studies soon to be published along with the latest evidence of the spread of COVID from humans to wild white-tailed deer where the virus has detected a series of new mutations. Additionally, in one case, COVID most likely later reverted from deer to a human. It’s a first.

These new discoveries — which follow a previous study about COVID in the white-tailed deer population — raise new concerns about the unpredictability of spillover events and the potential risks posed to humans. Here are some questions asked about deer fallout.

Did the Pennsylvania deer die of COVID?

No. “These are deer that died with COVID,” says Andre Marques, a doctorate in microbiology. student at the Perelman School of Medicine at the University of Pennsylvania. “It’s not deer that died from COVID.” Rather, they had been chased or hit by oncoming traffic. But a nearly 20% COVID positivity rate is, according to Marques, lead author of the Discoveries of Pennsylvania yet to be reviewed, “absolutely breathtaking when you consider the positivity rate in humans”, which is much lower. In Philadelphia, for example, the positive test rate currently hovers around 3%.

Of the 93 samples collected, eight were of high enough quality to have their genomes sequenced, a process that shows which variants were circulating in these wild deer. The results told Marques and his collaborators that the lineages they observed appear to have spilled over from humans. Some of them looked like the delta variant at a time when delta was common among people.

But others looked like the alpha, the first variant of concern at the end of 2020, “which is strange,” Marques says. The samples were collected months after delta became the dominant human strain. And that means the alpha strain, which had largely disappeared in humans, was still present in the environment – ​​inside those deer. That is to say, we cannot quite forget the variants that no longer affect us.

So how did the deer catch COVID?

We don’t know for sure. Marques admits: “It’s all speculation at the moment.” So let’s speculate.

It is possible that there was some form of direct interaction between deer and humans, possibly through people feeding the animals. Or maybe the deer drank human wastewater or untreated sewage and picked up circulating coronavirus, although Marques finds this possibility unlikely as the virus is not generally stable for long periods outside the body and typical sewage treatment would destroy virus particles. Or maybe COVID passed through one of the known intermediate animal host species like a mink, wildcat, or deer mouse.

Either way, once COVID hit the deer, it clearly spread among the animals. In fact, certain deer behaviors can increase the ease of transmission. “Deer sometimes touch their noses in greeting,” Marques says. And when exhaling, deer release clouds of vapor, just like other mammals. In humans, COVID is a respiratory disease that spreads through droplets in the air. The same is probably true in deer.

As for symptoms, other researchers have reported that most infected deer tend to show no noticeable symptoms.

/Ben Hasty/MediaNews Group/Reading Eagle via Getty Images

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Ben Hasty/MediaNews Group/Reading Eagle via Getty Images

It’s unclear how the deer became infected with SARS-CoV-2, but their foraging behavior could be a way of transmitting the virus between them.

Did you mention mutations?

Unfortunately yes. Some of the viruses identified by Marques and his collaborators had detected a few dozen mutations in their viral genetic sequence. Think of it as removing a handful of individuals from a parade of 30,000 people.

“Some of these people [might] play really important roles in the show,” says Marques. “And by changing those people, it can change the way the parade moves, the way the parade sounds. And we can think of that as an analogy to the virus where [a relatively small number of mutations] changes how the virus might spread. »

And I suspect it’s not just deer in Pennsylvania?

That’s right. the second study, also pending review, is outside southwestern and eastern Ontario. The, Samira Moubareka, a virologist at the Sunnybrook Research Institute and the University of Toronto, and his team tested nearly 300 deer. Some 6% had a COVID strain that was really retro.

“This one is from an even older line, so probably spilled over to deer at some point in 2020, maybe early 2021,” says Mubareka. This predates all variants of concern – delta, omicron, even alpha. Because this strain had presumably been circulating among deer for so long, it had time to accumulate 76 mutations, 23 of which had not previously been reported in deer.

And in sequencing the viral genomes, Mubareka and his colleagues found something puzzling. This constellation of mutations did not remain confined to deer. They found it in a sample from an infected person, compelling evidence that that person had caught the virus from a deer.

Minks and hamsters…and now deer? How worried should we be?

The results of this deer study are significant – after finding its way into a different species like this, where it gathered additional mutations, a new variant or strain of COVID could impact people, where it has the potential to create more problems. Fortunately, Mubareka and his research team found preliminary evidence that blood serum from vaccinated individuals neutralized this mutated strain.

Mubareka adds, “We don’t want people to worry about far and distant deer exposure.” Nevertheless, for those in close contact with wildlife and animals, it is important to take the appropriate precautions, including getting vaccinated and keeping your distance. This affects not only deer, but also mink, hamsters and some mice – all known reservoirs of SARS-CoV-2.

Are there any possible long-term consequences of COVID in deer?

If history is any guide, the answer is yes. “I can’t think of a single zoonotic disease that has established itself in an animal reservoir in the wild that we’ve successfully eradicated,” says Barbara Han, disease ecologist at the Cary Institute of Ecosystem Studies. She was not involved in either study, but says the work is essential to assess human risk. And she’s not surprised with the results.

Han says that across mammals (and vertebrates more broadly), “We all share some version of this [ACE2] receptor that the virus hijacks to enter our cells. But distinguishing which species are most likely to shed lots of viruses and transmit them is still very difficult. »

In fact, in a separate study, to assess spillover probabilities among 5,400 mammals, Han and his team used machine learning to train an algorithm to recognize characteristics of species whose ACE2 receptors bind tightly to the SARS-CoV-2 virus. The algorithm identified more than 500 of these species as possible suspects, including a range of primates, bats, carnivores (such as red foxes and spotted hyenas) and ungulates (such as deer and gazelles).

Although researchers aren't sure exactly how deer were initially infected with SARS-CoV-2, the animals are closely related to humans in many regions – as well as other animals known to harbor the virus.

/Daniel Slim/AFP via Getty Images

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Daniel Slim/AFP via Getty Images

Although researchers aren’t sure exactly how deer were initially infected with SARS-CoV-2, the animals are closely related to humans in many regions – as well as other animals known to harbor the virus.

Han says all of this work is essential to help calculate the risk. And she fears that once we see an overflow (like the deer), we’re in it for the long haul. “So the fact that we now have a semi-permanent reservoir species – and not just white-tailed deer, but mink and [laboratory] stag mouse – suggests to me that we now need to track the evolution of these species and constantly update our calculations of risk to humans.”

Copyright 2022 NPR. To learn more, visit https://www.npr.org.

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