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'Stunning' rate of COVID among deer...

edited March 2022 in The OT Bullpen
NPR is reporting that "Between October and December of last year, researchers swabbed the noses of 93 dead deer from across Pennsylvania. Nearly a fifth of the animals tested positive for COVID." Here is the entire NPR article:

Here's what it means for humans:
Between October and December of last year, researchers swabbed the noses of 93 dead deer from across Pennsylvania. Nearly a fifth of the animals tested positive for COVID.

This is one result from a new pair of soon-to-be-published studies with the latest evidence for COVID spillover from humans into wild white-tailed deer where the virus picked up a raft of new mutations. In addition, in one case, COVID most likely later spilled back from the deer into a human. That's a first.

These new findings — which follow an earlier study about COVID in the white-tailed deer population — are raising renewed concerns over the unpredictability of spillover events and the potential risks posed to humans. Here are a few questions being asked about the deer spillovers.

Did the Pennsylvania deer die from COVID?

No. "These are deer that died with COVID," says Andrew Marques, a microbiology Ph.D. student at the University of Pennsylvania's Perelman School of Medicine. "These aren't deer that died from COVID." Rather, they'd been hunted or struck by oncoming traffic. But an almost 20% COVID positivity rate is, according to Marques, lead author on the Pennsylvania findings still out for review, "absolutely stunning when we consider the positivity rate in humans," which is much lower. In Philadelphia, for instance, the positivity test rate is currently hovering 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 revealed to Marques and his collaborators that the lineages they observed seem to have spilled over from humans. Some of them resembled the delta variant at a time when delta was commonplace among people.

But others resembled alpha, the first variant of concern back in late 2020, "which is strange," Marques says. The samples were gathered months after delta had surged to become the dominant human strain. And that means that the alpha strain, which had largely disappeared in people, was still present in the environment — inside these deer. That's to say, we can't quite forget about variants no longer affecting us.

So how'd the deer catch COVID?

We don't know for sure. Marques admits, "Everything is basically speculation at the moment." So let's speculate.

It's possible there was some form of direct deer-human interaction, perhaps through people feeding the animals. Or maybe the deer drank human wastewater or untreated sewage and picked up circulating coronavirus, though Marques finds that possibility unlikely because the virus isn't typically stable for long periods of time outside the body and typical wastewater treatment would destroy viral particles. Or perhaps COVID passed through one of the known intermediate animal host species like a mink, feral cat or deer mouse.

However it happened, once COVID reached the deer, it clearly spread among the animals. In fact, certain deer behaviors may increase the ease of transmission. "Deer touch noses sometimes in a form of greeting," Marques explains. And when exhaling, deer release clouds of vapor, just as other mammals do. In humans, COVID is a respiratory disease that travels via droplets through the air. The same is likely true in deer.

As for symptoms, other researchers have reported that most infected deer tend not to have noticeable symptoms.

Did you say something about mutations?

Unfortunately, yes. Some of the viruses that Marques and his collaborators identified had picked up a few dozen mutations in their viral genetic sequence. Think of it as if you'd sub out a handful of individuals in a 30,000-person parade.

"Some of these people [might] play really important roles in the parade," Marques elaborates. "And by changing those people, that can change the ways the parade moves, the way that the parade sounds. And we can think of that as an analogy of the virus where [a relatively small number of mutations] changes the way that the virus might spread."

And I suspect this isn't just the deer in Pennsylvania?

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

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

And by sequencing the viral genomes, Mubareka and her colleagues found something unsettling. This constellation of mutations didn't stay confined to the deer. They found it in a sample from an infected person, a compelling piece of evidence that this individual had picked up the virus from deer.

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

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

Mubareka adds, "We don't want people to worry about distant and remote exposure to deer." Still, for those in closer contact with wildlife and animals, taking the proper precautions is important, which includes being vaccinated and keeping your distance. This pertains not just to 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 in an animal reservoir in the wild that we have been successful at eradicating," says Barbara Han, a disease ecologist at the Cary Institute of Ecosystem Studies. She wasn't involved with either of the two studies but says the work is critical for assessing human risk. And she isn't surprised by the results.

Han says that across mammals (and vertebrates more broadly), "We all share a version of that [ACE2] receptor that the virus is hijacking to get into our cells. But distinguishing between which species are the most likely to shed lots of virus and transmit onward is still really difficult."

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

Han says all of this work is critical for helping calculate risk. And she worries that once we see a spillover (like that of 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 in white-tailed deer but in mink and in [laboratory] deer mice — suggests to me that we now have to keep track of how it's evolving in these species and constantly update our calculations of what the risk is for humans."
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