COULD DEER BECOME A NATURAL COVID RESERVOIR?
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Researchers prepare to swab a white-tailed deer in College Station, Texas, to check for SARS-CoV-2.
COULD DEER BECOME A
NATURAL COVID RESERVOIR?
Hundreds of white-tailed deer in North America have tested positive for
SARS-CoV-2. Here’s why scientists aren’t panicking, yet. By Smriti Mallapaty
T
SERGIO FLORES/THE NEW YORK TIMES/REDUX/EYEVINE
esting deer for SARS-CoV-2 is a little meat-processing site or a butcher’s shop, In between estimating a deer’s age by
different from testing humans. The waiting to be turned into hamburgers, checking teeth and taking antler measure-
cotton swabs travel just a bit farther sausages, steaks, chops and more. ments, researchers wearing masks and gloves
into the animals’ cavernous nasal Researchers have worked with hunters wipe mud and grass from around the animal’s
passages, for example. “We’ll run for decades as part of regular wildlife sur- nostrils before inserting a swab to test for
out of swab before we, you know, hit veillance to manage deer populations and viral RNA. They then collect blood to check
anything,” says Andrew Bowman, a track the spread of infectious diseases, such for antibodies against the virus. Their work
veterinary epidemiologist at Ohio as chronic wasting disease and bovine tuber- has uncovered widespread infection in white-
State University in Columbus. culosis. But these days, the scientists are also tailed deer (Odocoileus virginianus) in North
And the deer in question are often looking for the virus that causes COVID-19 America, with hundreds of infected animals in
dead, in the back of a hunter’s truck, at a in humans. 24 US states and several Canadian provinces.
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Scientists want to understand how the virus DEER DETECTION
gets into deer, what happens as it spreads Nasal samples taken in Ohio from January to March 2021 revealed 129 out of 360 white-tailed
deer (Odocoileus virginianus) were positive for SARS-CoV-2. The recovered viral sequences
among them, and what risk these infections
resembled some of the strains that were circulating in local human populations at the time.
might pose for other wildlife and for humans.
Close to 30 million deer live in the United B.1 B.1.1.7 (Alpha) B.1.2 B.1.596 Other
States — one for every 10 people — and a few 80,000
million live in Canada.
Several teams have cobbled together the
funding to survey deer, says Samira Mubareka,
Weekly COVID-19 cases in humans, Ohio
a virologist at Sunnybrook Research Institute
in Toronto, Canada. 60,000
“We’ve mobilized an army of students,” says
Bowman.
The variants researchers found circulating
in deer typically mirror those spreading in 40,000
humans who live nearby, but some studies
suggest that SARS-CoV-2 in the wild could
already be exploring fresh avenues of evolu-
tion through mutations that alter the virus.
It’s not yet clear whether the virus can 20,000
spread in long chains of infection among
deer, or whether deer-to-human transmis-
sion could spark outbreaks. But researchers
are growing increasingly concerned about the
0
animals becoming a viral reservoir, serving as Dec Jan 2021 Feb Mar Apr
a recalcitrant source of outbreaks and poten-
tially breeding new variants. Some research-
ers think that the highly infectious Omicron
variant spent time in an animal reservoir
Sequence sleuthing
before popping up in people. Fourteen SARS-CoV-2 sequences recovered from
So far, infected deer aren’t turning up very infected deer in Ohio included six in late February that
SOURCE: REF. 3
unwell, but they could spread the infection seemed to be the result of deer-to-deer transmission.
to livestock or other wildlife that might be Human Deer
more vulnerable. And that’s a major worry.
“Once it gets into wildlife,” says Marietjie and goats, are fairly resistant to infection, samples from deer to test for SARS-CoV-2
Venter, a medical virologist at the University says William Karesh, chair of the Paris-based using the polymerase chain reaction — a pos-
of Pretoria in South Africa, “there is basically World Organisation for Animal Health work- itive result would be direct proof that the ani-
no way at the moment to control it.” ing group on wildlife. mals were infected. But until December 2020,
Thomas DeLiberto, SARS-CoV-2 coordi- “we were getting all negative samples”, says
Multiple outbreaks nator in the Wildlife Services programme of Vanessa Hale, an animal-health researcher at
Researchers have been concerned about the USDA Animal and Plant Health Inspection Ohio State University. Everything changed
wildlife infections since the beginning of the Service in Fort Collins, Colorado, says that the in the new year3. She and Bowman found
COVID-19 pandemic, but tracking the move- study was an eye-opener. “We said, ‘Well, we 129 deer that were positive for SARS-CoV-2
ments of such a promiscuous virus is tricky. better look and see if we’ve had exposure in viral RNA among about 360 animals sampled
To target surveillance efforts, they started by wild white-tailed deer.’” in Ohio between January and March 2021.
looking at ACE2, a host-cell protein that the DeLiberto and his colleagues started Suresh Kuchipudi, a virologist at Pennsyl-
virus typically uses to enter cells. Animals with 385 blood samples collected from deer vania State University in University Park, and
with an ACE2 receptor similar to that found in between January and March 2021, as part of his colleagues got a similar rate of positive
humans were considered at risk. Teams around regular wildlife disease-surveillance efforts tests in Iowa4. Of the 283 deer tested between
the world then began experimentally infecting across Illinois, Michigan, New York and April 2020 and January 2021, 33% were posi-
those animals to see whether they were suscep- Pennsylvania. Roughly 40% of the samples tive for SARS-CoV-2. Most of these turned up
tible and could pass the infection along. Among contained antibodies against SARS-CoV-2. in November and December 2020, coinciding
the prospects were cats, deer mice (Peromyscus The findings2, first reported in a July preprint with a peak in human infections.
maniculatus) and raccoon dogs (Nyctereutes last year, suggested that the deer had been Genome sequencing of more than half of
procyonoides), as well as white-tailed deer. exposed, but it wasn’t clear whether these the samples from infected Ohio deer revealed
In early January 2021, researchers at the US were one-off exposures or whether the virus variants similar to those circulating in human
Department of Agriculture (USDA) showed had spread among the animals. It was also communities across the state at the time3
that fawns in captivity could be infected with possible that the antibodies were the result (see ‘Deer detection’). It seemed that the
SARS-CoV-2, shed it in their nasal mucus and of other coronavirus infections in deer. virus had spilled over from humans on six
faeces, and spread the infection to other These results led to a slew of fresh separate occasions. Mutations in the genetic
fawns in adjacent pens1. Within a week, the deer-sampling efforts across North America, sequences also confirmed that the deer were
animals began producing antibodies against and a rush to publish the results of sampling spreading the infection among themselves.
the virus, but none was particularly ill. projects already under way. Since then, researchers have found positive
The results were “somewhat surprising”, In the first year of the pandemic, scientists deer in 24 of the roughly 30 US states where
because other ungulates, such as cows, sheep had begun to collect nasal swabs and blood sampling has been reported — as well as in
Nature | Vol 604 | 28 April 2022 | 613
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the Canadian provinces of Quebec5, Ontario6, direct contact in any of these scenarios to Occasionally, a doe might also go on an
Saskatchewan, Manitoba, New Brunswick and account for the hundreds of cases detected excursion of up to 100 kilometres, possibly
British Columbia, although the Canadian pos- so far, let alone the countless more that just “to visit family or friends”, returning days
itivity rates have been lower, at 1–6%. haven’t been recorded. or weeks later to her usual territory, says
In late December 2021, researchers found Another route of SARS-CoV-2 infection Tonkovich. And during heavy snow in some
the highly transmissible Omicron variant in could be environmental. Although transmis- northern states, groups of deer sometimes
white-tailed deer living in Staten Island, a part sion through contaminated surfaces has not travel to ‘deer yards’, where thick tree cover
of New York City7. And in March 2022, a mule been an established route in people, deer prevents snow from accumulating on the
deer (Odocoileus hemionus) in Utah tested could be picking the virus up by digging their ground and where they might encounter
positive for SARS-CoV-2. other groups. All of this time, the animals
The epidemic seems to be confined to are interacting and potentially spreading the
North America. “No one’s detected it in Euro- virus. There’s a lot of “nose-to-nose contact
pean deer so far, despite a lot of looking,” says among deer”, says Linda Saif, a virologist at
NO ONE’S DETECTED
Rachael Tarlinton, a veterinary virologist at the Ohio State University in Wooster.
University of Nottingham, UK. For example, All of the potential for viral spread has
IT IN EUROPEAN DEER
Alex Greenwood, an evolutionary virologist scientists concerned that deer could become
at the Leibniz Institute for Zoo and Wildlife a SARS-CoV-2 reservoir — a permanent home
Research in Berlin and his colleagues tested
roe deer (Capreolus capreolus), red deer SO FAR, DESPITE A for the virus and a regular source of out-
breaks in other animals, including humans.
(Cervus elaphus) and fallow deer (Dama dama)
in Austria and Germany8, and none of them
had SARS-CoV-2.
LOT OF LOOKING.” Camels, for example, are a natural reservoir
of the MERS-CoV coronavirus that causes
Middle East respiratory syndrome, which
Researchers say biological differences don’t occasionally jumps to people. Once estab-
seem to explain the discrepancy. “All the data noses into discarded masks, or gobbling flow- lished in deer, SARS-CoV-2 could mutate,
on ACE2 receptors suggest European deer ers and garden vegetables that humans have evolve and possibly recombine with other
species should be as susceptible as white- sneezed on, for instance. Hunters sometimes coronaviruses, says Saif. And it could evolve
tailed deer,” says Tarlinton. Rather, the North also feed and bait deer using maize (corn) or to better infect other grazing animals such
American epidemic seems to be the result of vegetables, which could be covered in virus. as sheep, goats and cows that share pastures
the high density of deer there, and people’s But Hale points out that the deer would have with deer, she says. “Once you have a single
frequent interactions with them. to arrive at just the right time to ingest infec- wild-animal reservoir, it’s conceivable it can
“In the Americas, the deer basically walk tious virus. “Is it possible? Yes. Is it likely? pass over to other wildlife, or even domestic
around wild, in people’s backyards,” says Again, I don’t know.” livestock.”
Venter, who adds that interactions with large Another route might be contaminated There is increasing evidence for that. The
ungulates are much less common where she waste water that trickles into the animals’ virus is showing signs of long-term evolution
works. “In Africa, mostly animals would be in water sources. Although many studies have in deer, for example. In a February preprint6,
wildlife reserves.” found viral RNA in sewage, they haven’t iso- Mubareka and her colleagues sequenced five
lated infectious SARS-CoV-2. Also, it’s not just SARS-CoV-2 genomes from deer sampled in
Human intervention urban deer that are getting infected; some live Ontario in November and December 2021.
How deer are getting infected remains a in the middle of nowhere, say researchers. The viruses had 76 mutations compared
mystery. “There’s a window open somewhere Other animals such as feral cats or wild mink with the original SARS-CoV-2 virus isolated
and we have no idea what it is,” says Bowman. could serve as a go-between for transmission, in Wuhan, China, including some that contrib-
Humans are known to spread pathogens in according to some reports. ute to amino-acid changes in the spike protein
the wild, such as the bacterium Escherichia “All of these things seem far-fetched until that the virus uses to infect cells. Such muta-
coli, the measles virus and the protozoan we can prove them,” says Hale. But there tions have been key to the success of highly
Giardia, among others. But these anthro- doesn’t have to be one single source of infec- transmissible variants.
ponotic jumps, or ‘spillbacks’, rarely result in tion, says Mubareka. Multiple routes are prob- The closest known relatives the research-
sustained transmission, if ever. ably involved. ers could find for these viral genomes were
Direct contact, for example when people from people in Michigan almost a year earlier.
pet or hand-feed animals, could be a culprit. Nose-to-nose The results suggested that the virus had been
White-tailed deer live in close proximity Once one deer catches the virus, there are spreading in animals for a long time. “It was
to people in towns and cities across North plenty of opportunities for SARS-CoV-2 to crazy. Honestly, I couldn’t believe it,” says
America — the deer live near to houses, spread in the broader population. White- Mubareka, adding, “The fact that we found
roam the streets and explore university cam- tailed deer are very social animals, says it with such sparse sampling, you really have
puses. “They’ve done very well to adapt to the Tonkovich. For most of the year, bucks live to wonder what else is going on?”
human-dominated landscape,” says Michael in loose bachelor groups of up to six, groom- A second preprint in February 9 found
Tonkovich, who oversees the deer programme ing and sparring with each other. Matriarchal the Alpha and Delta SARS-CoV-2 variants in
at the Ohio Department of Natural Resources does live with several generations of their Pennsylvania deer in November 2021. The
in Athens. female offspring and fawns. The animals Alpha genomes were distinct from those
Deer are farmed for meat in some US states, typically stick to their home ranges of several found in people, and were found in deer
and others have rehabilitation programmes square kilometres, but this all changes during months after Delta had become the dom-
for fawns orphaned by car accidents. Deer the breeding season: the winter months from inant human-infecting variant, suggesting
in captivity can have frequent contact with around October to February. that Alpha had been evolving independently
humans and with wild deer, or they could Bucks can travel several tens of kilometres, in the deer population.
escape or be released back into the wild. moving between groups of does and lock- Mubareka and her colleagues made
But Hale says there probably isn’t enough ing antlers with other bucks along the way. another unexpected finding: a viral sequence
614 | Nature | Vol 604 | 28 April 2022
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.DONALD M. JONES/NPL
An estimated 30 million deer live in the United States. They have adapted well to living around humans.
in a person from southwestern Ontario that experimental infection studies to see whether
was very similar to the viral genomes found in variants such as Omicron and Delta behave
deer6. Although the evidence is not definitive, differently in white-tailed deer, and what
IF THE ANIMALS ARE
scientists suspect that the person might have other wild animals are susceptible. They’ve
caught the virus from deer. found10 that red foxes (Vulpes vulpes) are, but
ABLE TO BE REINFECTED,
Deer-to-human transmission, if confirmed, not coyotes (Canis latrans), and they want to
would be concerning, as would reinfection look at mule deer and elk. They might also
among deer — something Kuchipudi might
have observed. From sampling this past JUST LIKE PEOPLE, try mixed-species studies, to see whether,
for example, mink can spread the infection
December and January, he identified a deer
infected with Omicron that also had antibodies THEN THE VIRUS to rodents.
A lot more work is needed to track these
against Delta7. “If the animals are able to be rein-
fected, just like people, then the virus will not
fade out; it will continue to circulate,” he says.
WILL NOT FADE OUT.” rapidly unfurling events, says Mubareka.
“These are just the early chapters.”
Researchers say there’s not enough evi- Smriti Mallapaty writes for Nature from
dence yet to indicate whether deer are a researchers have embarked on longitudinal Sydney, Australia.
breeding ground for dangerous variants. studies in which they revisit sampling sites
1. Palmer, M. V. et al. J. Virol. 95, e00083-21 (2021).
Karesh says he would need to see many more over several hunting seasons. 2. Chandler, J. C. et al. Proc. Natl Acad. Sci. USA 118,
spillover events — to people from deer — to In March 2021, the USDA received a e2114828118 (2021).
call them a reservoir for human infection. US$300-million grant to survey animals 3. Hale, V. L. et al. Nature 602, 481–486 (2022).
4. Kuchipudi, S. V. et al. Proc. Natl Acad. Sci. USA 119,
Bryan Richards, a wildlife biologist and susceptible to SARS-CoV-2, and has sampled
e2121644119 (2022).
emerging-disease coordinator at the US Geo- deer through the 2022 hunting season in at 5. Kotwa, J. D. et al. Preprint at bioRxiv
logical Survey National Wildlife Health Center least 27 states. DeLiberto says his group plans https://doi.org/10.1101/2022.01.20.476458 (2022).
in Madison, Wisconsin, agrees that deer don’t to study footage of how deer interact with 6. Pickering, B. et al. Preprint at bioRxiv
https://doi.org/10.1101/2022.02.22.481551 (2022).
yet seem to pose a risk. “Out of millions of people and other animals to quantify their 7. Vandegrift, K. J. et al. Preprint at bioRxiv
humans who interacted with deer, hunting modes of engagement. And Richards says https://doi.org/10.1101/2022.02.04.479189 (2022).
this last year, we now know of a grand total more sampling to determine which types of 8. Moreira-Soto, A. et al. Microorganisms 10, 748 (2022).
9. Marques, A. D. et al. Preprint at medRxiv
of one that may have been infected,” he says. deer are at highest risk — bucks or does, urban
https://doi.org/10.1101/2022.02.17.22270679 (2022).
Truly understanding the situation will or rural — could offer further clues. 10. Porter, S. M. et al. Preprint at bioRxiv
require more sampling of animals. Some Scientists are also planning more https://doi.org/10.1101/2022.01.27.478082 (2022).
Nature | Vol 604 | 28 April 2022 | 615
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