Accelerated Evolution of SARS-CoV-2 in US Deer Populations

Ohio white-tailed deer carry SARS-CoV-2 and it may look very different from the variants we're worried about right now.

Transmission of SARS-CoV-2 between humans and animals and then back again is well documented in several species. The list of animals that have been documented transmitting SARS-CoV-2 to humans includes deer, mink (ferrets also), cats, and hamsters.

Zoonotic transmission is the spread of a virus between humans and animals. Numerous viruses have adapted to infect both animals and humans. Animal to human virus transmission is the most scientifically well supported likely source of initial SARS-CoV-2 infections, and there may have been two distinct animal to human transmission events in November of 2019: The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2, Pekar, J.E. et al, Science 2022

Image Credit: U.S. Government Accountability Office from Washington, DC, United States, Public domain, via Wikimedia Commons

When wildlife carries viruses that can mutate or reassort (Influenza does both) viruses continue to evolve and mutate into variants that may be highly divergent from the last version that infected the human population. This becomes problematic when the highly mutated variant is transmitted back to the human population and has changed so much that the human population’s immune system does not recognize the virus as well and does not provide protection to the new variant.

Today in Nature Communications the Bowman (Ohio State University College of Veterinary Medicine) and Nelson (National Institutes of Health) groups published a research article detailing accelerated evolution of SARS-CoV-2 in the Ohio white-tailed deer population. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer, McBride, D.S. et al, Nature Comm. 2023

The 27+ researchers that complied the study asked the question: what does SARS-CoV-2 evolution look like in a wild animal species that has been known to transmit the virus back to humans?

The group collected nasal swabs from 1522 white tailed deer in both urban and rural counties in the state of Ohio. Note: Deer all over the US and Canada have tested positive for SARS-CoV-2.

Here is what they found:

• 30 instances of human to deer transmission of SARS-CoV-2 over ~5 months (Nov. 2021 to March 2022) transmitting both the alpha and delta variant to the deer population.

• Deer had a roughly 10% positivity rate

• SARS-CoV-2 evolution occurred 3x faster in the deer population relative to the human population

• Virus evolution in deer was driven by different selection pressures and mutational biases

• Deer in both urban and rural counties tested positive for SARS-CoV-2

Fig. 1: Geographic distribution of SARS-CoV-2 in Ohio by county. Counties classified as urban are colored gray and rural counties are white. The size of circles plotted over the county centroids indicate the number of samples collected and the color scale indicates SARS-CoV-2 estimated prevalence in each county by rRT-PCR (a) and seroprevalence by surrogate virus neutralization (b). Counties that are outlined in bold borders indicate counties from which we obtained SARS-CoV-2 genomic sequences (Table S2). Counties marked with an asterisk indicate counties from which samples were collected from culled WTD as a part of population management programs (Table S1). Map created with ArcMap (ESRI) using base layers and data from Esri, Garmin, OpenStreetMap, GIS user community, Infogroup and the US Census Bureau.”

Mutations in the white tailed deer population were found to occur at 3x the rate of mutations in the human population (Fig. 4a). Notably, the time these samples were taken vaccines were widely available in the United States and it has been documented that vaccination reduces mutational frequency. In Fig. 4b, mutations in the spike protein that were distinct from the human delta variant are show in orange, the mutations distinct from the human alpha variant are show in green. The mutation L18F was positively selected for in six distinct clusters of virus spread in deer and two single positive deer. The same mutation was found in Hong Kong in hamster to human infection, and this mutation found in the human gamma variant contributed to immune evasion.

The group goes on to characterize in vitro and in vivo properties of the isolated variants from Deer, showing that the current vaccines were in fact protective from severe disease in a Syrian Golden Hamster model (a common SARS-CoV-2 model animal). And in human cells the variants were capable of infecting the cells, but some did not replicate as well as their parental variant.

Taken together, this data indicates that rapid viral evolution in wildlife populations can produce variants that have evolved to be more immune evasive and are capable of infecting humans.

Parallel evolution of SARS-CoV-2 in a different species posses a serious risk to the human population given the pathogenicity of this virus, and is a likely future source of highly divergent variants. It is also possible that as SARS-CoV-2 becomes more adapted to the wild deer population it may be less pathogenic in humans, however it is unknown which direction viral evolution will take relative to pathogenicity in humans.

Monitoring wild animal and livestock populations for possible zoonotic diseases is nothing new. A global network of laboratories that accept samples and sequence viruses to monitor for possible pandemic causing disease outbreaks has actively tracked influenza variants for decades. March 7th, 2022 the WHO issued a joint statement with the FAO (Food and Agriculture Organization), and OIE (Organization for Animal Health) re: prioritizing monitoring of SARS-CoV-2 infection in wildlife and reducing establishment of animal reservoirs, encouraging the global community to monitor animals for the development of new variants.

People often ask me if there will ever be a COVID-19 free future, with a heavy heart, the honest answer is: No.

A significant part of the reason is that we have widespread establishment of SARS-CoV-2 in wild animal populations.

It is still a tough reality to face.

I remember vividly the day in early 2021 when this became abundantly clear to me, that we would not establish herd immunity and that the world would continue down this path of infection and chronic re-infection.

As a scientist I went through stages of grief, disbelief, anger and a sick unsettled acceptance were high on that list.

Today, I sit with a sense of wistful remorse, did we really have a chance? Could we have stopped this? I believe at the very least we could have kept it at bay in a more significant way, a feat which would have required so more public will and cooperation. But scientists (a once highly trusted profession), were brutally kneecapped by those wishing to weaponize the infection by downplaying it, grifters capitalizing off of telemedicine prescriptions of snake oil, and the forces that pressed on for a “return to normal” an impossible promise. As scientists should we have tried harder to educate, screamed louder? I think perhaps, yes.

Should the government have curbed disinformation and foreign propaganda, and outright lies pedaled by grifters, MLMs… all at the risk of revolt by those who decry “Free Speech”? I think yes too, if only temporarily. However, they did not, and now those who said they would die to protect Free Speech about masks and vaccines and SARS-CoV-2, most likely will.