#16,585
While SARS-CoV-2 is believed to have emerged from a non-human host species (likely a bat) in 2019, it has become a remarkably human-adapted pathogen, sweeping the world repeatedly, and reinventing itself along the way (as Alpha, Delta, Omicron, etc.).But at the same time, COVID has also spilled over into other hosts (e.g. mink, deer, dogs, cats, etc.), raising genuine concerns that SARS-CoV-2 could follow a different evolutionary trajectory in these animal hosts, and `spill back' into humans at a later date.
Although a theoretical concern at first, in November of 2020 we saw this scenario play out in Denmark, when several new strains of COVID emerged from infected farm-raised mink, and went on to infect humans in the community (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus).
While quickly supplanted by a more aggressive Alpha variant, this accidental field experiment proved a point; humans could infect other species with COVID, and those new hosts could generate a new variant, which could jump back into humans.
More than 2 dozen non-human species have been identified as being susceptible to SARS-CoV-2 infection (includes experimentally infected animals), with deer and mink thus far the most commonly reported.
Fortunately, most farmed animals (pigs, chickens, cattle, etc.) are poor hosts for the SARS-CoV-2 virus. Dogs and cats are mildly susceptible, but since they don't have contact with hundreds of other animals, aren't as likely to generate mutations.
While there are several species in the wild that are believed capable of hosting, and spreading, SARS-CoV-2, so far North American Deer are showing the greatest promise.
Last summer North American white-tailed deer were identified as hosting the virus in multiple states (see USDA/APHIS: White-Tailed Deer Exposed To SARS-CoV-2 Detected In 4 States).
They appeared to carry the virus asymptomatically, and seemed capable of transmitting the virus to other deer, but their overall threat remained unquantified.
We've revisited this topic several times, including COVID Reservoir Roundup: Cambodian Bats, Farmed Mink In Utah & North American Deer and Two New Reports Find Widespread SARS-CoV-2 In North American Deer). In More Documented Spillovers Of COVID-19 Into North American Deer we saw evidence of new spillovers into deer with the Omicron variant.
Last fall, China's CCDC Weekly published a perspective article on the continual spread of SARS-CoV-2 from humans to other animal hosts, and warned `The host expansion of SAR-COV-2 is not over'.
All of which brings us to a new preprint by researchers at the University of Pennsylvania which presents evidence of "deer-derived alpha variants" that "diverged significantly from those in humans".
You'll want to follow the link to download the full 20-page PDF, as I've only posted the abstract and a short excerpt below. I'll have a postscript when you return.
Evolutionary Trajectories of SARS-CoV-2 Alpha and Delta Variants in White-Tailed Deer in PennsylvaniaAndrew D Marques, Scott Sherrill-Mix, John Everett, Hriju Adhikari, Shantan Reddy, Julie C Ellis, Haley Zeliff, Sabrina S Greening, Carolyn C Cannuscio, Katherine M Strelau, Ronald G Collman, Brendan J Kelly, Kyle G Rodino, View ORCID ProfileFrederic D Bushman, Roderick B Gagne, Eman Anisdoi: https://doi.org/10.1101/2022.02.17.22270679
Abstract
The SARS-CoV-2 pandemic likely began by spillover from bats to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus are infected in the United States at substantial levels, raising concerns about the formation of a new animal reservoir and potential of spill-back of new variants into humans1.
Here we characterize SARS CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 93 nasal swab samples analyzed by RT-qPCR, 18 (19.3%) were positive for SARS-CoV-2. Seven whole-genome sequences were obtained, which were annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer.
The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.
(SNIP)
In summary, a survey of SARS-CoV-2 in 93 deer in Pennsylvania over the fall-winter of 2021 showed 19% of the deer sampled to be positive. Prior surveys carried out over the fall and winter of 2020 showed similarly high point prevalence of infection in Iowa (33.2%)9 and Ohio (35.8%)10.
We report the first examples of the alpha and delta lineages in wild white-tail deer, likely derived from at least four independent spillovers from humans to deer. Given that there are estimated to be 30 deer per acre in PA, and over a million deer total, this suggests an enormous number of spillovers and infected deer in the state13,14.
Mechanisms of infection and transmission are incompletely understood. Studies of experimental infections show efficient transmission between deer, potentially involving the common practice of individuals touching noses when in groups, but the mechanism of efficient transmission from humans to deer remains obscure.
At present it is unclear to what degree SARS-CoV-2 is evolving in new directions in the deer host.
Our findings of alpha persistence in deer after replacement of alpha by delta in humans, and the divergence seen between our deer and human alpha genomes, are all consistent with long-term persistence and spread of the alpha variant in deer.
Although the emergence of another - even more problematic SARS-COV-2 variant - from deer, mink, or some other animal host is far from certain, it remains a real possibility.
As does the spillover of other bat-borne viruses (think Nipah, MERS-CoV, Hendra, Ebola, etc.) into humans (see Curr. Opinion Virology: Viruses In Bats & Potential Spillover To Animals And Humans).
To that we can add the threats from novel flu viruses, emerging pox viruses (see PLoS NTD: The Changing Epidemiology of Human Monkeypox—A potential threat?), and Virus X; the one that isn't even on our radar.
Six months ago, in PNAS Research: Intensity and Frequency of Extreme Novel Epidemics, researchers suggested that the probability of novel disease outbreaks will likely grow three-fold in the next few decades.
Which means the next global public health crisis may be much closer than we think.
