Thursday, November 04, 2021

Two New Reports Find Widespread SARS-CoV-2 In North American Deer


While SARS-COV-2 most likely emerged from a bat host, and jumped to man via an (as yet, unidentified , intermediate species), it remains primarily a disease that infects and spreads easily among  humans (see Science Perspective: The Animal Origin of SARS-CoV-2).  

We have seen examples of reverse zoonosis - where companion animals (mainly dogs, and cats), and some captive or farmed animals (mink, big cats in zoos, etc.) have been infected - through exposure to humans.  

While a variety of other coronaviruses are known to infect, and transmit efficiently, among birds (IBV), swine (PED & TGE), and cattle (BCoV), reassuringly the evidence continues to suggest that common livestock (poultry, swine, cattle, etc.) are not particularly susceptible to SARS-CoV-2 infection (see EID Journal: Susceptibility of Domestic Swine to Experimental Infection with SARS-CoV-2).

The notable exception being mink, which are easily infected, and spread the virus efficiently (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus).

All of this matters because controlling the pandemic virus becomes far more difficult if the virus establishes itself in a non-human host.  Not only does it provide a `safe harbor' for the virus - where it is harder to eliminate using vaccines -  it can often lead to additional evolutionary pathways for the virus. 

Although the news has been generally reassuring, over the summer we saw a report from the USDA (see USDA/APHIS: White-Tailed Deer Exposed To SARS-CoV-2 Detected In 4 States) finding evidence of SARS-CoV-2 in wild deer across multiple states.  

Yesterday the full open-access report from researchers at USDA/APHIS was published in PNAS. 
SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus)

Jeffrey C. Chandler, Sarah N. Bevins, Jeremy W. Ellis, Timothy J. Linder, Rachel M. Tell, Melinda Jenkins-Moore, J. Jeffrey Root, Julianna B. Lenoch, Suelee Robbe-Austerman, Thomas J. DeLiberto, Thomas Gidlewski, Mia Kim Torchetti, and Susan A. Shriner
Widespread human SARS-CoV-2 infections combined with human–wildlife interactions create the potential for reverse zoonosis from humans to wildlife. We targeted white-tailed deer (Odocoileus virginianus) for serosurveillance based on evidence these deer have angiotensin-converting enzyme 2 receptors with high affinity for SARS-CoV-2, are permissive to infection, exhibit sustained viral shedding, can transmit to conspecifics, exhibit social behavior, and can be abundant near urban centers.
We evaluated 624 prepandemic and postpandemic serum samples from wild deer from four US states for SARS-CoV-2 exposure. Antibodies were detected in 152 samples (40%) from 2021 using a surrogate virus neutralization test. A subset of samples tested with a SARS-CoV-2 virus neutralization test showed high concordance between tests. These data suggest white-tailed deer in the populations assessed have been exposed to SARS-CoV-2.

These results indicate that some WTD examined in the four states were exposed to SARS-CoV-2. The high seroprevalence observed in multiple counties and states suggests the possibility of within-herd spread. While serological data alone cannot confirm infection, SARS-CoV-2 infection in WTD in Ohio has now been confirmed (16), supporting the findings presented herein.

An important consideration in evaluating these results is the potential for assay cross-reactivity. Testing of human serum samples with the sVNT achieved 99.93% specificity and 95 to 100% sensitivity (17), with no cross-reactivity observed for several human coronaviruses and only minor cross-reactivity between SARS and SARS-CoV-2 (1719). In contrast, no cross-reactivity has been identified for SARS-CoV-2–specific VNT for closely related human coronaviruses (1719) or animal viruses (20).

Limited research has been conducted on coronaviruses in WTD for baseline information on potential cross-reactivity. Bovine-like coronaviruses have been identified in cervids in the United States (21). However, differences in the receptor affinity of these viruses, genetic variability, and previous evaluations of serological cross-reactivity suggest limited potential for cross-reactivity to antibodies to SARS-CoV-2 (21, 22).

Several transmission routes are possible for exposure of wild deer to SARS-CoV-2. In the case of outbreaks in farmed mink, direct transmission of the virus from infected humans to mink is the only definitive transmission route identified to date (23, 24). Multiple activities bring deer into direct contact with people, including captive cervid operations, field research, conservation work, wildlife tourism, wildlife rehabilitation, supplemental feeding, and hunting (10). Wildlife contact with contaminated water sources has also been suggested as a potential transmission route (11), although transmissibility of SARS-CoV-2 from wastewater has yet to be conclusively demonstrated (25). Transmission from fomites or other infected animal species cannot be discounted.

These results emphasize the need for continued and expanded wildlife surveillance to determine the significance of SARS-CoV-2 in free-ranging deer. We also recommend SARS-CoV-2 surveillance of susceptible predators and scavengers that interact with deer. Future wildlife surveillance should be designed to detect, isolate, and genetically characterize SARS-CoV-2 and to identify potential variants, as well as other endemic coronaviruses. These methods are needed to shed light on how zoonotic pathogen spillback into novel wildlife reservoirs may affect pathogen adaptation, evolution, and transmission.

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The second report is a preprint, posted on the BioRxiv site, which comes from researchers at Penn State.  First a link and the abstract from the preprint, followed by excerpts from a press release from Penn State University. 

Suresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michelle Yon, Ruth H. Nissly, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Kurt J. Vandegrift, Costas D. Maranas, Nicole Levine, Katriina Willgert, Andrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur



Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns transmit the virus to other captive deer. 

To test the hypothesis that SARS-CoV-2 may be circulating in deer, we evaluated 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between Nov 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. 

The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive “One Health” approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.

One-Sentence Summary SARS-CoV-2 was detected in one-third of sampled White-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover events and deer-to-deer transmission.

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This press release from Penn State University. 

Deer may be reservoir for SARS-CoV-2, study finds

NOVEMBER 03, 2021

By Sara LaJeunesse

UNIVERSITY PARK, PA. — More than 80% percent of the white-tailed deer sampled in different parts of Iowa between December 2020 and January 2021 tested positive for SARS-CoV-2. The percentage of SARS-CoV-2 positive deer increased throughout the study, with 33% of all deer testing positive. The findings suggest that white-tailed deer may be a reservoir for the virus to continually circulate and raise concerns of emergence of new strains that may prove a threat to wildlife and, possibly, to humans.

“This is the first direct evidence of SARS-CoV-2 virus in any free-living species, and our findings have important implications for the ecology and long-term persistence of the virus,” said Suresh Kuchipudi, Huck Chair in Emerging Infectious Diseases, clinical professor of veterinary and biomedical sciences, and associate director of the Animal Diagnostic Laboratory, Penn State.
These include spillover to other free-living or captive animals and potential spillback to human hosts. Of course, this highlights that many urgent steps are needed to monitor the spread of the virus in deer and prevent spillback to humans.

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Although the concerns that SARS-CoV-2 could circulate in deer (or other non-human hosts), and evolve over time into a new variant - and then spill back into humans - are largely theoretical, we do have at least once instance where this has already happened. 

A full month before the B.1.1.7 (Alpha) variant was announced by the UK's Health Secretary in December 2020, Denmark was frantically trying to contain a SARS-CoV-2 variant that had arisen as the virus swept through millions of farmed mink. 
In early November of 2020, Denmark announced the discovery of a mutated SARS-CoV-2 virus in both Mink and in humans, prompting authorities to order the depopulation of 17 million mink (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus).
In response, Denmark temporarily locked down North Jutland where most of the human cases had been identified, and the UK quickly banned travel to and from Denmark.

Actually, there were multiple `mink variant's' (B.1.1.298 lineage), but only one - dubbed `Cluster 5' - appeared to pose any enhanced threat over the `wild type' COVID  (see EID Journal: SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark).  

The arrival of a more transmissible Alpha variant in December averted a mink variant crisis, but it did provide a proof of concept that a mutated SARS-COV-2 virus could evolve in another non-human species, and spill back into humans. 

A little over a month ago, in CCDC Weekly Perspectives: COVID-19 Expands Its Territories from Humans to Animals, we looked at a report from Chinese scientists who warned that the "The host expansion of SARS-CoV-2 is not over."

How that plays out is anyone's guess - but since its already happened with mink - we'd be negligent to assume it can't happen again.