Sunday, December 26, 2021

Nature: SARS-CoV-2 Infection in Free-ranging White-tailed Deer



Although SARS-CoV-2 emerged from a non-human host species (likely a bat), it has become a remarkably human-adapted pathogen, and has swept the globe repeatedly over the past 2 years.

 It is not exclusively a human disease, however, as we've seen that other species - including dogs, cats, mink, and deer - are susceptible to infection. 

Of these, mink and deer appear to be the most susceptible, although other species - not yet identified - could be equally so.  We've also seen evidence that new variants may have expanded COVID's host range (see PrePrint: The B1.351 and P.1 Variants Extend SARS-CoV-2 Host Range to Mice).

The concern is these non-human hosts could provide COVID with an alternate evolutionary path, and allow for the creation of new, potentially more dangerous variants, that could spill back into humans

And a little over a year ago - just before the Alpha variant emerged - discovery of a mink COVID variant infecting humans was the world's biggest pandemic concern. 

ECDC Rapid Risk Assessment: Detection of New SARS-CoV-2 Variants Related to Mink

EID Journal: SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark

WHO 2nd Update: SARS-CoV-2 mink-associated variant strain – Denmark 

The emergence of the Alpha variant quickly overpowered, and supplanted, Denmark's mink variant - but it's emergence and spill-back into humans serves as a proof-of-concept - and there are indications that similar mink-to-human transmission may have occurred in other countries. 

The good news - so far - is that most 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 one known exception is deer, which last summer 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 appear to be infected asymptomatically, and seem 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). 

Late last week the Journal Nature published an early version of a study on active SARS-CoV-2 infection in American White-Tailed Deer.  We've the abstract, and excerpts form a press release from Ohio State University on their findings. 

Published: 23 December 2021
Humans have infected a wide range of animals with SARS-CoV-2 viruses1–5, but the establishment of a new natural animal reservoir has not been observed. Here, we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2 virus, are exposed to a range of viral diversity from humans, and are capable of sustaining transmission in nature.
SARS-CoV-2 virus was detected by rRT-PCR in more than one-third (129/360, 35.8%) of nasal swabs obtained from Odocoileus virginianus in northeast Ohio (USA) during January-March 2021. Deer in 6 locations were infected with 3 SARS-CoV-2 lineages (B.1.2, B.1.582, B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. Probable deer-to-deer transmission of B.1.2, B.1.582, and B.1.596 viruses was observed, allowing the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are infrequently seen in humans.
No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have the capacity to transmit in US wildlife, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive “One Health” programs to monitor deer, the environment, and other wildlife hosts globally.

          (Continue . . . )


Dec 23, 2021

COVID-19 infection detected in deer in 9 Ohio locations

Scientists unsure if wild deer could be SARS-CoV-2 virus reservoir

Emily Caldwell Ohio State News
Scientists have detected infection by at least three variants of the virus that causes COVID-19 in free-ranging white-tailed deer in six northeast Ohio locations, the research team has reported.

Previous research led by the U.S. Department of Agriculture had shown evidence of antibodies in wild deer. This study, published today in Nature, details the first report of active COVID-19 infection in white-tailed deer supported by the growth of viral isolates in the lab, indicating researchers had recovered viable samples of the SARS-CoV-2 virus and not only its genetic traces.

Based on genomic sequencing of the samples collected between January and March 2021, researchers determined that variants infecting wild deer matched strains of the SARS-CoV-2 virus that had been prevalent in Ohio COVID-19 patients at the time. Sample collection occurred before the Delta variant was widespread, and that variant was not detected in these deer. The team is testing more samples to check for new variants as well as older variants, whose continued presence would suggest the virus can set up shop and survive in this species.

The fact that wild deer can become infected “leads toward the idea that we might actually have established a new maintenance host outside humans,” said Andrew Bowman, associate professor of veterinary preventive medicine at The Ohio State University and senior author of the paper.

“Based on evidence from other studies, we knew they were being exposed in the wild and that in the lab we could infect them and the virus could transmit from deer to deer. Here, we’re saying that in the wild, they are infected,” Bowman said. “And if they can maintain it, we have a new potential source of SARS-CoV-2 coming in to humans. That would mean that beyond tracking what’s in people, we’ll need to know what’s in the deer, too.

“It could complicate future mitigation and control plans for COVID-19.”

A lot of unknowns remain: how the deer got infected, whether they can infect humans and other species, how the virus behaves in the animals’ body, and whether it’s a transient or long-term infection.

          (Continue . .  )

Last September, 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 might affect the future course of COVID in humans is anyone's guess - but since its already happened with mink - we'd be negligent to assume it can't happen again.