CoVid in US deer going its own way

[url]https://www.researchsquare.com/article/rs-2574993/v1[/url] or https://www.researchsquare.com/article/rs-2574993/v1;

While SARS-CoV-2 has sporadically infected a wide range of animal species worldwide1, the virus has been repeatedly and frequently detected in white-tailed deer in North America2–7. 

The zoonotic origins of this pandemic virus highlight the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. 

Here, we detected SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. 

Subsequently, deer-to-deer transmission persisted for 2-8 months, which disseminated across hundreds of kilometers. 

We discovered that alpha and delta variants evolved in white-tailed deer at three-times the rate observed in humans. 

Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only faster in white-tailed deer but driven by different mutational biases and selection pressures. 

White-tailed deer are not just short-term recipients of human viral diversity but serve as reservoirs for alpha and other variants to evolve in new directions after going extinct in humans. 

The long-term effect of this accelerated evolutionary rate remains to be seen as no critical phenotypic changes were observed in our animal model experiments using viruses isolated from white-tailed deer. 

Still, SARS-CoV-2 viruses have transmitted in white-tailed deer populations for a relatively short duration, and the risk of future changes may have serious consequences for humans and livestock.

DJ, I put the most serious concern in bold...

[url]https://www.wormsandgermsblog.com/2022/02/articles/animals/other-animals/are-deer-strains-of-sars-cov-2-emerging/[/url] or https://www.wormsandgermsblog.com/2022/02/articles/animals/other-animals/are-deer-strains-of-sars-cov-2-emerging/ almost a year old...

One thing we’ve been watching for with SARS-CoV-2 in animals is whether we will see establishment of “animal” variants. Humans have done an effective job of infecting a wide variety of animal species with this primarily-human virus. Fortunately, thus far these infections usually die out rapidly in that animal or group of animals (mink being a notable exception). In that scenario, the broader implications of spillover into animals are limited, because there’s not enough long-term transmission for animals to become true reservoirs or for new variants to emerge.

White-tailed deer have been a particular concern lately because they are quite susceptible to infection with SARS-CoV-2, they can spread the virus effectively deer-to-deer, and they live in large enough groups that the virus could potentially be maintained in the deer population even without regular contact with infected people.

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The good news aspect of the low prevalence is offset by some bad news about the genetic makeup of the viruses that were found. Sequence analysis was only possible for a subset of positive samples. (There can be various reasons for that. Most often, it’s because there’s enough virus to yield a positive PCR result but not enough to be able to get good sequencing data). Using a couple of techniques, they ultimately managed to get full sequence data from 5 samples and partial genomes from 2.  The deer SARS-CoV-2 viruses belonged to the B1 lineage, which encompasses a wide group of common strains. However, the deer samples formed their own group that was very different from other reported sequences in B1 lineage, with the closest “relatives” being sequences from people collected in Michigan in November/December 2020 (where they had also seen spillover into the deer populations there)

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Potential deer-to-human transmission

Another noteworthy aspect of this report is information about a potential deer-to-human transmission event. One human sample from Ontario from December 2021 was found with most (80 of 90) of the same mutations and was consistent with this deer-group of viruses. It wasn’t possible to say where this strain fit into the timing of viral evolution, i.e. was it a step along the way of the progression to the deer lineage, or was it derived from a deer strain?  The human sample pre-dates the deer sampling, but we have to be careful interpreting timing of deer samples because collection occurs during a defined time of year: hunting season. So, while these strains were first found in deer in samples from November/December 2021, we have to assume that they were present earlier. There’s also a plausible epidemiological link between the infected person and deer, as there was known “close contact” with deer.  Note: that’s contact with deer, not the known-positive deer.  Further details of the “close contact” were not provided.

This gets us back to the “chicken vs egg” discussion.  Did this person get infected from deer, or were they a source of infection for deer?  Until December 2021, virtually all PCR-positive samples in Ontario were being sequenced, so it’s unlikely this strain was emerging in people in a lead up to a spillover into deer. There was less testing (and sequencing) in humans in late 2021 as the omicron surge overwhelmed testing capacity in Ontario.

Have there been more human cases of this strain?

• That’s hard to say, since this was a very recent observation in deer and the risk of spillback into people was probably most likely during the recent hunting season. Omicron blasted through Ontario at the same time, and there were severe limitations in testing. At that point only a minority of people got tested, particularly of otherwise healthy people from the community (who would be at greatest likelihood of deer exposure). There’s currently no evidence of onward human-to-human spread, but we have to realize that surveillance decisions made by the province impact the ability to detect spread of new variants.

I won’t get much into the genomics themselves, since this post is pretty long and the story above is the key. More details about these new finding are in the paper. However, the quick version is that many of the mutations that were found in the strains from the deer are consistent with those found in animals such as bats, cats, hamsters, mink and, yes, other deer. When a virus jumps to a different host, we can see some more common genetic changes as it adapts to that new species.

Ultimately, to answer these and other questions, we need more samples from deer from different areas and over time, and more comparison with human-derived virus sequences. The current story is based on a small number of samples from a narrow window in time, but the story is pretty compelling and concerning.

If this is truly a deer strain of SARS-CoV-2, what does that mean?

That’s still hard to say. The big question is what happens over time.  Will this strain (or others) be maintained in deer? If so, will deer become a true reservoir, where they can then potentially infect people and other animals?

The “other animals” component is often neglected, but it’s important. If deer are a reservoir, they could spread it to other potential reservoir species, amplifying the problem. They could also spread it to other susceptible species that are not likely to become reservoirs based on numbers and population dynamics, but that have closer contact with people. For example, we’re not going to see a reservoir in domestic cats because there’s not much chance of sustained cat-to-cat spread in most situations. However, cats are highly susceptible and indoor-outdoor cats have abundant contact with wildlife (including deer) so they could plausibly be a bridge from wildlife reservoirs to people.

A closing piece of good news is that it looks like these deer variants are as effectively neutralized by vaccine antibodies as other lineages.

DJ, Vaccination by now is limited to only high risk groups...Level of (rural) vaccination -in general- may be low. So deer-SARS-2 may be a growing risk in rural areas with urban population still higher level of vaccinations...

Of course most of the risks could be in "deer-CoViD" spreading into other wildlife...carnivors, but also via "droppings/urine"...