Nature: SARS-CoV-2 infection in free-ranging white-tailed deer

[NNadir]

I really shouldn't post in GD, but I'm not feeling well, can't get a Covid test, (and neither can my wife who is more ill than I am) and well, what the hell, I'm already in a bad mood, but only mildly ill, not necessarily from Covid.

This paper comes with the following disclaimer from Nature:

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

The full preliminary publication can be found here: SARS-CoV-2 infection in free-ranging white-tailed deer. The full text can be downloaded as a PDF, including graphics and experimental details. I am logged into Nature, but Nature Springer keeps Covid papers open sourced, and the full text should be available to anyone.

The authors are largely from institutions in Ohio, with some participants working at the NIH in Maryland.

I'm personally not panicked by this result; and I live in what may be in a deer festival zone, I can't go outside for more than an hour without seeing one or more deer.

I do not know if any of the deer from this report in Ohio, or the deer all over the place in New Jersey, ever went to a secret lab in Wuhan, or whether any of them bought anything at the Wuhan market, but for what it's worth, here's the report.

[hlthe2b]

1. That's the thing about infectious agents in nature. You look, you find. Its implications are likely

not what many of the lay public might think except to say there are a LOT of coronaviruses out there and susceptibility (asymptomatic or subclinical) is probably a lot wider than we'd imagine. Given how readily SARS-Cov-2 is picked up in wastewater monitoring, incidental environmental exposure to a number of species may well be more than we'd like to think. If we had sufficient resources to randomly screen the nation's pet dogs and cats in sufficient numbers, my guess is one hell of a lot of them may be seropositive for antibodies as well. Someone will undoubtedly do that sooner or later, but the penchance for the public misinterpreting potential findings would be a real deterrence.

[NNadir]

2. I saw a report a few weeks ago, possibly in Nature or Science news sections, offering...

...several theories on the source of Omicron.

Relying on memory, if I'm correct, the four were 1) in unvaccinated populations in the third world, 2) in a very sick individual, 3) in vaccinated people with a mild infection subjecting viruses to natural selection in vivo 4) re-infection from an animal species to which the virus jumped.

#3, if I'm remembering correctly, seems improbable.

I have never ascribed to the theory of a lab leak based on my reading, in particular a report from the team that went to Wuhan to evaluate potential sources.

I have always thought the most probable origin was that the infection came from a viral pool of animals, subject to mutation, and that transmission involved increased human incursion into the wilderness. Humanity is very active in the massive destruction of wilderness.

However, I am hardly an expert on virology but am only relying on impressions from general reading and my long ago participation in the development of AIDS drugs.

[femmedem]

3. Thanks, NNadir. And I hope you and your wife are feeling better soon.

Mr. Femmedem is quarantining with covid, and of course we spent a lot of time together before his symptoms started a few days ago. Fortunately, we had bought a couple boxes of home tests thinking that would be better than going out and exposing people if we ever developed symptoms. So far I'm testing negative but it's still a little early.

The thing about the deer is that I always think I'm relatively safe if I'm outside and not spending too much time in one place talking maskless to someone. But no one is standing close to deer for an extended period. It makes me wonder how likely it is for humans to catch it from each other even outside.

[NNadir]

4. Thanks. I'm not all that sick, just fatigue and a mild sore throat, digestive symptoms.

My wife is in worse condition, but improving.

I wish Mr. Femmedem a quick recovery!

I don't know where you are, but we're in New Jersey.

There are no home testing kits available here, and the NJ website for getting an appointment produces no results after hours of going through it. Apparently there was testing at a local arena, but it wasn't listed on the website. We will not be able to get tested until 2022.

My wife and son both work at Universities where testing is available, but this involves them going to work. My son is not sick...yet. My other son is a graduate student finishing up a thesis. He's home with us for the holidays.

I'm not entirely convinced it is Covid that we have. We are of course, all vaccinated and boosted; I personally felt worse after Moderna dose one, and the booster, but was fine with Moderna boost two.

My sister-in-law arrived at our home on Christmas and stayed over. Her boyfriend got sick here. The most serious symptoms involve the digestive tract for everyone involved, my sister-in-law's boyfriend, my sister-in-law (who got it after they left), my wife and myself.

My wife has been vomiting; it's a joke around here that I've only vomited once since the 1970's when I got drunk in Ensenada on 25 cent Tequila Sunrises. I've had mild nausea, but it's against my religion to throw up since Mexico in the 70's.

I've taken the week off anyway, and have been using the time to catch up with the scientific literature, including but not limited to Covid variants, since this is a current concern among us.

I'm cautiously optimistic that it won't be as bad as advertised, but I am in no way an expert or qualified to say.

As for the deer variants...

The deer variants seem to have some mutations not found in humans, but considerable homology nonetheless. That is, I think, a good thing. The best thing is that we now have technology to rapidly develop vaccines using our spectacular analytical tools, for which I credit President Clinton's efforts on the Human Genome project, which made sequencing everything, from viruses to monkeys, to potatoes to human beings relatively straight forward.

Viruses are slippery, but interesting little beings or nonbeings, and it's kind of cool that we can track them so well.

It is, as once remarked, the best of times and the worst of times. Interesting periods in history always qualify for that statement.

I hope and trust you and your family will be well, safe, and enjoy a wonderful rewarding New Year!

[femmedem]

5. Thanks for the well wishes, NNadir.

We're in Connecticut, where the omicron surge kicked in a little later than New Jersey's. It's in full force now: test positivity rate over 20% reported yesterday, with .2% of the population testing positive daily--and that doesn't include home tests, of course. (We're running low now on home tests here, too, but we bought a few tests last week, figuring we'd better have some on hand.)

What a nightmare for your family, all sick at once. I hope you'll all be joking about it years from now.

Mr. Femmedem isn't doing too badly. No digestive issues, just a very runny nose, a sore throat, now starting to cough on day 3. Mostly he is very tired. He slept for twelve hours, woke for three, fell asleep for four more. But he is vaxxed and boosted and he's in good spirits. And if he were here beside me, I'm sure he'd be joining me in wishing you and your family a happy New Year!