Did the omicron variant come from human to mouse to human migration?

[Lawyer Daggett]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702434/

This paper proposes that the variation observed in the spike
protein in Omicron is evidence of selection for viral infectivity
in mice and mutational tendencies in mice. I'm not prepared
to vouch for this hypothesis yet but it would convince me to
fund some studies to start catching South African rodents and
looking for evidence of an intermediate between Omicron and
B.1.1. I'd also be doing some detective work with older rodent
droppings to see if evidence can be found from "aged" samples.

I wonder who wants to tell that story about their PhD thesis project?

[Glenn]

"Infected rodents pose no immediate danger to humans"

https://www.nytimes.com/2021/03/31/health/coronavirus-mice-animals.html

[Zen Cycle]

Try reading the links before you post misleading headlines, sparky. Your link was published in march, and doesn't discuss the omicron variant. Daggets was published in december, and see a specific link to zoonotic transmission.

"our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak. "

[RonO]

Most of the articles that I have seen indicate that there isn't a high
chance of getting covid from infected animals. No one seems to be
worried that cats and dogs can be infected and even get sick from Covid
19. It seems obvious to me that a virus that has an airborne as well as
other contact infection routes is something that you don't want your
pets spreading around the house. There is no stretch of the imagination
that people that allow their dogs to lick their faces are in danger of
infection. If your dog gets the virus by sniffing another dogs butt,
the virus will be in your household.

Apparently the virus uses other means (different receptors) to enter the
cells of some other mammals. They can adapt to better infecting those
hosts during the infection cycle or by spreading it to others of the
same species. The latest worry is that deer in the US seem to be
spreading the virus among themselves. The next deer season or sooner
with poachers we may be getting a new strain from deer. The virus is
obviously going to be mutating in the deer population just as it does
among humans, and it will be an independently evolving lineage.

Omicron sequence is odd in that it looks like it was mutating in
isolation for a long time. It has a lot of unique mutations that
differentiate it from the original virus. I've seen speculation that it
might have been associated with long term infections, evolving a lot, or
that it reinfected a small population of humans over and over before
spreading to other populations. Having that population be another
species likely isn't out of the realm of possibility.

Ron Okimoto

[jillery]

Viral cross-species infections are well-known, among birds, among
mammals, and between birds and mammals. For a virus to cross-infect
other species, it must be able to attach to and pass through different
species' cell membranes, and then to take over those cells' chemistry
to duplicate itself. That it happens at all is evidence of how
similar all species' biochemistries are. That it happens so rarely is
evidence that even the smallest differences can prevent infection.

--
You're entitled to your own opinions.
You're not entitled to your own facts.

[Lawyer Daggett]

Come on. The cited paper includes an analysis of how the mutations in
Omicron appear to be positively selected for a better match to mouse ACE2.
They specifically modeled the structure of mouse ACE2 and the mutated
viral spike protein. Please don't go off on some silly tangent about adapting
to completely different receptors in response a paper that proposes a very
clear and direct thesis about adaption to a specific cross species ortholog.

[Ernest Major]

On 04/01/2022 12:32, RonO wrote:
> Most of the articles that I have seen indicate that there isn't a high
> chance of getting covid from infected animals.  No one seems to be
> worried that cats and dogs can be infected and even get sick from Covid
> 19.  It seems obvious to me that a virus that has an airborne as well as
> other contact infection routes is something that you don't want your
> pets spreading around the house.  There is no stretch of the imagination
> that people that allow their dogs to lick their faces are in danger of
> infection.  If your dog gets the virus by sniffing another dogs butt,
> the virus will be in your household.
>

Mink to human transmission does seem to have occurred, but the
mink-specific strain seem to have gone extinct, at least in humans.
(Provided it didn't get into wild mink populations, culling of mink will
hopefully extirpated it in that species.)

In the short term, with high rates of human to human transmission any
animal to human backtransmission of circulating strains is going to be
lost in the noise.

--
alias Ernest Major

[RonO]

I didn't claim anything that would negate any of the papers conclusions.
The other research that I have seen indicates that some other mammals
are infected not using ACE2, but covid 19 infects them some other way.
Once infected a reasonable adaptation would be to adapt to the current
host ACE2 because that is the primary means of infection in other hosts.
The sequence of the mouse ACE2 probably isn't that much different from
human.

Ron Okimoto

[*Hemidactylus*]

Well now that it’s out and about here’s someone who speaks to my heart
about OmicRon DeSantis:

https://youtu.be/zdf539e_ofk

My new hero. Ben Frazier!

[*Hemidactylus*]

One of the balcony muppets who used to post here a Mister Waldorf has
opined on this very thing.

https://sandwalk.blogspot.com/2022/01/the-effect-of-spike-protein-mutations.html

“One idea is that the ancestor of the Omicron variant jumped to another
species and evolved in that species for 18 months before jumping back into
humans. This would account for the lack of intermediates seen in screening
infected patients. Several of the key mutations in the spike protein
sequence are similar to variants that have adapted to bind to the mouse
version of the receptor (ACE2) (Sun et al. 2021) and the Omicron spike
protein binds strongly to mouse ACE2. (The original SAR-CoV-2 variants do
not infect mice.) I think it's safe to conclude (tentatively) that Omicron
evolved in mice and jumped back to humans in October or November 2021.”

He might irk Racaniello with talk of transmissibility. Could it be…fitness.
Larry can’t be neutral on that right?

Also a thumb in the eye of that John Campbell guy:
“There's a lot of speculation that the Omicron variant causes less severe
forms of COVID-19 but the data is complicated by the fact that vaccinated
and convalescent patients are also suffering from COVID-19 and they are
partially protected. I don't think it's really known whether naive
(unvaccinated and not previously infected) individuals have a milder form
of the disease and I know we don't have any data on the long-term effect of
Omicron infection. Please let me know of any studies that have been
released.”

Long term effects in the naive? Good point.

[jillery]

On Wed, 05 Jan 2022 19:16:05 -0600, *Hemidactylus*
<ecph...@allspamis.invalid> wrote:

>Also a thumb in the eye of that John Campbell guy:
>“There's a lot of speculation that the Omicron variant causes less severe
>forms of COVID-19 but the data is complicated by the fact that vaccinated
>and convalescent patients are also suffering from COVID-19 and they are
>partially protected. I don't think it's really known whether naive
>(unvaccinated and not previously infected) individuals have a milder form
>of the disease and I know we don't have any data on the long-term effect of
>Omicron infection. Please let me know of any studies that have been
>released.”

<https://www.whitehouse.gov/briefing-room/press-briefings/2022/01/05/press-briefing-by-white-house-covid-19-response-team-and-public-health-officials-77/>

<https://tinyurl.com/2p8ryu5m>

Note the date of this briefing is the same as your post above.

Short version: Data from South Africa, United Kingdom, and Canada (Hi
Larry) all show deaths and significant effects from Omicron are much
less than from previous variants. That's Good New(c) for those who
contract it.

So thumb in the eye back atcha.

However, the Omicron variant is far more transmissible, which makes
its impact on healthcare systems far worse than previous variants. As
of this post, 854,000 USians have died of Covid-19.

Even for those who think Covid-19 doesn't justify the "hysteria", the
fact remains hospitals can't provide other treatments when their bed
are filled with Covid-19 patients. The issue is, was, and always will
be, that pandemic countermeasures are necessary to prevent
overwhelming healthcare systems.

[Öö Tiib]

As every 13th USian seems currently counted as "active case" it looks
more like strategy to gain herd immunity by going through of it
rather than trying to be saving towards healthcare system.

[jillery]

On Wed, 19 Jan 2022 13:23:22 -0800 (PST), Öö Tiib <oot...@hot.ee>
wrote:

Who did the counting to get your statistic? Wikipedia claims only 1.4
million total Covid-19 cases in the U.S since Jan. 2020, which isn't
remotely close to 1 in 13 *active* cases.

As for "strategy", it's more a case of realities imposing consequences
on people. With Omicron leaping past pandemic isolation, and about
half the population acting as if the risk of dying from Covid-19 is
less than the risk of Bill Gates controlling their minds, it may very
well turn out that enough people will ultimately get that "natural
immunity" they claim is better than vaccinations.

[Öö Tiib]

How can it be that 0.88 millions did die from 1.4 total? That makes
62.8% lethality?
<https://www.worldometers.info/coronavirus/country/us/>
Says that almost 70 millions total and 25 millions active.
I thought U.S. itself reports it.

[jillery]

On Wed, 19 Jan 2022 17:06:44 -0800 (PST), Öö Tiib <oot...@hot.ee>

I acknowledge I read and quoted the wrong chart. I regret my error.

[Matt Beasley]

, ootlib wrote:

> jillery wrote:
> > >>
> > >As every 13th USian seems currently counted as "active case" it looks
> > >more like strategy to gain herd immunity by going through of it
> > >rather than trying to be saving towards healthcare system.
> > Who did the counting to get your statistic? Wikipedia claims only 1.4
> > million total Covid-19 cases in the U.S since Jan. 2020, which isn't
> > remotely close to 1 in 13 *active* cases.
> How can it be that 0.88 millions did die from 1.4 total? That makes
> 62.8% lethality?
> <https://www.worldometers.info/coronavirus/country/us/>
> Says that almost 70 millions total and 25 millions active.
> I thought U.S. itself reports it.

-------
Yeah, we're adding one billion people every 12 years,
and wildlife numbers are down 50-60% in the last
50-60 years! That's not justice; that's JUST US!
--
--

[Bob Casanova]

On Thu, 20 Jan 2022 22:16:26 -0800 (PST), the following
appeared in talk.origins, posted by Matt Beasley
<less...@gmail.com>:

>...we're adding one billion people every 12 years,

>and wildlife numbers are down 50-60% in the last
>50-60 years! That's not justice; that's JUST US!
>

AAAHHHHH!!! We're all DOOMED! DOOMED! Genuflect to Gaia! And
run away! Run away!

Piss off.
>
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Athel Cornish-Bowden]

I spent the first few days of this week in hospital. We wanted a single
room (and were ready to pay 78€ per night for it), but were told that
all the single rooms were needed for Covid-19 patients.

> The issue is, was, and always will
> be, that pandemic countermeasures are necessary to prevent
> overwhelming healthcare systems.


--

Athel -- French and British, living mainly in England until 1987.

[jillery]

>> are filled with Covid-19 patients. The issue is, was, and always will

>> be, that pandemic countermeasures are necessary to prevent
>> overwhelming healthcare systems.
>
>I spent the first few days of this week in hospital. We wanted a single
>room (and were ready to pay 78€ per night for it), but were told that
>all the single rooms were needed for Covid-19 patients.

You don't say why you went to hospital, but apparently you were not a
Covid-19 patient. If you went for what some call "elective therapy",
you were lucky to be admitted at all. Perhaps it would be better if
Covid-19 patients were placed in a common isolation ward, like used to
happen with polio patients.

I hope you're better now than you were before you went to hospital.