Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern" & BA.2 sub-variant, XE

[Emily]

I don't think we know for sure yet where it emerged.

[sharon sanders]

Fauci says early reports encouraging about omicron variant


U.S. health officials said Sunday that while the omicron variant of the coronavirus is rapidly spreading throughout the country, early indications suggest it may be less dangerous than delta, which continues to drive a surge of hospitalizations.

President Joe Biden's chief medial adviser, Dr. Anthony Fauci, told CNN's “State of the Union” that scientists need more information before drawing conclusion's about omicron's severity.

Reports from South Africa, where it emerged and is becoming the dominant strain, suggest that hospitalization rates have not increased alarmingly.

more...

https://www.clickorlando.com/news/national/2021/12/05/fauci-says-early-reports-encouraging-about-omicron-variant/

[blacknail]

It is a startling phrase, however, the study shows that the partially vaccinated people had higher viral loads than the fully vaccinated people, and that a high proportion of the deceased were immunocompromised. Given all that, I don't think they are saying there is any direct evidence of ADE, just something that needs further study.

[Chicagogal]

Saw a startling phrase this morning:

https://www.medrxiv.org/content/10.1101/2021.12.03.21267155v1

High viral loads: what drives fatal cases of COVID-19 in vaccinees? an autopsy study

Klaus Hirschbuehl, Tina Schaller, et al View ORCID

Background: The rate of SARS-CoV-2 breakthrough infections in vaccinees is becoming an increasingly serious issue. Objective: To determine the causes of death, histological organ alteration, and viral spread in relation to demographic, clinical-pathological, viral variants, and vaccine types.

Results: Autopsies were performed on 16 partially and 13 fully vaccinated individuals. Most patients were elderly and suffered from several relevant comorbidities. Real-time RT-PCR (RT-qPCR) identified a significantly increased rate of generalized viral dissemination within the organism in vaccinated cases versus nonvaccinated cases (45% vs. 16%, respectively; P = 0.008). Vaccinated cases also showed high viral loads, reaching Ct values below 10, especially in the upper airways and lungs. This was accompanied by high rates of pulmonal bacterial or mycotic superinfections and the occurrence of immunocompromising factors such as malignancies, immunosuppressive drug intake, or decreased immunoglobulin levels. All these findings were particularly accentuated in
partially vaccinated patients compared to fully vaccinated individuals. A fatal course after vaccination occurred in only 14% of all COVID-19 deceased in Augsburg. Limitations: Restricted number of cases Conclusions: Fatal cases of COVID-19 in vaccinees were rare and often associated with severe comorbidities or other immunosuppressive conditions. Interestingly, we observed striking virus dissemination in our case study, which may indicate a decreased ability to eliminate the virus in patients with an impaired immune system. However, the potential role of antibody-dependent enhancement must also be ruled out in future studies.

If ADE is a factor, Omicron "mild" infections will rip through previously hard-hit areas.

[Emily]

Prof. Penny Moore on why neutralization assay will take weeks - "It is complicated by the number of mutations this variant has."
(I cued this to start at her segment.)

https://www.youtube.com/watch?v=Vh4XMueP1zQ&t=3439s

[Emily]

Or equus asinus? (aka: "utter nonsense")

https://twitter.com/alchemytoday/status/1467320245438361602/photo/1

[Emily]

Continued mass vaccination will only push the evolutionary capacity of SARS-CoV-2 Spike protein beyond the Omicron version

Updated 7:41 AM EST, Tue November 30, 2021

By By G. Vanden Bossche, DVM, PhD
...

As the scientifically perverse narrative continues to add fuel to the fire, it is difficult to believe that Omicron will be the end station of the pandemic train that’s out of control. Omicron is likely to start out as a mild disease because short-lived, poorly functional anti-S antibodies (Abs) that resulted from previous asymptomatic infection (e.g., with another previously dominant variant) will no longer recognize Omicron. It is, indeed, highly likely that resistance of Omicron will not be limited to vaccinal Abs but also to naturally induced low affinity Abs that result from asymptomatic/ mild infection. Consequently, Abs from such previous infection would no longer compete with relevant innate Abs for binding to the virus. Individuals who previously contracted asymptomatic/ mild infection will, therefore, be able to fully rely on their first line of immune defense to deal with Omicron. This will leave our ‘experts’ with the impression that the virus (in fact Omicron) is becoming less virulent (than Delta) and is on its way to transit into endemicity. However, the overall pattern of ‘mild’ disease would only prevail until Omicron becomes dominant and causes high infection rates. When this happens, short-lived, low affinity anti-S Abs will start to compete with innate Abs in an increasing part of the population as a direct result of the enhanced likelihood of re-exposure shortly after previous infection. High Omicron infection rates will prevent short-lived, poorly functional anti-S Abs from declining in large parts of the population. This, combined with continued mass vaccination with (inevitable?) anti-Omicron vaccines, will enable large populations to exert immune pressure on Omicron’s infectiousness. None of these immune responses is, however, capable of curtailing viral transmission (it’s now widely acknowledged that the type of C-19 vaccines used by the industry is not capable of blocking transmission)....

[Pathfinder]

Translation Google

Omicron Variant: What if the appearance of this "super variant" was good news?

The new strain could be less dangerous by dint of having mutated. But scientists believe it is still too early to support such a hypothesis.

Audrey Parmentier
Published on 12/04/2021 at 12:59, updated to 22:55

The sentence seems so surprising that it has been repeated in many media: The Omicron variant "could be good news", said virologist Yves Van Laethem in the Belgian daily La DH . While the new strain detected in South Africa worries the whole world which is barricaded , the specialist affirms that it could be "a very beautiful gift from Saint-Nicolas, in the sense that a less virulent variant would replace the other and allow to the unvaccinated to be immunized. If the patients have a cold and 37.7 fever, this is less of a problem. " In other words, he believes that the mutation of a virus can lead to a decrease in its lethality and thus make the disease mild. If the Omicron variant causes milder forms of the disease while being transmitted more quickly, it could therefore reverse the Delta variant - the main source today. For the time being, no death linked to this new mutant has been detected in the world, recalled the WHO on Saturday.

Other specialists abound in this direction: "This new variant is perhaps the light at the end of the tunnel. It is a very contagious variant, but perhaps not as aggressive as is feared", also advanced the November 30, Zvika Granot, professor of immunology at the Hebrew University of Jerusalem. These remarks echo those of the president of the Association of South African Physicians, Angelique Coetzee who said last week that she had received patients with positive Covid tests with unusual symptoms. "What brought them to my practice" in Pretoria, "was extreme fatigue," she said. "I'm not saying that there won't be serious illnesses" but "for now even the patients we have seen who were not vaccinated have mild symptoms," she said. . In the process, Dr Coetzee recalls that very little is known about the dangerousness of this variant that the WHO has however qualified as "worrying".

Between hope and concern, the Omicron variant is at the heart of scientific discussions. Among the questions that flow: Could Sars-CoV-2 turn into a mild disease with this new strain? Asked by L'Express, virologist Hervé Fleury and professor emeritus at the CNRS and the University of Bordeaux, replied that several options are on the table: "You have to be patient and wait a few weeks before being able to respond." In order to obtain a more precise picture of the Omicron variant, the evolution of current patients in the coming days will make it possible to assess the seriousness of the situation. Note that in South Africa- country most affected by the new variant - a peak in infections among children was reported by health authorities on Friday. With 16,000 new cases per day - due to the Omicron variant - South African pathogenicity data is eagerly awaited. "The tragedy is that everyone is making assumptions, but no one yet has solid data," annoys Hervé Fleury.

Omicron "disabled" by dint of having transferred

While conclusions cannot be drawn immediately, the virologist admits that the hypothesis that the Omicron variant could be good news is one of the possibilities to be considered. While the highly transmissible Delta variant contains nine mutations on the Spike protein, which plays an important role in infection, the Omicron variant has 32 mutations in this protein and around 50 in all. According to Hervé Fleury, the new strain could end up "handicapped" by having so much mutated. If it gained in transmissibility - because it had no other choice to maintain itself - it could have lost in virulence by dint of being transformed. "The Omicron variant has so many mutations that it could be less pathogenic. If this is confirmed, it could become a very interesting strain for the human species", underlines the professor emeritus who takes care to use the conditional each time .

Pending the results, the Delta variant continues to kill in France and remains the number one enemy. Until Omicron replaces it, maybe. "It could become a type of benign coronavirus that we already know in winter in our regions and which affects children", continues Professor Fleury before adding that this obviously remains to be proven. Across the Atlantic, the discourse is the same. "What we must do is simply continue to monitor the situation, obtaining as much information and data as possible," said Antony Fauci, White House adviser on the health crisis, on Friday. In France, scientists are divided on the assumptions about Omicron. On Twitter, medical biologist Claude-Alexandre Gustave recalls that "variants have also always been more contagious ... without being less virulent."
...
According to some scientists, the virus needs to produce viral particles in order to be transmitted. "If a variant is more contagious, there is a chance that it will be more virulent", declared Mircea Sofonea, epidemiologist and specialist in the modeling of infectious diseases at the University of Montpellier, in the columns of Le Figaro . For now, there is therefore nothing to confirm that a virus that has become more transmissible would be less dangerous. "Among the other options on the table, the Omicron variant could be more dangerous, more transmissible and escape vaccines", continues Hervé Fleury. Especially since according to a study made available Thursday on the pre-publication site medRxiv,, but which has not yet been peer-reviewed, reinfection of infected subjects is three times more frequent with the Omicron variant compared to waves linked to the Beta and Delta variants. "We must also take this into account. We have hypotheses which are also not very good", concludes the virologist.

https://www.lexpress.fr/actualite/so...e_2163684.html

[Pathfinder]

Omicron Up Close: South Africa’s Experts Tell Their Stories

By Janice Kew and Michael Cohen
December 3, 2021, 2:11 AM CST
...
Richard Friedland, chief executive officer of Netcare Ltd., which operates the largest private health-care network in South Africa:

“If in the second and third wave we’d seen these levels of positivity to tests conducted, we would have seen very significant increases in hospital admissions and we’re not seeing that. In our primary care clinics it is mainly people under 30-years-old.”

“So I actually think there is a silver lining here and this may signal the end of Covid-19, with it attenuating itself to such an extent that it’s highly contagious, but doesn’t cause severe disease. That’s what happened with Spanish flu.”
...

Shabir Madhi, a vaccinologist from the University of the Witwatersrand, who led trials of both AstraZeneca Plc’s and Novavax Inc.’s shots in South Africa:
...
“I’m optimistic that in this resurgence, while the total number of cases will probably be greater, hospitalizations and deaths will be lower than what we experienced during the course of any of the first three waves.
...

Anne von Gottberg, a clinical microbiologist at South Africa’s National Institute for Communicable Diseases:

“All the data has shown that children have a less severe clinical course and we’ve had some anecdotal reports from hospitals in South Africa, that yes, they are seeing a few more children in some of the hospitals and are admitting them, but many of them have an uncomplicated clinical course during the few days that they are in hospital.”
...
“This virus may be similar to delta in its ability to spread or in being contagious. However, it’s the susceptibility of the population that is greater now because previous infection used to protect against delta and now, with omicron, it doesn’t seem to be the case.”

“However, we believe that with the reinfections the disease will be less severe and the same would hold for those that are vaccinated. So that would be good news.”

...

https://www.bloomberg.com/news/articles/2021-12-03/omicron-up-close-south-africa-s-experts-tell-their-stories

[sharon sanders]

bump this

[Shiloh]

Source: https://www.fxempire.com/news/articl...d-virus-830065

Omicron variant may have picked up a piece of common-cold virus
By:Reuters
Updated: Dec 4, 2021, 04:21 EST•2min read

By Nancy Lapid NEW YORK (Reuters) – The Omicron variant of the virus that causes COVID-19 likely acquired at least one of its mutations by picking up a snippet of genetic material from another virus – possibly one that causes the common cold – present in the same infected cells, according to researchers.

This genetic sequence does not appear in any earlier versions of the coronavirus, called SARS-CoV-2, but is ubiquitous in many other viruses including those that cause the common cold, and also in the human genome, researchers said.

By inserting this particular snippet into itself, Omicron might be making itself look “more human,” which would help it evade attack by the human immune system, said Venky Soundararajan of Cambridge, Massachusetts-based data analytics firm nference, who led the study https://osf.io/f7txy posted on Thursday on the website OSF Preprints....

[Emily]

https://twitter.com/ydeigin/status/1466879569261207552

Yuri Deigin @ydeigin


Hmm. Durban is where the lab is.


3:17 PM · Dec 3, 2021·Twitter for iPhone



Yuri Deigin
@ydeigin
10h
Replying to@ydeigin





github.com
Sequence of traveller from South Africa failed to get assigned to any lineage by pangolin, with a...
This sequence we got this morning is from a return traveller from South Africa. Pangolin failed to assign any lineage to it, neither scorpio. On UShER tree it is close to one sequence from South Af...



Yuri Deigin
@ydeigin




pubmed.ncbi.nlm.nih.gov
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma - PubMed
SARS-CoV-2 variants of concern (VOC) have arisen independently at multiple locations1,2 and may reduce the efficacy of current vaccines that target the spike glycoprotein of SARS-CoV-23. Here, using...

3:18 PM · Dec 3, 2021·Twitter for iPhone




valentin bruttel @VBruttel

Replying to@ydeigin

So to sum this up: 1) SARS2 Omicron genome looks like it was "separated/frozen" between June 2020 and late summer 2021 - This has never before been seen in nature, only in lab leaked pandemics



en.wikipedia.org
1977 Russian flu - Wikipedia

5:57 PM · Dec 3, 2021·Twitter Web App




valentin bruttel

@VBruttel
7h

Replying to@VBruttel
and@ydeigin

2) SARS2 Omicron has 25:1 non-synonymous:synonymous mutations ratio. https://twitter.com/P_J_Buckhaults/s...374038530?s=20

Natural evolution would result in 25:50-100 ratios. The only logical explanation here is targeted manipulation.


Dr B.@P_J_Buckhaults

· Nov 30

Omicrons (B.1.1.529) most recent common ancestor is AV.1. Relative to this MRCA, Omicron has 25 nonsynonymous and 1 synonymous mutation in Spike, and 13 nonsynonymous and 6 synonymous mutations in the entire rest of the genome. This is very strange & I don't understand.




valentin bruttel
@VBruttel

Replying to@VBruttel
and@ydeigin

3) No SARS2 Omicron predecessors have been detected between June 2020 and fall 2021, despite their supposedly already higher infectivity. So in this time, - a single isolated patient bred more mutations than >100Mio others? - survived continous infection in complete isolation?

6:19 PM · Dec 3, 2021·Twitter Web App



valentin bruttel
@VBruttel·
7h

Replying to@VBruttel
and@ydeigin


4) Omicron is better adapted to humans and likely also to vaccinated/recovered humans. If this was acquired in a large pool of humans, we would have seen predecessors of this variant before. Evolution in animals should have resulted in a less-well adapted variant.



valentin bruttel

@VBruttel·
7h

5) The only plausible explanation how this huge number of mutations could have been acquired completely below the radar is: - scientists enabled SARS2 samples to escape antibody responses by passaging them in presence of diluted convalescent serum on human/humanized cell lines.

[silylene]

Gauteng hospital data. Hospitalization is now up 6x compared to a couple weeks ago. 604 cases in ICU. Most likely about a third of these will become fatalities.

[JJackson]

If it follows the progression of other variants this is a little early to expect to see deaths. The first week is the active viral phase then week 2 the virus begins to clear but the immune pathology kicks in, by week 3 most are beginning to get better but some will progress to severe disease, week four onward those that are not going to make it will start to appear in the statistics. Given this typical time scale a month ago there were not enough cases to be picked up by sequencing. In short it is too soon to know where this variant will fit amongst the others in terms of morbidity and mortality.

[Pathfinder]

Christian Lindmeier:
"I have not seen reports of Omicron related deaths yet."

Translation Google

Omicron: no deaths related to the reported variant (WHO) | AFP
3 Dec 2021

The World Health Organization (WHO) spokesman said on Friday that "all information" was not yet known about Omicron but that to his knowledge, no deaths were yet linked to the Covid variant.

https://www.youtube.com/watch?v=4pYYEntEJEg