Covid Variant Omicron (B.1.1.529)

[pinball1970]

There have been several premier league matches postponed due to a COVID outbreak in one team or other.

In truth, the vaccination rate is probably not particularly significant, but it's evidence that Omicron is out of control already.

They premiership should insist on it. Not all the players and management are idiots though. (My reason on why they are not vaccinated)

"I follow the advice of smart, educated people who know their field because they've dedicated their lives to it and have studied it," said Klopp.

"Ignore those who pretend to know. Ignore lies and misinformation. Listen to people who know best. If you do that, you end up wanting the vaccine and the booster."

The German revealed on Wednesday that his entire squad has been double-vaccinated and those eligible for a booster had already had it.

 

[Sagittarius A-Star]

The German revealed on Wednesday that his entire squad has been double-vaccinated and those eligible for a booster had already had it.

Omicron has a German twitter account
https://twitter.com/realB11529

 

[Sagittarius A-Star]

Preliminary experimental data on T cell cross reactivity to Omicron
...
Summary & Conclusion

• T cell responses maintained to Omicron compared to ancestral Spike in Pfizer vaccinees
• Although there is a consistent decrease in the CD4 T cell response to Omicron, 70% of the response is preserved
• The majority of vaccinees mounting a CD8 Spike response are unaffected by Omicron mutations, with a fraction losing their CD8 response
• Infection prior to vaccination gives some advantage
• JnJ vaccinees (1x and 2x) currently being tested

Source:
https://cdn.who.int/media/docs/defa...hoconsulation_15dec2021.pdf?sfvrsn=2a2a7479_7

 

[valenumr]

Im assuming at this point that omicron is as contagious and vaccine resistant as warned. Hawaii reported almost 800 cases today, almost double yesterday's numbers, and near our delta peak. Just two days ago, the speculation was that we might reach 500 cases per day by the end of this month. Yikes!

https://www.khon2.com/coronavirus/hawaii-reports-797-covid-cases-2-new-deaths/amp/

 

[StevieTNZ]

Three more cases detected at the border - https://www.1news.co.nz/2021/12/17/three-more-omicron-covid-19-cases-reported-in-miq/

NZ is trying to keep this new variant out of the community for as long as possible.

 

[jim mcnamara]

2 points:

https://www.frontiersin.org/articles/10.3389/fimmu.2019.00438/full
https://en.wikipedia.org/wiki/Somatic_hypermutation
First point --
The links explain Somatic Hypermutation (SHM) in the immune system, specifically in antigen-activated germinal center B cells. Germinal centers are in lymph nodes The Bcells there are involved in affinity maturation - a map for antigen Ig synthesis.

What does this mean?
SHM is specifically designed to keep up with possible antigen changes in pathogens. e.g., Delta, Omicron at al.
A. it works well only after maturation - many weeks after exposure. Time required may vary with the pathogen, diet, and other problems like inflammatory diseases example: Lupus, Type II diabetes,
B. function is marked improved with multiple exposures to antigens i.e. boosters. Over extended time.
C. This not like the very first response we see in newly immunized patients.
D. So, after several months the response is to prevent disease even from variants. NOT infection.
E. Immunocompromised patients do not do SHM well, which may be why some physicians may have administered more than three Covid vaccines to this patient population. Second point --
A. Vaccines are designed from the get-go to depend primarily on SHM.
B. Vaccines are unusual if they provide "upfront" protection from infection
C. Covid mRNA vaccines do protect against infection. Upfront. Even though they do the SHM thing as well.
D. Some Covid vaccines (like AstraZeneca) do not use mRNA. So, infection protection is not like mRNA vaccines.
E. Infection protection induced by a few vaccines wanes. But for Covid we are expecting it to do something it was never intended to do: Protect against infection.

So these points explain why we use boosters over time -
example tetanus antitoxin boosters every 10 years or so.
They also explain the why of inoculation strategies for children.
They explain why it may be possible for Omicron to be less pathogenic.

I'll let you work it out...

 

[kyphysics]

Im assuming at this point that omicron is as contagious and vaccine resistant as warned. Hawaii reported almost 800 cases today, almost double yesterday's numbers, and near our delta peak. Just two days ago, the speculation was that we might reach 500 cases per day by the end of this month. Yikes!

https://www.khon2.com/coronavirus/hawaii-reports-797-covid-cases-2-new-deaths/amp/

I feel like this is a rerunning movie. We keep underestimating COVID and variants in the media and socially.
I think exponential growth also tricks people's minds. You see just a few cases and think it's nothing. Even a few weeks later, it's just a bit more. But, once you go parabolic, it can explode out of nowhere and now you've got a full blown pandemic. It's frustrating. This wasn't hard to predict. Omicron was known very early on to be much more infectious than the already super infectious Delta. What did people expect?

It's like "out of sight out of mind." ...Exponential growth works that way...flat curve for a while and then an explosion straight up. That's why we needed to be careful early on. Not when it's gone exponential. Kinda too late now as the math takes over.

 

[valenumr]

I feel like this is a rerunning movie. We keep underestimating COVID and variants in the media and socially.
I think exponential growth also tricks people's minds. You see just a few cases and think it's nothing. Even a few weeks later, it's just a bit more. But, once you go parabolic, it can explode out of nowhere and now you've got a full blown pandemic. It's frustrating. This wasn't hard to predict. Omicron was known very early on to be much more infectious than the already super infectious Delta. What did people expect?

It's like "out of sight out of mind." ...Exponential growth works that way...flat curve for a while and then an explosion straight up. That's why we needed to be careful early on. Not when it's gone exponential. Kinda too late now as the math takes over.

Yep. Hawaii dropped basically all gathering restrictions (group sizes, venue capacity limits, etc) December 1st even with omicron in the news. No plans on going back as far as I can see.

 

[collinsmark]

I feel like this is a rerunning movie. We keep underestimating COVID and variants in the media and socially.
I think exponential growth also tricks people's minds. You see just a few cases and think it's nothing. Even a few weeks later, it's just a bit more. But, once you go parabolic, it can explode out of nowhere and now you've got a full blown pandemic. It's frustrating. This wasn't hard to predict. Omicron was known very early on to be much more infectious than the already super infectious Delta. What did people expect?

It's like "out of sight out of mind." ...Exponential growth works that way...flat curve for a while and then an explosion straight up. That's why we needed to be careful early on. Not when it's gone exponential. Kinda too late now as the math takes over.

Yes, I've experienced that with people.

Whenever I'm chatting with someone, and it becomes more and more apparent that they don't understand exponential growth, I'll slyly steer the conversation to this riddle:

A movie at the cinema starts at noon. At 11:45 AM, the first person walks into the theater. It's a very large theater, by the way, if you're curious. A minute later, two people enter. A minute after that 4 people enter. This continues for a while: with each minute, the number of people entering doubles. At exactly 12:00 noon, the last person enters and the theater is completely full. The question is: when is the theater half full?​

A typical question they may ask: "How big is the theater?"
Which I'll answer with: "It doesn't really matter. I could tell you the number*. It's big. But you don't need that to solve the problem. There's an easier way."

The answer to the riddle, of course, is 11:59 AM. A mere 1 minute before noon. That usually gets them to think, particularly with this pandemic going on.

I'll then mention that a mere 3 or 4 minutes or so before noon, it may seem that the theater is almost empty, with 9 out of 10 or so seats open, free for the taking. Then I might sneak in something about how people working at hospitals might feel when exponential growth happens.

*(65535)

 

[Astronuc]

NY State will release the numbers on variants later today. The state reports variant distribution on a two week basis. For two weeks ending 04 Dec, Omicron was reported as 1.1% (up from 0.6%) of infections typed.

CDC reported for Region 2 that Omicron accounted for 2% of infections for the week ending 04 Dec. For the week ending 11 Dec, CDC reports that 13.1% infections are Omicron.

HHS/CDC Region 2 includes New Jersey, New York, The Commonwealth of Puerto Rico and The U.S. Virgin Islands (St. Croix, St. Thomas and St. John).

From California - https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/COVID-Variants.aspx
Variants being tracked/detected/monitored

• B.1.1.7 (Alpha) variants are associated with approximately 50% increased transmission, and likely with increased disease severity and risk of death. Appears to have minimal impact on the effectiveness of treatments with antibodies.
• B.1.351 (Beta) variants are associated with approximately 50% increased transmission. May have moderately decreased response to antibody treatments.
• P.1 (Gamma) variants may have moderately decreased response to some antibody treatments.
• B.1.526 (Iota) is associated with significantly reduced efficacy of some antibody treatments.
• B.1.525 (Eta), and P.2 (Zeta) variants may have moderately decreased response to some antibody treatments.
• B.1.617.1 (Kappa) may have moderately decreased response to some antibody treatments.
• B.1.427 and B.1.429 (Epsilon) are associated with approximately 20% increased transmission. There is significantly reduced efficacy of some antibody treatments.
• B.1.621 (Mu) may have moderately decreased response to antibody treatments

Two variants of concern

• B.1.617.2 (Delta) variants are associated with approximately 200% increased transmission. May have moderately decreased response to antibody treatments. (Delta totals include all Delta AY sublineages).
• Omicron (B.1.1.529) is a new SARS-CoV-2 variant that was designated as a Variant of Concern by the WHO on November 26, 2021. California reported its first case of Omicron variant on December 1, 2021. As of December 15, 2021, 49 confirmed cases associated with the Omicron variant have been reported to the state.

Importantly, with respect to sequencing variants in California,

As of December 15th 299,708 samples have been sequenced in California. In August 2021, 16% of cases in California were sequenced, and this percent is expected to increase in coming weeks as more data becomes available. In July 2021, 23% of cases in California were sequenced.

In Texas, SARS-Cov-2 is predominantly Delta, with Texas recently indicating 100%.
https://www.dshs.texas.gov/coronavirus/variants-data/

A more detailed assessment of Central Texas during the past summer and before Omicron.
https://onlinelibrary.wiley.com/doi/10.1002/jmv.27373

 

[kyphysics]

The answer to the riddle, of course, is 11:59 AM. A mere 1 minute before noon. That usually gets them to think, particularly with this pandemic going on.

I'll then mention that a mere 3 or 4 minutes or so before noon, it may seem that the theater is almost empty, with 9 out of 10 or so seats open, free for the taking. Then I might sneak in something about how people working at hospitals might feel when exponential growth happens.

*(65535)

What does the *(65535) represent, collinsmark?

That's a pretty surprising illustration of exponential growth. Very powerful actually. I wouldn't have guessed 11:59 AM myself even! I don't know what I'd guess, but not THAT close to 12 PM. I might borrow this example.

 

[jim mcnamara]

How many minutes? So we double the number of new people every minute. Right? Doubling means two times itself. 4 doubled is 8.

Looking at it another way:
2^x - 1 = 65535. So. x is what number?

Plus you absolutely cannot do that theater trick for an hour, right? Tell us why... Hint: 1152921504606846975

 

[kyphysics]

How many minutes? So we double the number of new people every minute. Right? Doubling means two times itself. 4 doubled is 8.

Looking at it another way:
2^x - 1 = 65535. So. x is what number?

Plus you absolutely cannot do that theater trick for an hour, right? Tell us why... Hint: 1152921504606846975

x= 16
makes sense

Nice reorienting of the calculation there. No matter how much I intuitively recognize the power of exponential growth, seeing it in real examples still stuns me.

U.S. is in bad shape guys...the world is in bad shape. The only positive I can think of is that Omicron might not be any more deadly than Delta. But, that's not great comfort when you've got the beginnings or happenings of parabolic growth (not enough people vaxxed, nor boostered). The next month or two will be absolutely horrible, I'm guessing. After the peak, hopefully we recover okay.

 

[kyphysics]

 

[kyphysics]

Plus you absolutely cannot do that theater trick for an hour, right? Tell us why... Hint: 1152921504606846975

What if these were super midgets?

Interestingly, the reverse of exponential growth can be exponential decline:

https://www.nytimes.com/2020/03/13/science/coronavirus-math-mitigation-distancing.html
Good article on the power of STOPPING JUST 1 INFECTION.

The only problem is people have abandoned masks in many places. We don't have social cooperation here in the U.S. to leverage the power of exponential decline.

 

[Astronuc]

NY State will release the numbers on variants later today. The state reports variant distribution on a two week basis. For two weeks ending 04 Dec, Omicron was reported as 1.1% (up from 0.6%) of infections typed.

Perhaps the data on variants won't be released until Monday. Today, NY State reported 21,908 positive cases for yesterday, which eclipsed the previous all time high of 21,027 new cases the day before. Fatalities were 62 and 60, respectively. In January of this year, the mortality rates were 2 or more times those numbers, but there may be a lag of a week or two. If the COVID-19 infection is less severe with Omicron, hopefully, NY will not experience the higher levels of mortality experienced earlier this year.

 

[kyphysics]

Perhaps the data on variants won't be released until Monday. Today, NY State reported 21,908 positive cases for yesterday, which eclipsed the previous all time high of 21,027 new cases the day before. Fatalities were 62 and 60, respectively. In January of this year, the mortality rates were 2 or more times those numbers, but there may be a lag of a week or two. If the COVID-19 infection is less severe with Omicron, hopefully, NY will not experience the higher levels of mortality experienced earlier this year.

Mortality could also be lower, b/c the more vulnerable are already fully vaxxed.

Like you said, it'll be interesting in a few weeks. Deaths report with a lag. But, Omicron is also more infectious than Delta, so that could drive things due to high absolute infection rates.

 

[kyphysics]

 

[kyphysics]

 

[Astronuc]

Mortality could also be lower, b/c the more vulnerable are already fully vaxxed.

Like you said, it'll be interesting in a few weeks. Deaths report with a lag. But, Omicron is also more infectious than Delta, so that could drive things due to high absolute infection rates.

Yes, the vaccination of many of 60+ will help, even if Omicron is more infectious. New York has not reported their estimates of Omicron, but CDC has last week at 13% up from ~1-2% in the prior week, so perhaps New York is 20-25% Omicron this past week. Other states seem to be lagging.Edit/update: NY State reported two new deaths in the age range of 10 to 19. One death was reported on 15 Dec and the second on 16 Dec, bring the total to 20, which is low compared to hundreds or thousands in other age groups. The number of death in the 0-9 age group stands at 17, also low, but l think of the parents who lost their child and the grandparents who lost a granchild.

 

[StevieTNZ]

All of NZ's cases of Omicron are being detected at the border, thus it is not in the community. Yet anyway. They're looking at reducing the interval of getting a 2nd dose of Pfizer then a booster from six months to perhaps three. It is expected in early January, 5 - 11 year olds will be able to get vaxxed.

 

[kyphysics]

I promise I'm not Eric Ding.

 

[nsaspook]

I promise I'm not Eric Ding.

I think we need to be careful either way because there is minimal evidence of what 'mild' actually means. If 'mild' means a simple reduction of sickness and death by some set factor that's one thing but if 'mild' really means equivalent to a non-serious 'cold' in most vaccinated people that's a different set of numbers

 

[kyphysics]

I think we need to be careful either way because there is minimal evidence of what 'mild' actually means. If 'mild' means a simple reduction of sickness and death by some set factor that's one thing but if 'mild' really means equivalent to a non-serious 'cold' in most vaccinated people that's a different set of numbers

There's definitely a vaxxed/boostered vs. unvaxxed dichotomy.

There is also a global/poverty vs. G7 divide. Africa has only 10% of its total population vaxxed, for example. If Omicron hits, given its infectiousness, it could be devastating there. This thing has gone global.

Pray for the world. Many are not vaccinated.

 

[valenumr]

There's definitely a vaxxed/boostered vs. unvaxxed dichotomy.

There is also a global/poverty vs. G7 divide. Africa has only 10% of its total population vaxxed, for example. If Omicron hits, given its infectiousness, it could be devastating there. This thing has gone global.

Pray for the world. Many are not vaccinated.

No it's bad. Like really really bad. Here in Hawaii we have around 75 percent vax rate total population, indoor mask mandates, proof of vax requirements for gyms, restaurants, bars, theaters, etc, as well as proof of vax for entering the state. And it is spreading fast here. Faster than Delta when we did not have a lot of vaccines. Many establishments are shutting down because a majority of the staff have covid. Establishments that require their employees to be vaccinated. Time will tell how virulent the strain is in vaxxed and unvaxxed individuals, but it is definitely very infectious. UK reported almost 100k new cases yesterday. That is nuts. The sheer numbers are going to be problematic.

 

[valenumr]

Oops, that was meant in reply of @nsaspook

 

[kyphysics]

https://www.cnbc.com/2021/12/20/mod...ron-in-tests-will-still-develop-new-shot.html

Moderna said Monday its Covid-19 booster does appear to provide protection against omicron, but the drug company will still be developing a new shot specific to the variant currently surging across the world.

In an announcement early Monday, Moderna said preliminary data from lab testing found the version of its booster currently in use in the United States and elsewhere provided increased antibody levels to neutralize the virus. But it also found that a double dose of the booster shot provided a much greater increase in those levels.

 

[kyphysics]

I am not related to Eric Ding.

 

[StevieTNZ]

https://www.stuff.co.nz/national/po...sters-postpones-end-to-miq-because-of-omicron

- boosters now being delivered four months after second doses of Pfizer

It was also planning to allow fully vaccinated Kiwis and residents to travel into the country from Australia without going through managed isolation from mid-January.
That has been pushed back until the end of February to give the country more time to give far more Kiwis time to get their booster shot – with about 82 per cent of over-12s eligible for a booster at that point.
The Government has also announced that vaccinations for 5 – 11-year-olds will begin from January 17.
The suite of measures is designed to combat the newly-dominant Omicron variant, which is not yet been found in the community in New Zealand.

 

[kyphysics]

I promise I'm not Eric Ding's wife.

 

[Astronuc]

The Wall Street Journal and Bloomberg had headlines yesterday that indicated that 73% of new Covid infections are Omicron. I'm still waiting to see the different states including NY.

https://www.bloomberg.com/news/arti...s-to-nearly-three-quarters-of-u-s-virus-cases

https://www.wsj.com/articles/omicro...73-of-u-s-covid-19-cases-cdc-says-11640040586

 

[pinball1970]

I think we need to be careful either way because there is minimal evidence of what 'mild' actually means. If 'mild' means a simple reduction of sickness and death by some set factor that's one thing but if 'mild' really means equivalent to a non-serious 'cold' in most vaccinated people that's a different set of numbers

12 deaths in the UK so far (EDIT 14 deaths)

https://assets.publishing.service.g...042543/20211220_OS_Daily_Omicron_Overview.pdfSouth Africa looking more optimistic

https://www.telegraph.co.uk/global-...9-hospitalisations-fall-sharply-south-africa/

 

[Evo]

So, with so many more people getting Covid now, does this mean that there are so many more opportunities for Covid to mutate into another possibly more lethal variant again?

 

[BillTre]

So, with so many more people getting Covid now, does this mean that there are so many more opportunities for Covid to mutate into another possibly more lethal variant again?

Yes. More virus reproducing, more opportunities for changes to occur.

However, not all opportunities are equally productive in making new versions of virus.
An explanation proposed for new versions (that have accumulated a lot of genetic changes, and thus have new properties), is that they were able to reproduce, for long periods of time, within a single person. South Africa, supposedly, with lots of untreated HIV patients, would have a lot of people with a poorly functioning immune system where a virus could survive a long time.

Some would argue that this would be a more opportune oportunity for a virus to make big genetic changes.

 

[Astronuc]

New York State and CDC (for Region 2) have reported SARS-Cov-2 Variants for two weeks and the week ending 18-Dec, respectively. NY State reports on a two week basis. I'm trying to reconcile the different numbers for Omicron. New York reports 11.1% of cases being Omicron, 88.5% Delta. However, for the week ending 11-Dec, CDC reports Region 2 as 25.4% Omicron, 74.2% Delta and for the week ending 18-Dec, Region 2 has 92% Omicron, 7.9% Delta. Is there are measurement bias?

New York is seeing more deaths in the 20-29, 30-39, 40-49, 50-59, which have increased during the last month.