Covid Variant Omicron (B.1.1.529)

[PeroK]

We do not have and will never have all the answers. People do not and will not behave as rational actors. To predicate our actions on these assumptions is foolish and to proselytize on this basis is reckless. So we do the best we can here in the real world.

COVID is the last straw for my belief that universal healthcare, free at the point of use, is sustainable. Nominally, that is what we have in the UK but in a practical sense we simply no longer have healthcare except for emergencies. I'm already dependent on my private health insurance to get a telephone appointment with a "family doctor" - GP as they are callled here. There is no prospect of my seeing an NHS GP face-to-face or even on the telephone.

I have arthritis and it would take forever to see a GP, then a specialist, then have a scan, then see the specialist again and finally get treatment. This would nominally be free on the NHS, but in practical terms this sort of non-emergency treatment is no longer readily available (*). No one wants to face the political realities of a healthcare system that can barely cope in any case and now has to content with unvaccinated COVID patients - all demanding their unlimited free healthcare.

It seems that we have too many scared cows now and sooner or later we have to choose one to be slaughtered.

(*) Last year I went through that cycle privately in 2-3 weeks.

 

[Phil Core]

With Omicron the real alarm is the number of mutations that have arisen in a relatively short period of time.

Here's the genetic sequence with mutations for Omicron - https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant -

"The variant has a large number of mutations, of which some are concerning.[11] Thirty-two mutations affect the spike protein, the main antigenic target of antibodies generated by infections and of many vaccines widely administered. Many of those mutations had not been observed in other strains.[12][13] The variant is characterised by 30 amino acid changes, three small deletions and one small insertion in the spike protein compared with the original virus, of which 15 are located in the receptor binding domain (residues 319-541). It also carries a number of changes and deletions in other genomic regions. Of note, the variant has three mutations at the furin cleavage site.[14] The furin cleavage site increases SARS-CoV-2 infectivity.[15] The mutations by genomic region are the following:[16][10]

• Spike protein: A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
  • Half (15) of these 30 changes are located in the receptor binding domain-RBD (residues 319-541)
• ORF1ab
  • nsp3: K38R, V1069I, Δ1265, L1266I, A1892T
  • nsp4: T492I
  • nsp5: P132H
  • nsp6: Δ105-107, A189V
  • nsp12: P323L
  • nsp14: I42V
• Envelope protein: T9I
• Membrane protein: D3G, Q19E, A63T
• Nucleocapsid protein: P13L, Δ31-33, R203K, G204R"

vs the genetic sequence with mutations for Delta - https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant

What is it about the spike protein sequences (genetic structure) that generates increasing mutations rates?

 

[cmb]

At least everyone is learning the Greek alphabet, but not heard of the xi variant. Probably too much like '6' and skipped?

 

[DrGreg]

At least everyone is learning the Greek alphabet, but not heard of the xi variant. Probably too much like '6' and skipped?

“‘Nu’ is too easily confounded with ‘new,’” Tarik Jasarevic, a W.H.O. spokesman, said on Saturday. “And ‘Xi’ was not used because it is a common last name.” -- https://www.nytimes.com/2021/11/27/world/africa/omicron-covid-greek-alphabet.html

 

[atyy]

Yikes. We had that happen with Delta. It was going around everywhere, and we just kept opening up. Then we had a massive spike in cases. Granted the guidelines were based on vaccination rates, but those were based on science of Covid classic.

Where?

 

[kyphysics]

So, if they are working on "better boosters" would it be wise for someone already vaccinated to wait for these to be distributed? Or smarter to get the available booster now?

My view of boosters is that if you're in a vulnerable category, then getting one now is warranted and worth it. Otherwise, it's maybe not the biggest problem in the world to not get one if you're healthy and relatively young.

Boosters mainly offer an additional layer of protection (upping your active neutralizing antibodies, which decay over time - often heavily depleted or even gone after a few months) vs. those who are fully vaccinated w/o the booster yet. Those antibodies will give you a small advantage in preventing infection, but probably not much of one in regards to severe health complications.

The "original full vaccinations" already give you long-term protection in the form of memory T and memory B cells, which help your body fight the infection if you get COVID. Whereas antibodies decay over time, memory T & B cells increase over time, from cell division. This will mean years of protection from severe illness, even if infection protection wanes over time w/o boosters.

eta: ...assuming Omicron doesn't break through memory T & B cell illness protection, of course.

The question I have is:
If a booster for omicron comes out (or some other new and improved one), how quickly can a person who has already had a booster get the latest/best one? E.g.,

If I got a Moderna booster today and tomorrow it was announced that an omicron booster is available, could I get it immediately?

 

[Sagittarius A-Star]

If I got a Moderna booster today and tomorrow it was announced that an omicron booster is available, could I get it immediately?

The Omicron booster will not be be available tomorrow.

The Berlin virologist Christian Drosten is worried about the new Omikron variant of the corona virus. “I'm pretty worried at the moment,” said Drosten on Sunday evening in the ZDF “heute journal”.

You don't know too much about the new variant. Reports of mild courses did not yet have a lot of substance in view of only a good 1000 cases. Here you have to wait for the clinical course.

You can see, however, that it occurs frequently among young people in South Africa and also affects people who have already had an illness. He is concerned that the first real "immune escape mutant" is in front of him.

It is also not yet possible to say how the variant behaves in this country, where many people have been vaccinated.

“Nobody can say at the moment what is in store for us. The only thing you can really say for sure is: it's better to be vaccinated. It's even better when you're boosted, ”said Drosten. The available vaccines would probably protect against a serious course of the disease.

Source
https://www.bz-berlin.de/berlin/dro...mutation-bin-schon-ziemlich-besorgt-im-moment

via Google translate:
https://translate.google.com/?hl=de...Krankheitsverlauf wohl schützen.&op=translate

 

[kyphysics]

Yes, it was a hypothetical question.

I did see Fauci, however, answer the "wait for a tweaked booster" question by saying not to wait. We cannot know for sure if/when a better/tweaked booster will come out, so he recommends not playing these games and just getting boosted now. Sounds like solid advice.

 

[valenumr]

Where?

Hawaii.

 

[valenumr]

Hawaii.

This happened: https://www.worldometers.info/coronavirus/usa/hawaii/

 

[artis]

Then there was India that initially looked fine and everyone said how well they had done, then it surged and folks said how badly they'd dealt with the second wave, now at 330/M deaths, they're looking pretty good by comparison with USA and, say, UK at 2,100/M.

Now I wouldn't be too confident in these statistics especially from countries like India, the simply reason being that many of the Covid deaths never appeared on the papers because many sick people never got to the hospital and simply were sick at home and then died. Given the overcrowding of their health care system I am highly suspicious that those "at home" deaths ever got reported and most likely they "flew" under the radar.

COVID is the last straw for my belief that universal healthcare, free at the point of use, is sustainable.

Well, has it ever really worked anywhere except for a few small countries with extremely good rates of GDP and healthy population?

After Covid I decided to see a cardiologist and make some checkups, the state given one would be 6 months in waiting so I just went from my own pocket, not to mention the attitude you get while paying yourself is quite different.
All in all the best way to fight any virus and take load off from healthcare system is to not make bad life choices that eventually lead to conditions like obesity etc.
One of the unspoken yet major factors in Covid deaths is obesity and probably the reason US is in the lead of deaths. Others conditions also included.
Take no offence but given this is a science forums I think we should practice what we preach and stop the fear posting and just wait for reliable data to come out and then judge.
Also life is a probability , a virus that affects mostly vulnerable people I think the most logical approach is to isolate that group instead of everybody because someone has to go and work and pay for all the expenses we have not to mention we shouldn't write off our future because of a single event that will most likely go away.
We have nothing to fear , but fear itself , once said one man...

 

[atyy]

What we do know is what the doctor that spotted this has said about it;-

https://www.standard.co.uk/news/uk/omicron-symptoms-mild-doctor-angelique-coetzee-b968715.html

I mean, sure, take precautions but let's get it understood quickly to avoid unnecessary hardships.

In South Africa, 70-80% of the population has been previously infected, 24% vaccinated, and the average age is relatively young, all of which are expected to provide protection against Covid, so this may be why all of the cases Dr Angelique Coetzee (Chairperson, board of the South African Medical Association) had encountered at that point were mild.

Notably, https://news.yahoo.com/south-african-doctor-says-omicron-205354980.html added: "What we have to worry about now is that when older, unvaccinated people are infected with the new variant, and if they are not vaccinated, we are going to see many people with a severe [form of the] disease ..."

Dr Rudo Mathivha, (head of ICU at Chris Hani Baragwanath Hospital in South Africa) indicates that there are severe cases of Omicron among the young: "We have already seen a change in the demographic profile of Covid patients. We are seeing young 20s to just over their late 30s presenting at our hospital with with moderate to severe Covid disease, and some of them needing critical care intervention. Of note is 65% of those have not been vaccinated, and the rest have only been half-vaccinated (so took the first Pfizer jab, and were still thinking of going for the second Pfizer jab) ... How do we attract those young people that do not want to be vaccinated to realize that they would want to be vaccinated now? Because that is where our strength will lie when those young people come and be vaccinated ..."

 

[Sagittarius A-Star]

Also life is a probability , a virus that affects mostly vulnerable people I think the most logical approach is to isolate that group instead of everybody

Who does not belong to the vulnerable people?

Germany Covid-19 cases in ICU per age group:

Source:
https://www.mdr.de/wissen/corona-intensivstationen-altersstruktur-100.html

 

[cmb]

I'd like to see some clear data on all these variants showing the mortality rate from Covid of those without underlying conditions.

The data here in the UK initially showed this, and then it seemed to just stop being mentioned.

 

[pinball1970]

I'd like to see some clear data on all these variants showing the mortality rate from Covid of those without underlying conditions.

The data here in the UK initially showed this, and then it seemed to just stop being mentioned.

https://www.ons.gov.uk/peoplepopula...icles/coronaviruscovid19latestinsights/deaths

You can get to the raw data of age groups and add up male deaths from 65-79 and they are about 75 death short of your average containing age range.

Pre-existing below

 

[Astronuc]

Thirteen cases of the new Omicron Coronavirus variant have been found among players of Portugal’s top-flight football club Belenenses SAD, according to initial results from the country's national health institute (INSA).

One of the players has recently returned from South Africa, where the new strain was discovered last week, the institute said.

“Preliminary tests carried out at INSA, strongly suggest that all 13 cases associated with players of Belenenses SAD are linked to the variant of concern Omicron,” the institute said in a statement sent to Portuguese media.

https://www.politico.eu/article/portugal-13-omicron-coronavirus-cases-football-club-belenenses/

INSA also noted that tests carried out on 218 passengers who arrived in Lisbon from Mozambique on Saturday detected two cases of COVID-19. One was of the Delta variant and the other was not possible to identify, the institute said.

 

[hutchphd]

The way the statistics stand at the moment in the UK is the contradictory conclusion that you will live longer if you have Covid.

Average life expectancy in the UK; 81 years old

Average age of death from Covid; 83 years old.

What does this mean? That you live 2 years longer if you catch Covid?

This is a gross and trivial misuse of statistics. Your supposition that more complete data would allow you to figure out proper policy is, to be kind, doubtful.

Incidentally, as an old person, it really matters not one whit to me whether I die from COVID or with COVID. Please be more concerned about brotherhood than about Big Brother.

 

[kyphysics]

https://www.bloomberg.com/news/arti...pital-cases-in-omicron-epicenter?srnd=premium

Children under the age of 2 account for about 10% of total hospital admissions in the omicron epicenter Tshwane in South Africa, according to the National Institute for Communicable Diseases.

More kids are being admitted than during the early stages of the country entering the current fourth wave of infections, although a similar trend occurred during the third wave when delta was dominant, said Waasila Jassat, public health specialist at the institute.

 

[wywong]

Many countries are urging citizens to get booster jabs early to counter Omicron. Given that a mismatched booster may render a subsequent matched booster less effective thanks to original antigenic sin ( https://www.cambridge.org/core/jour...ov2-variants/C8F4B9BE9E77EB566C71E98553579506 ), is early booster a wise decision?

 

[artis]

is early booster a wise decision?

What do you consider early one might ask?
3 moths after your second shot?
I don't think these are the type of decisions to be made online. I myself always check with my doctor and make actual blood tests to make a decision like that.
That being said it also depends on your medical condition and age. If you are not in a risk group or are young having a booster VS just being doubly vaccinated the difference is hard to tell
Take a look at this study recently from Israel
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02249-2/fulltext#seccestitle150

we estimated that a third dose of the BNT162b2 mRNA COVID-19 vaccine is effective in preventing severe COVID-19-related outcomes. Compared with two doses of the vaccine administered at least 5 months before, adding a third dose was estimated to be 93% effective in preventing COVID-19-related admission to hospital, 92% in preventing severe disease, and 81% in preventing COVID-19-related death, as of 7 or more days after the third dose.

Then just further down from the same study

Third-dose vaccine effectiveness against admission to hospital and severe disease was estimated to be similar between males and females, and between individuals aged 40–69 years and at least 70 years. In those aged 16–39 years, the rate of these severe outcomes was too small for meaningful estimation of the booster effectiveness.

https://www.bmj.com/content/375/bmj.n2814

A study by the UK Health Security Agency (UKHSA) found that at least 20 weeks after being fully vaccinated with two doses of the AstraZeneca vaccine effectiveness against symptomatic disease was 44.1%, while for Pfizer it was 62.5%.

But two weeks after receiving the booster dose, protection against symptomatic infection increased to 93.1% (95% confidence interval, 91.7 to 94.3) in those who initially had two doses of the Oxford AstraZeneca vaccine, and 94.0% (95% CI, 93.4 to 94.6) for those who had Pfizer.

So it really depends on your immunity , existing antibody levels, age and other factors , anyway a decision you have to make with your doctor. On a side note, given in my country there is no Omicron yet (not to say that it will be worse as we don't know yet), we dealt with a delta wave recently and despite the freezing weather which is normal here as winter has come we are now down to the levels seen before mid waves. More interestingly we fell back down before Europe as there the wave still somewhat continues.
We have about 60% vaccination status and quite many have had the virus itself so the overall immunity might be well over 80+%
What is interesting is that now for actually quite a while we have almost equal numbers of positive cases in the vaccinated VS unvaccinated groups.
The only statistic that hasn't equalized is the deaths, those are still higher in the unvaccinated.
Here are the official statistic links
https://www.worldometers.info/coronavirus/country/latvia/

One can open up the numbers of individual days and they will link to the government twitter account for these statistics.

 

[atyy]

Many countries are urging citizens to get booster jabs early to counter Omicron. Given that a mismatched booster may render a subsequent matched booster less effective thanks to original antigenic sin ( https://www.cambridge.org/core/jour...ov2-variants/C8F4B9BE9E77EB566C71E98553579506 ), is early booster a wise decision?

In original antigenic sin, the response to variants would be less effective than to the original virus. Data shows that antibodies after the second dose are more effective at neutralizing the original virus than to the Beta variant. A booster at 9 months not only increases antibody levels, but also makes the antibodies almost equally effective at neutralizing the original virus and the Beta variant. So there is no sign of original antigenic sin. In fact, available data remains consistent with the still untested hypothesis that the third dose might broaden antibody neutalization sufficiently to even deal with Omicron.

You can also see the brief comment (without evidence, but it's pretty expert opinion) not to worry about original antigenic sin by Ali Ellebedy in response to a similar question.

 

[wywong]

What do you consider early one might ask?
3 moths after your second shot?
I don't think these are the type of decisions to be made online. I myself always check with my doctor and make actual blood tests to make a decision like that.

In response to Omicron, UK has halved the minimum gap for booster shots from 6 months to 3 months to counter the likely reduced vaccine protection, and the new groups of people who are eligible for the booster vaccine will be invited to get a jab. I think such a blanket recommendation is not warranted. Worse, if a tweaked vaccine for Omicron is available soon, those who get a mismatched booster now may gain less from the matched booster then because of original antigenic sin.

 

[PeroK]

In response to Omicron, UK has halved the minimum gap for booster shots from 6 months to 3 months to counter the likely reduced vaccine protection, and the new groups of people who are eligible for the booster vaccine will be invited to get a jab. I think such a blanket recommendation is not warranted. Worse, if a tweaked vaccine for Omicron is available soon, those who get a mismatched booster now may gain less from the matched booster then because of original antigenic sin.

Given the number of unvaccinated people in the UK and that they continue to dominate the hospital admissions, it does seem pointless to focus so much on those already vaccinated. One could argue that promoting the booster is the only politically viable course of action, given that tackling the unvaccinated is politically taboo.

 

[Nugatory]

The way the statistics stand at the moment in the UK is the contradictory conclusion that you will live longer if you have Covid.

Average life expectancy in the UK; 81 years old

Average age of death from Covid; 83 years old.

What does this mean? That you live 2 years longer if you catch Covid?

At the risk of stating the obvious….
The 81 year life expectancy from birth is irrelevant. The life expectancy to look at is that of an 83 year old, which is 7.86 years(female, 2018-2020 data set, UK).

(But even that comparison is seriously misleading, as the 83 year “average age of death from Covid” is exactly that - it is an average, so necessarily includes many much younger people).

 

[atyy]

Given the number of unvaccinated people in the UK and that they continue to dominate the hospital admissions, it does seem pointless to focus so much on those already vaccinated. One could argue that promoting the booster is the only politically viable course of action, given that tackling the unvaccinated is politically taboo.

Do the unvaccinated really dominate hospital admissions in the UK? Aren't many cases in the older age groups fully vaccinated? It's those who would benefit the most from the booster. Vaccinating younger age groups might also help reduce transmission. Also, if neutralizing antibodies contribute to protection against severe disease, then the booster would help, even in younger age groups, against Omicron.

 

[PeroK]

Do the unvaccinated really dominate hospital admissions in the UK? Aren't many cases in the older age groups fully vaccinated? It's those who would benefit the most from the booster. Vaccinating younger age groups might also help reduce transmission. Also, if neutralizing antibodies contribute to protection against severe disease, then the booster would help, even in younger age groups, against Omicron.

You're right. The percentage of unvaccinated has reduced to about 35%. You're about 5-10 times more likely to be hospitalised if you are unvaccinated, but because 90-95% of vulnerable people are vaccinated, the numbers are what they are.

It still means that hospital admissions could be lower by one third. That's still quite significant, I guess!

 

[pinball1970]

You're right. The percentage of unvaccinated has reduced to about 35%. You're about 5-10 times more likely to be hospitalised if you are unvaccinated, but because 90-95% of vulnerable people are vaccinated, the numbers are what they are.

It still means that hospital admissions could be lower by one third. That's still quite significant, I guess!

some numbers week 43-46 below cases, hospital and deaths pages 30-31

https://assets.publishing.service.g...047/Vaccine_surveillance_report_-_week_47.pdf

this link on age groups – vaccine uptake

https://coronavirus.data.gov.uk/details/vaccinations?areaType=nation&areaName=England

If you hover over the age group (see below) using the link, you can see uptake month by month, I hovered over 80-84 = 95.8%

 

[russ_watters]

Given the number of unvaccinated people in the UK and that they continue to dominate the hospital admissions, it does seem pointless to focus so much on those already vaccinated. One could argue that promoting the booster is the only politically viable course of action, given that tackling the unvaccinated is politically taboo.

It's not politically taboo in the US but it is largely pointless to "focus" on the unvaccinated. There's enough vaccine in circulation we can just encourage as many people to get jabs as possible, whether first or booster*. Right now something like half of those being administered are boosters (from memory).

*That said I'm not having an easy time getting my booster scheduled.

 

[russ_watters]

At the risk of stating the obvious….
The 81 year life expectancy from birth is irrelevant. The life expectancy to look at is that of an 83 year old, which is 7.86 years(female, 2018-2020 data set, UK).

At the risk of belaboring; how the COVID pandemic affects life expectancy is undetermined and depends on the framing of the point, but it may well be higher for the survivors than pre-COVID due to elimination of at-risk people from the average. But one thing is certain: the life expectancy of someone who died of COVID is zero.

 

[Nugatory]

At the risk of belaboring….

It’s worth belaboring - life expectancy statistics are so easily abused.