Covid Variant Omicron (B.1.1.529)

[nsaspook]

https://www.technologynetworks.com/...vs-pfizer-vaccine-first-data-available-356640

Next, the researchers looked at the ability to neutralize Omicron in two groups of individuals:

The individuals that had previously tested positive for SARS-CoV-2 infection did so in the first wave of the pandemic in South Africa, during which the prominent form of the virus was D614G.

Plasma samples were collected from each of the 12 participants.

“Geometric mean titer (GMT) FRNT50 (inverse of the plasma dilution required for 50% reduction in infection foci number) was 1321 for D614G,” the authors write in the paper. These samples therefore had very strong neutralization capabilities against this variant of SARS-CoV-2.

So what happens when the samples are tested against Omicron?

“GMT FRNT50 for the same samples was 32 for Omicron, a 41-fold decline,” the authors write.

While this figure might seem frightening, the researchers emphasize that neutralization escape by Omicron was not incomplete; five of the participants that had been previously infected – in addition to being vaccinated – demonstrated seemingly high neutralization titers against Omicron.
Click to expand...

Keep calm, get your booster and carry on
“It is important to interpret the data cautiously, as the investigators themselves point out. While the amount of virus-killing observed in the lab is reduced markedly – up to 40-times reduction – there is still measurable virus neutralization, especially in those who were vaccinated and previously infected,” Dr. Jonathan Ball, professor of molecular biology at the University of Nottingham, told the SMC. “This group effectively mimics what we would expect in people who had had two doses of vaccine plus a boost.”

https://www.ahri.org/wp-content/uploads/2021/12/MEDRXIV-2021-267417v1-Sigal.pdf

 

[kyphysics]

It's been interesting to see people's predictive takes/fears/non-fears...

Some think E-Ding is closer to the alarmist side. But, he makes good arguments too.

 

[Astronuc]

New York state has reported as of December 4, 0.6% of new positive Covid-19 cases are of the Omicron variant. Counties with lower vaccination rates report higher rates of infection.

The state of Rhode Island is seeing a high rate of hospitalizations as is the state of Michigan.

The state [of Rhode Island] has one of the highest COVID-19 infection rates in the country, as the Northeast, including Massachusetts and Connecticut, have seen a surge in cases during colder weather.

Nearly 85% of all Rhode Islanders have gotten at least one dose of the COVID-19 vaccine, according to state data. That includes over 96% of adults. While breakthrough cases have steadily increased in recent weeks, the vast majority of new cases are in unvaccinated people, state data shows. Under 7% of all patients hospitalized for COVID-19 have been fully vaccinated, according to state data.

https://www.msn.com/en-us/health/me...vid-19-cases-hospitalizations-rise/ar-AARGk2Z

this week Michigan had more patients hospitalized for Covid-19 than ever before. Covid-19 hospitalizations jumped 88% in the past month, according to the Michigan Health & Hospital Association.

https://www.msn.com/en-us/news/us/c...king-a-toll-on-health-care-workers/ar-AARFiEX

"Since January, we've had about 289 deaths; 75% are unvaccinated people," Dover said. "And the very few (vaccinated people) who passed away all were more than 6 months out from their shot. So we've not had a single person who has had a booster shot die from Covid."

And, Michigan is reporting more cases in younger people.

 

[Ygggdrasil]

Here's another twist. The Omicron variant of SARS-Cov-2 apparently shares genetic code with a common cold coronavirus! https://thehill.com/homenews/corona...-be-more-transmissible-due-to-sharing-genetic

https://www.cdc.gov/coronavirus/general-information.html
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204879/

The news that the Omicron variant shares genetic code with a seasonal Coronavirus comes from this non-peer reviewed manuscript posted on the website of a company founded by some of the authors:

Omicron variant of SARS-CoV-2 harbors a unique insertion mutation of putative viral or human genomic origin
https://nference.com/publications/YamgzBMAADIAxXym

Specifically, the claim comes from the fact that a specific 9 nucleotide insertion in the viral genome (ins214EPE) resembles the sequence found in a common cold-causing Coronavirus (specifically HCoV 229E). However, there are some major flaws in the authors' argument:

1. The sequence doesn't actually resemble any extant sequence in the virus genome. Here's the figure that the authors make showing the sequence:

The 9 nucleotide insertion in the Omicron genome matches the backwards sequence of the reverse complement of a sequence from the HCoV 229E genome. However, as anyone who has studied any molecular biology could tell you, 5'-GAGCCAGAA-3' is very different from 3'-GAGCCAGAA-5' and I don't think there would be a way for that backward sequence to recombine with Omicron to insert itself into the Omicron genome.

2. 9 nt is a very short sequence. Given that there are 4 different nucleotides, we would expect GAGCCAGAA to occur once every 4^9 = 262,144 nucleotides. The HCoV 229E genome is 27,271 nucleotides long, so it might be somewhat surprising to see that sequence in the HCoV 229E genome. However, it looks like the authors not only considered the sense strand of the HCoV 229E genome, but also its reverse complement and the backwards forms of each, giving a total of 109,084 nucleotides analyzed. Finding the occurrence of a 9 nt sequence that occurs once every 262,144 nt in 109,084 nt is not too surprising statistically and could reasonably occur by chance. Furthermore, the authors also likely considered the other endogenous common cold-causing coronaviruses, which even further increases the likelihood that they would find a match for the 9 nt insert by chance.

 

[kyphysics]

Thanks for sharing, Astronuc. Good info. to have!

The stat about no deaths from boostered people is pretty amazing.

 

[atyy]

However, as anyone who has studied any molecular biology could tell you, 5'-GAGCCAGAA-3' is very different from 3'-GAGCCAGAA-5' and I don't think there would be a way for that backward sequence to recombine with Omicron to insert itself into the Omicron genome.

That's the politest way I've seen of saying the paper is completely nonsensical.

 

[atyy]

UKHSA has released preliminary estimates of vaccine effectiveness against symptomatic illness: 2x AZ ~ 0%, 2x Pfizer ~30%. Boosting AZ/AZ/BNT or 3xBNT ~70%. So boosting helps.

Protection against severe illness can remain high even if there are large falls in protection against symptomatic illness. No numbers yet, but anecdotal reports from South Africa are that Omicron still causes severe respiratory illness requiring ventilation, but that double vaccination is significantly protective against serious illness. Caveats even given that these are anecdotal, is that the likely Omicron cases are probably detected by SGTF in PCR tests, but SGTF is also present in a small percentage of Delta cases.

 

[StevieTNZ]

What about this gronk -- https://www.nzherald.co.nz/nz/covid...lth-investigating/2ZDJLPLPM2NFG5KW5N4LEGRKWY/ -- who:

... was vaccinated against Covid-19 up to 10 times in one day on behalf of other people ...

Is he well and truly protected against Omicron, or (and I hope) suffer ill-effects of his stupidity?

 

[nsaspook]

https://www.reuters.com/world/afric...s-hospital-data-amid-omicron-wave-2021-12-10/

JOHANNESBURG, Dec 10 (Reuters) - South African scientists see no sign that the Omicron Coronavirus variant is causing more severe illness, they said on Friday, as officials announced plans to roll out vaccine boosters with daily infections approaching an all-time high.

South Africa alerted the world to Omicron late last month, prompting alarm that the highly mutated variant could trigger a new surge in global infections.Hospital data show that COVID-19 admissions are now rising sharply in more than half of the country's nine provinces, but deaths are not rising as dramatically and indicators such as the median length of hospital stay are reassuring.

Although scientists say more time is needed to arrive at a definitive conclusion, Health Minister Joe Phaahla said the signs on severity were positive."Preliminary data does suggest that while there is increasing rate of hospitalisation ... it looks like it is purely because of the numbers rather than as a result of any severity of the variant itself, this Omicron," he said.

 

[kyphysics]

UKHSA has released preliminary estimates of vaccine effectiveness against symptomatic illness: 2x AZ ~ 0%, 2x Pfizer ~30%. Boosting AZ/AZ/BNT or 3xBNT ~70%. So boosting helps.

Protection against severe illness can remain high even if there are large falls in protection against symptomatic illness. No numbers yet, but anecdotal reports from South Africa are that Omicron still causes severe respiratory illness requiring ventilation, but that double vaccination is significantly protective against serious illness. Caveats even given that these are anecdotal, is that the likely Omicron cases are probably detected by SGTF in PCR tests, but SGTF is also present in a small percentage of Delta cases.

Hey, atty:

What are the distinctions between symptomatic illness, severe illness, and serious illness? I take the latter two to be synonymous and just two words for one concept.

Are we talking about any hospitalization and above for "severe" or "serious" illness? Or, would it require ICU-level hospitalization, etc.? I take symptomatic illness as just stuff like fatigue, running nose, cough, etc. But just thought I'd check. Thanks.

 

[atyy]

Hey, atty:

What are the distinctions between symptomatic illness, severe illness, and serious illness? I take the latter two to be synonymous and just two words for one concept.

Are we talking about any hospitalization and above for "severe" or "serious" illness? Or, would it require ICU-level hospitalization, etc.? I take symptomatic illness as just stuff like fatigue, running nose, cough, etc. But just thought I'd check. Thanks.

Usually symptomatic illness means testing positive with symptoms, even mild ones. You'd have to read the paper carefully to see how they defined it. It's possible the definition of symptomatic illness changes from study to study, especially if it depends on people figuring out whether they have mild symptoms or not. For example, a study in healthcare workers may pick up more symptomatic cases, because healthcare workers may be more conscientious in picking up their own mild symptoms, whereas others may just think they are a little "off" that day. Probably @berkeman will know better, since he's a healthcare worker :)

For severe illness and serious illness, I was sloppily meaning roughly the same thing in a non-technical sense (so hospitalization or worse). However, these are also technical terms. You can see one definition here: https://www.covid19treatmentguidelines.nih.gov/overview/clinical-spectrum/.

 

[kyphysics]

 

[Sagittarius A-Star]

UK has Omicron Covid patients in hospital, government confirms
Top UK medical adviser says growing number of people going to emergency departments diagnosed with Omicron
...
No deaths have been reported so far from Omicron, although it is just over two weeks since the variant was first detected in the UK, and there is normally a time lag of three to four weeks between infection and death, should that happen. “I think it’s too early to make any assumption at this point in time,” Hopkins said.

Source:
https://www.theguardian.com/world/2...ovid-patients-in-hospital-government-confirms

 

[AlexCaledin]

Most of the 43 COVID-19 cases caused by the Omicron variant identified in the United States so far were in people who were fully vaccinated, and a third of them had received a booster dose, according to a U.S. report published on Friday.

The U.S. Centers for Disease Control and Prevention (CDC) said that of the 43 cases attributed to Omicron variant, 34 people had been fully vaccinated. Fourteen of them had also received a booster, although five of those cases occurred less than 14 days after the additional shot before full protection kicks in.

https://www.reuters.com/world/us/mo...ses-have-hit-fully-vaccinated-cdc-2021-12-10/

 

[kyphysics]

 

[Astronuc]

The U.S. Centers for Disease Control and Prevention (CDC) said that of the 43 cases attributed to Omicron variant, 34 people had been fully vaccinated. Fourteen of them had also received a booster, although five of those cases occurred less than 14 days after the additional shot before full protection kicks in.

From the same article,

Among the Omicron cases, 25 were in people aged 18 to 39 and 14 had traveled internationally. Six people had previously been infected with the coronavirus.

Most of them only had mild symptoms such as coughing, congestion, and fatigue, the report said, and one person was hospitalized for two days. Other symptoms reported less frequently including nausea or vomiting, shortness of breath or difficulty breathing, diarrhea and loss of taste or smell.

Seems most of those cases identified as Omicron are relatively mild compared to Delta cases.

One should ask, 'how frequently are positive cases typed for variant?'

One factor not discussed is whether those infected wore masks to prevent infection and maintained distance in public places. Six of those people had previously been infected with the coronavirus, but the article doesn't indicate which variant(s). So, 'natural immunity' from previous infection doesn't necessarily work too well, eh?

Best to face SARS-Cov-2 with appropriate vaccinations.

 

[Sagittarius A-Star]

At least one person in UK has died with Omicron, says Boris Johnson
PM says idea that Omicron is ‘milder version’ of virus should be set aside as he confirms death of patient from Covid variant

Source:
https://www.theguardian.com/world/2...n-uk-has-died-with-omicron-says-boris-johnson

 

[pinball1970]

reports suggest mass outbreaks after social gatherings – even among people who have had a Covid booster

https://www.theguardian.com/world/2...s-to-be-infecting-britain-despite-the-vaccine

The vaccine does not stop you getting Covid Omicron or otherwise or passing it on, it reduces the risk of severe disease, hospitalization and death.

 

[kyphysics]

See bottom post 9).

One word: boosters

 

[hutchphd]

Yes it is complicated. This is actually a balanced presentation of the questions involved and concludes that we may need periodic boosters and that they do work. Nowhere does it yell "the sky is falling"

Credit to you for finally providing a reference that actually contains information.
.

 

[Ygggdrasil]

This concern [antibodies against the vaccine] applies only to the adenoviral vector vaccines (AstraZeneca or Johnson & Johnson) and not the mRNA vaccines (Pfizer or Moderna). Because the AZ and J&J vaccines use viruses to introduce DNA encoding the spike protein into cells, there is a concern that the body could develop antibodies against the adenovirus and prevent subsequent doses of the adenoviral vaccine from delivering sufficient spike protein DNA to generate immunity. The concern is not that a booster dose of an AZ and J&J would reduce existing immunity to the virus, just that the booster dose would not be as effective at increasing the level of immunity.

However, these concerns are hypothetical (though well founded scientifically), and not currently supported by existing data. Studies of COVID booster shots have shown that, for individuals initially immunized with two doses of the AZ adenoviral vaccine, a booster dose of the AZ adenoviral vaccine (or boosting with other types of vaccine) are effective at boosting the levels of neutralizing antibodies (for example, see the study below):

Safety and immunogenicity of seven COVID-19 vaccines as a third dose (booster) following two doses of ChAdOx1 nCov-19 or BNT162b2 in the UK (COV-BOOST): a blinded, multicentre, randomised, controlled, phase 2 trial
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02717-3/fulltext

Even if it is shown that the effeciveness of repeated boosters with adenoviral vaccines wanes due to immunity against the adenoviral vector, other vaccines are available to use as boosters (e.g. the mRNA vaccines from Pfizer or Moderna).

[Moderator's note: edited since it was an answer to a deleted post.]

 

[pinball1970]

The overwhelming evidence from the greatest mass Vaccine program on the planet says 1/It works (all of them with some variation) 2/ It is safe.
You never cite this part and seem to prefer mine quote and mine ref like a creationist looking for that fringe view, paper, comment.
This is just me as a neutral position, non Scientist. Just an observer. You may well be more qualified or in a Science position work wise rather than periphery than like me.
This is not a personal attack on you. It's a question regarding your ideas/position which is fair game.

[Moderator's note: edited since it was an answer to a deleted post.]

 

[Rive]

The vaccine does not stop you getting Covid Omicron or otherwise or passing it on...

At least a reduced transmission was expected, and as I recall it was observed too.
And this was a key point about keeping the speed new variants emerging with low (due lower number of copies/mutations).
I'll wait for more data, but an outbreak amongst vaccinated would be definitely a concern.

 

[berkeman]

Thread closed temporarily for Moderation...

 

[berkeman]

Thread is reopened. Thank you to @Ygggdrasil for the helpful reply.

 

[valenumr]

Latest confirmed count in Hawaii is 12 cases. A 27 case outbreak of general Covid is being investigated as well, from a nightclub. They should be requiring proof of vaccination at the door, and local reporting hasn't indicated that they weren't, so far.

 

[atyy]

At least a reduced transmission was expected, and as I recall it was observed too.
And this was a key point about keeping the speed new variants emerging with low (due lower number of copies/mutations).
I'll wait for more data, but an outbreak amongst vaccinated would be definitely a concern.

Yes. But for Omicron, there's very much reduced antibody neutralization, and reduced protection against symptomatic infection. This is consistent with estimates that Omicron is more able to reinfect, so it's likely there are more breakthrough infections also. But it's possible that the prior infection or double vax still provides high protection against severe disease, which is thought to contribute to the Omicron wave in South Africa resulting in a lower percentage of cases being severe compared to previous waves. The ability to protect against severe disease may remain high even if neutralization is low, because there are other mechanisms involved such as T cells and non-neutralizing antibodies.

 

[jim mcnamara]

An anthropomorphic point about human immunity:

The first cells that act to kill infected cells are not something you want running around forever. Why? They can cause problems like immune diseases because they get "bored" with nothing to kill, and as soon as there is some kind of activity from an unrelated allergen (for example) making inflamed tissue - the lonely cells kick off a stream of chemicals that damages cells. Cells that should not be damaged. They are not the original target cells that should be zapped.

This is a way to think about about allergies and autoimmune responses.

Anyway, the immune system evolved to taper off production of killer cells so that this will not happen. It uses eicosanoids, in part, to do this. When all types of eicosanoids can be produced all is well. But. Eicosanoid production is ultimately dietary because it depends on the presence essential polyunsaturated fatty acids in the diet.

You can think of eicosanoids as the the inflammatory on/off switches at the cellular level.

Most of the "on switch" eicosanoid family derives from omega-6 fatty acids, like vegetable oils. The "off switch" eicosanoids mostly depend on omega-3 fatty acids, found in animal based fats. So, if you consume omega-6 without omega-3 you increase the likelihood of those nasty immune cells not getting the "stop". The reverse is probably true. Anyway. As a result, out of place inflammatory responses result. They are also involved in a lot of other regulatory pathways. Both types of fatty acids are required.

So, there is a LOT more to this:

The eicosanoids include the
prostaglandins (PG),
thromboxanes (TX),
leukotrienes (LT),
lipoxins (LX).

Here is a discussion of more extreme events - Eicosanoid storms

https://www.nature.com/articles/nri3859

 

[pinball1970]

At least a reduced transmission was expected, and as I recall it was observed too.
And this was a key point about keeping the speed new variants emerging with low (due lower number of copies/mutations).
I'll wait for more data, but an outbreak amongst vaccinated would be definitely a concern.

If the growth continues we will hit 1,000,000 cases by xmas (page 28)
https://assets.publishing.service.g...t_data/file/1040076/Technical_Briefing_31.pdf

10 in hospital 1 death so far

https://assets.publishing.service.g...0898/20211214_OS_Daily_Omicron_Overview-1.pdf

Huge push for the booster programme, 24 million already boosted

https://coronavirus.data.gov.uk/details/vaccinations

Cutting out the 15 minute wait to increase flow too.

https://www.gov.uk/government/publi...ith-mrna-vaccine-for-covid-19-uk-cmos-opinion

 

[StevieTNZ]

https://www.stuff.co.nz/national/he...covid19-new-zealands-first-omicron-case-found

The first case of the Omicron Covid-19 variant has been found in New Zealand.
The case is in managed isolation in Christchurch, Stuff understands.
...
The Ministry of Health is expected to issue a statement about the case later on Thursday afternoon.
The World Health Organization (WHO) has warned Omicron is spreading at an “unprecedented rate” after being reported in 77 countries, and is likely to outpace Delta.

EDIT: further details have emerged: https://www.stuff.co.nz/national/he...h-omicron-had-flown-from-germany-six-days-ago

 

[Astronuc]

New York State just reported the third highest daily number (18,276) of positive SARS-Cov-2 cases since March 2020. The highest daily case numbers were 19942 on 14 Jan 2021 and 18832 on 7 Jan 2021. The daily fatalities have increased from less than 10/day (during the summer) to more than 60/day (during the past week). Yesterday, 74 deaths due to Covid-19 were reported. The total confirmed death toll due to Covid-19 stands at 47370 with another ~13000 probable (those dying outside of a medical or care facility.

New York State will report on the variant distribution on 18 Dec. They report every two weeks.

I just listened to a talk by a pathologist who studies respiratory illnesses, and the doctor indicated that mortality in the US from SARS-Cov-2 is about 10x that of influenza.

Locally, in our county, we've gone from 1 death per month during the past summer to 1 death per day during the past week. Many folks have chosen to go without wearing masks in public, and it is still those 60+, who are immunocompromised, or have one or more comorbidities, who are at most risk for mortality. Locally, those hospitalized tend to be those who are unvaccinated.

 

[kyphysics]

Worrisome paragraph:
https://nypost.com/2021/12/16/columbia-university-finds-omicron-vaccine-resistance/

A new study out of Columbia University says the Omicron variant is “markedly resistant” to vaccines and boosters might not do much to help, spelling bad news for the country as Omicron spreads and COVID-19 cases rise nationally.

“A striking feature of this variant is the large number of spike mutations that pose a threat to the efficacy of current COVID-19 vaccines and antibody therapies,” according to the study authored by more than 20 scientists at Columbia and the University of Hong Kong.

 

[atyy]

Worrisome paragraph:
https://nypost.com/2021/12/16/columbia-university-finds-omicron-vaccine-resistance/

I'm pretty sure boosters will help a lot! For 2xRNA vax, there is a major loss of antibody neutralization with Omicron, but protection against severe disease is expected to remain significant. Remarkably, 3xRNA not only increases antibody levels, but also broadens antibody neutralization, so that there is now significant neutralization of Omicron. 3xRNA generates Omicron neutralization that is a significant fraction of, and sometimes even comparable to the "super-immunity" generated by the combination of infection and vaccination. So 3xRNA is in a sense qualitatively better than 2xRNA in generating protection that is resistant to viral mutations.

https://www.medrxiv.org/con.../10.1101/2021.12.12.21267646v1
https://www.medrxiv.org/con.../10.1101/2021.12.14.21267755v1
https://www.medrxiv.org/con.../10.1101/2021.12.14.21267769v1
https://www.medrxiv.org/con.../10.1101/2021.12.13.21267670v1
https://www.biorxiv.org/content/10.1101/2021.12.12.472269v1

 

[pinball1970]

New York State just reported the third highest daily number (18,276) of positive SARS-Cov-2 cases since March 2020. The highest daily case numbers were 19942 on 14 Jan 2021 and 18832 on 7 Jan 2021. The daily fatalities have increased from less than 10/day (during the summer) to more than 60/day (during the past week). Yesterday, 74 deaths due to Covid-19 were reported. The total confirmed death toll due to Covid-19 stands at 47370 with another ~13000 probable (those dying outside of a medical or care facility.

New York State will report on the variant distribution on 18 Dec. They report every two weeks.

I just listened to a talk by a pathologist who studies respiratory illnesses, and the doctor indicated that mortality in the US from SARS-Cov-2 is about 10x that of influenza.

Locally, in our county, we've gone from 1 death per month during the past summer to 1 death per day during the past week. Many folks have chosen to go without wearing masks in public, and it is still those 60+, who are immunocompromised, or have one or more comorbidities, who are at most risk for mortality. Locally, those hospitalized tend to be those who are unvaccinated.

A similar story in the UK for cases. Two weeks ago we had a few dozen cases and today over 88,000 cases were reported in 24 hours.
The highest since it started.
Deaths will lag behind by a few weeks so we will have to see if the booster program can out run this surge.

In terms of who is at risk, 25 million boosted already so elderly and vulnerable should be covered. However there is a this missing % that is around the 20-50 group. They are not vaccinated.
As an aside but related, the BBC reported this morning that 25% of premiership footballers are not vaccinated. I was shocked by this, those guys have access to the best, and probably most expensive one to one medical care, advice and technology available in the UK. No jab??

 

[PeroK]

As an aside but related, the BBC reported this morning that 25% of premiership footballers are not vaccinated. I was shocked by this, those guys have access to the best, and probably most expensive one to one medical care, advice and technology available in the UK. No jab??

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.