COVID Covid Variant Omicron (B.1.1.529)

[kyphysics]

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 ..."

Interesting demographic background.

One question I have is whether NPIs (non-pharmaceutical interventions) are common and well-received in that population? Do they wear masks and social distance?

NPIs can affect infection rates. Sometimes younger, healthy people have the mentality that they're not at risk (maybe not thinking of others) and don't worry about wearing masks or distancing. I see it all the time in my city. Crowds of teens will gather to play sports (maskless) and young adults often don't care to mask at the grocery and retail stores. I thought I saw a statistic that less than 10% of the South African population was over the age of 65. Could be wrong on the exact figure...but I know it was an unusually low number.

 

[Sagittarius A-Star]

You're right. The percentage of unvaccinated has reduced to about 35%.

That's differently in ICUs:

The head of the Oxford jab programme says almost every Covid-19 patient in intensive care units (ICUs) has not been vaccinated.

Source:
https://metro.co.uk/2021/11/24/almo...care-are-unvaccinated-doctors-claim-15658481/

 

[Jarvis323]

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

Actually it's not. The number in the table for the average was 80.3. The median was 83.

 

[atyy]

That's differently in ICUs:

Source:
https://metro.co.uk/2021/11/24/almo...care-are-unvaccinated-doctors-claim-15658481/

"Professor Sir Andrew Pollard warned that those who have not had a jab are now virtually the only ones struggling to breathe in the UK." So is the interpretation of all the data that for hospitalizations and deaths in the UK, most are vaccinated elderly (covid complications, mostly not severe acute respiratory distress); but for icu (especially for respiratory distress), most are unvaccinated younger people?

 

[artis]

@atyy I find this BBC article rather enlightening , it considers the statistics of Wales not the full UK but I suspect Wales is not that far off from the average UK situation so take a look
https://www.bbc.com/news/uk-wales-58680204

So is the interpretation of all the data that for hospitalizations and deaths in the UK, most are vaccinated elderly (covid complications, mostly not severe acute respiratory distress); but for icu (especially for respiratory distress), most are unvaccinated younger people?

I am not sure about the last part but given the statistics in the link I gave it indeed seems that elderly make up a lot of the hospitalization statistic. It also makes sense since the elderly are the most vaccinated group in UK.
It also shows the leaky nature of the Covid vaccines because if you compare someone in their 30/40s with someone in their 80s if both are vaccinated but both catch the virus and have symptoms then it is only natural to assume the 80 year old will have a higher chance on developing life threatening symptoms or have complications with a preexisting condition worsen.
So the message that I take away from this is that the vaccine actually helps more younger adults if we compare just between those that are vaccinated, because younger adults can easily survive a mild Covid infection without any bad effects in most cases while the elderly often cannot.

 

[Sagittarius A-Star]

but for icu (especially for respiratory distress), most are unvaccinated younger people?

For Germany, yes.

My explanation:

Old people have a higher vaccination rate, which helps that not so many appear in ICU.

The new-infections-incidence is much higher than 1 year ago, because many places are now open, which where closed 1 year ago, for example schools, and because of the more infectious Delta variant. Therefore, more younger (not vaccinated) people than 1 year ago are now in ICU.

 

[pinball1970]

For Germany, yes.

My explanation:

Old people have a higher vaccination rate, which helps that not so many appear in ICU.

The new-infections-incidence is much higher than 1 year ago, because many places are now open, which where closed 1 year ago, for example schools, and because of the more infectious Delta variant. Therefore, more younger (not vaccinated) people than 1 year ago are now in ICU.

It is what we should expect from an older immune response – good details in the link below

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266981/

Age ranges below My previous post was out thanks @atyy - I will just leave the table this time

 

[Astronuc]

https://www.bbc.com/news/uk-wales-58680204

The takeaway is that 'it is best to face SARS-Cov-2 being fully vaccinated'.

 

[Astronuc]

First case of Omicron variant in US.

“The California and San Francisco departments of public health and the CDC have confirmed that a recent case of COVID-19 among an individual in California was caused by Omicron variant,” Fauci said.

The individual was a fully vaccinated traveler who returned from South Africa on Nov. 22 and tested positive on Nov. 29, Fauci said.

https://news.yahoo.com/first-confirmed-case-of-omicron-in-the-us-185518322.html

 

[kyphysics]

First case of Omicron variant in US.

https://news.yahoo.com/first-confirmed-case-of-omicron-in-the-us-185518322.html

Which means there are many more. ...Let's hope we don't get exponential Omicron growth heading into the colder, winter months. Thanksgiving could have accelerated spread already.

 

[Astronuc]

Let's hope we don't get exponential Omicron growth heading into the colder, winter months. Thanksgiving could have accelerated spread already.

Positive cases of Delta have increased in some areas following Halloween (October 30-31) gatherings. We have seen this locally. Gatherings at Thanksgiving (November 25) will probably involve another surge in positive cases. We have seen this last year, including after Christmas and New Years celebrations.

Note the first case was someone returning from S. Africa on Nov. 22, but testing positive on Nov. 29. The spread in California will depend on who was exposed to this person, and other persons returning from S. Africa. Spread elsewhere in the nation will depend on how many persons returning from S. Africa with infections of Omicron and/or Delta variants and how many persons who are exposed.

How 2 Flights to Europe May Have Spurred Spread of New Variant
https://www.nytimes.com/2021/11/30/world/europe/omicron-variant-plane-travel.html

 

[kyphysics]

Positive cases of Delta have increased in some areas following Halloween (October 30-31) gatherings. We have seen this locally. Gatherings at Thanksgiving (November 25) will probably involve another surge in positive cases. We have seen this last year, including after Christmas and New Years celebrations.

Yeah, major holidays have historically led to case jumps with COVID. Although, I did see this Thanksgiving headline:

https://www.cnbc.com/2021/11/27/bla...drops-28percent-from-pre-pandemic-levels.html

Black Friday shopping in stores drops 28% from pre-pandemic levels as shoppers spread spending throughout the season​

When driving out that weekend, I also seemed to notice less people out than expected. Maybe less people out = less virus spread...I hope, at least.

 

[atyy]

In terms of age and deaths you can see how much impact the vaccine has looking at the below table for the UK a 3 week period NOV
50-59 age group 2.2 and 13 deaths per 100,000 vaccinated/unvax respectively so unvaxed dying at a rate 5.9 greater than vaccinated

This is the largest difference so a good immune response but in an age group where you will have heart and lung issues beginning to manifest?

Lowest difference is ≥ 80 which 2.4 where the immune response is weakest.

All the rest are between 3 and 4 times greater unvaccinated groupView attachment 293397

Can you check p26-28 of the report and the footnotes? I think the unadjusted rates might be misleading (underestimate vaccine effectiveness). I don't expect the vaccine to provide only a 2.4x advantage in ages 80+, I think the advantage should be more like 8x?

 

[pinball1970]

Can you check p26-28 of the report and the footnotes? I think the unadjusted rates might be misleading (underestimate vaccine effectiveness). I don't expect the vaccine to provide only a 2.4x advantage in ages 80+, I think the advantage should be more like 8x?

Ill check and edit thanks!

 

[pinball1970]

Yeah, major holidays have historically led to case jumps with COVID. Although, I did see this Thanksgiving headline:

https://www.cnbc.com/2021/11/27/bla...drops-28percent-from-pre-pandemic-levels.html

Black Friday shopping in stores drops 28% from pre-pandemic levels as shoppers spread spending throughout the season​

When driving out that weekend, I also seemed to notice less people out than expected. Maybe less people out = less virus spread...I hope, at least.

32 cases in the UK now

https://www.standard.co.uk/news/uk/more-cases-omicron-confirmed-england-covid19-b969448.html

 

[kyphysics]

32 cases in the UK now

https://www.standard.co.uk/news/uk/more-cases-omicron-confirmed-england-covid19-b969448.html

It's in 3 states now in the U.S: https://www.cnbc.com/2021/12/02/min...vid-case-in-resident-who-traveled-to-nyc.html
California
Minnesota
Colorado


Omicron in SA seems to be surging faster than other waves.

 

[Astronuc]

California confirmed the first case of omicron in the US on Wednesday (yesterday); the person is fully vaccinated.

Minnesota health authorities confirmed the 2nd U.S. case of the Omicron variant, in a resident who recently returned from New York City. The man, who was fully vaccinated and has since recovered. The individual had traveled to NY City for a convention Nov. 19-21.

Colorado health authorities confirmed the 3rd U.S. case later today in a woman who was fully vaccinated but had not received a booster shot.

https://www.cnbc.com/2021/12/02/min...vid-case-in-resident-who-traveled-to-nyc.html
https://www.cnbc.com/2021/12/02/omi...-coming-days-ny-health-commissioner-says.html

New York State has seen a sudden surge of positive COVID cases, which are expected to be mostly Delta. In the last two days, new positive cases numbered 9462 and 11300 cases, the first time since 5 February over 11,000 positive cases in one day. Then NY State was coming off the winter surge. The number of fatalities related to Covid-19 has increased from about 30-32 per day to 48 during the last two days. It is likely to continue to rise. The sudden rise in positive cases may be partly related to increased testing following the discovery of the Minnesota man who tested positive. For some unexplained reason, NY State did not report/post numbers yesterday.

https://www.wsj.com/articles/scient...see-rise-in-covid-19-reinfections-11638456463

Scientists in South Africa tracking the spread of the Omicron variant said Thursday they are seeing a rise in reinfections in people who had recovered from Covid-19 as the country reported another sharp daily rise in new cases.

https://www.reuters.com/world/afric...d-higher-risk-reinfection-omicron-2021-12-02/

JOHANNESBURG, Dec 2 (Reuters) - The new Omicron variant of the Coronavirus poses a threefold higher risk of reinfection than the currently dominant Delta variant and the Beta strain, a group of South African health bodies said on Thursday.

 

[valenumr]

It's in 3 states now in the U.S: https://www.cnbc.com/2021/12/02/min...vid-case-in-resident-who-traveled-to-nyc.html
California
Minnesota
Colorado


Omicron in SA seems to be surging faster than other waves.

I was just looking at this data elsewhere. It still early, but that looks pretty bad. Also, the Colorado edit: Minnesota case is concerning, I think it predates the timeline for omicron in South Africa.

 

[valenumr]

California confirmed the first case of omicron in the US on Wednesday (yesterday); the person is fully vaccinated.

Minnesota health authorities confirmed the 2nd U.S. case of the Omicron variant, in a resident who recently returned from New York City. The man, who was fully vaccinated and has since recovered. The individual had traveled to NY City for a convention Nov. 19-21.

Colorado health authorities confirmed the 3rd U.S. case later today in a woman who was fully vaccinated but had not received a booster shot.

https://www.cnbc.com/2021/12/02/min...vid-case-in-resident-who-traveled-to-nyc.html
https://www.cnbc.com/2021/12/02/omi...-coming-days-ny-health-commissioner-says.html

New York State has seen a sudden surge of positive COVID cases, which are expected to be mostly Delta. In the last two days, new positive cases numbered 9462 and 11300 cases, the first time since 5 February over 11,000 positive cases in one day. Then NY State was coming off the winter surge. The number of fatalities related to Covid-19 has increased from about 30-32 per day to 48 during the last two days. It is likely to continue to rise. The sudden rise in positive cases may be partly related to increased testing following the discovery of the Minnesota man who tested positive. For some unexplained reason, NY State did not report/post numbers yesterday.

https://www.wsj.com/articles/scient...see-rise-in-covid-19-reinfections-11638456463https://www.reuters.com/world/afric...d-higher-risk-reinfection-omicron-2021-12-02/

Michigan is a total disaster as well.

 

[valenumr]

It's in 3 states now in the U.S: https://www.cnbc.com/2021/12/02/min...vid-case-in-resident-who-traveled-to-nyc.html
California
Minnesota
Colorado


Omicron in SA seems to be surging faster than other waves.

Just reported a case in Hawaii.

 

[Astronuc]

Minnesota health authorities confirmed the 2nd U.S. case of the Omicron variant, in a resident who recently returned from New York City. The man, who was fully vaccinated and has since recovered. The individual had traveled to NY City for a convention Nov. 19-21.

He developed symptoms shortly after returning and tested positive on Nov. 22.

The question would be 'was the individual infected in Minnesota, traveled to NYCity, returned, and then tested positive'? Or was this person exposed upon arrival in NY City and then incubated for three days, or less? Who else has been exposed in the following 10 days?

 

[valenumr]

Follow up: https://www.hawaiinewsnow.com/2021/...t-holds-news-conference-discuss-covid-hawaii/

Individual previously had covid, no travel history. It's been here for a while.

 

[kyphysics]

 

[Astronuc]

Follow up: https://www.hawaiinewsnow.com/2021/...t-holds-news-conference-discuss-covid-hawaii/

Individual previously had covid, no travel history. It's been here for a while.

Axios reported "Hawaii became on Thursday the fifth state to confirm the newly discovered Omicron variant after New York announced five new cases earlier in the day.

In Hawaii, the variant was found in an unvaccinated O'ahu resident with moderate symptoms who had previously been infected with COVID-19, per a state health department statement."

And NY State has confirmed 5 cases of Omicron variant: Two cases were in Queens, one in Brooklyn and a fourth, from a test on Nov. 30, in Suffolk County. The location of the fifth individual was unidentified.

https://www.axios.com/omicron-cases-confirmed-3-us-states-4040d14b-1669-4168-b95a-4c639a5662b6.html

 

[artis]

I personally am not worried about the spread of it as that is already inevitable rather I care to see whether it is a milder form or a worse one. So far it seems everyone who has had it is doing fine. Including the original news from South Africa.

 

[Rive]

twitter

I can't actually guess the actual level of immunized (by any means) people in the population, but I think that at this point it's significant enough that the real deciding factor between the speed of spreading already would be about the success of bypassing that previously built immunities, and not just the raw R0 value.

I wonder if there is any study about 'repeaters' having consistent 'easy' or 'hard' cases (with or without different variants/variants noted)?

 

[kyphysics]

I personally am not worried about the spread of it as that is already inevitable rather I care to see whether it is a milder form or a worse one. So far it seems everyone who has had it is doing fine. Including the original news from South Africa.

The highly infectious Delta wreaked tremendous havoc, so if Omicron is even more transmissible (seems like it from early data and worries about the large number of spike protein mutations), this could make for yet another potentially stressful winter.

While Delta wasn't more virulent/deadly in generating worse health complications than other strains, the sheer impact of higher transmissibility on absolute numbers of people ending up hospitalized and taxing our ICUs across the U.S. was a concern.

Even if Omicron is not more deadly than other strains, if it's more infectious than the already super infectious Delta, and people are getting COVID reinfections with Omicron (from early reports), we could have a similar situation. Just from the sheer number of people getting it - even if it's not more deadly - lots of people could end up hospitalized and straining our systems again. Let's hope not! But, better to over-prepare than under-prepare just in case.

 

[nsaspook]

It will be interesting to see if spreading Omicron infections breaks the current US North vs South case barrier. Delta seems to be in a steady low ebb below a moving north wave. SA was in much the same low case condition before Omicron.

https://www.nytimes.com/interactive/2021/us/covid-cases.html
https://covidestim.org/

 

[artis]

I find this explanation by Dr. Mobeen Syed rather well, what I found interesting in the study is that it seems these Omicron mutations have happened multiple times before and at varying times in the infection.
I do wonder one thing, do we have any estimates or is it possible to estimate how many different working mutations can the S protein for example evolve in total? The reason I ask this is because I would suspect that a protein much like a cell or any other mechanism cannot have infinite amount of possible states in which it can exist and still function.
Do we have any such simulations or are they possible which could tell us for example the possible changes/mutations that a certain protein or other biological entity can undergo and still be functional and how they affect the functionality of it? To rephrase I'm asking is it possible to simulate a virus knowing it's RNA and details without actually waiting for it to undergo the changes it makes with time in real biological organisms as it spreads?

https://www.medrxiv.org/content/10.1101/2021.06.03.21258228v1.full

 

[kyphysics]

Age Group of 0-4 years old in a SA metro seeing huge rise in hospitalizations.
3rd Wave: ~15 hospitalizations vs.
4th Wave: ~110 hospitalizations

Age Group of 5-9 years old
3rd Wave: ~7 hospitalizations vs.
4th Wave ~20 hospitalizations

Age Group of 10-19 years old
3rd Wave: ~10 hospitalizations vs.
4th Wave: ~45 hospitalizations

Age Group of 20-29 years old
3rd Wave: ~20 hospitalizations
4th Wave: ~120 hospitalizations

Look at a reversal as you get higher in age? Is it due to the elderly having a higher vaccination rate maybe? Other factors going on? It's interesting.