Covid Variant Omicron (B.1.1.529)

[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.

 

[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.