Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern" & BA.2 sub-variant, XE

[sharon sanders]

Good fortune with Omicron

[Shiloh]

Source: https://www.bloombergquint.com/onweb...-african-study

Pfizer Course Has 23% Efficacy Vs. Omicron in S. African Study Antony Sguazzin 10:11 PM IST, 11 Dec 2021 10:56 PM IST, 11 Dec 2021

(Bloomberg) -- A two-shot course of Pfizer Inc.’s vaccine has just 22.5% efficacy against symptomatic infection with the omicron variant, but can thwart severe disease, according to laboratory experiments in South Africa...

[gsgs]

strange,unexpected,big decline in infections and positive-rates and
-to lower degree- also hospitalisations in the last 2 days.
NICD has data issues and we have weekend, but that doesn't really seem to explain it.
I.e. the positive rate should not be affected.
And not in all provinces ?!

But what else could be the reason ? Tshwane is 1 week ahead of Gauteng
and Gauteng is 1 week ahead of other provinces, so I'd expect it to
peak in Tshwane first.

https://twitter.com/gsgs2/status/1469879399369609222

https://twitter.com/BallouxFrancois/...33674426023936

https://twitter.com/tomtom_m/status/1469954026347315211

http://magictour.free.fr/zaf2i.GIF

---------------------------------------------------------
5,?,26,67,105,150,?,242,368,504,624,?,954 daily omicrons at cog_UK
1,1,3,7,7,19,40,65,31,81,100,107,118,125,150,74,13 ,12 by collection date since Nov20
more than delta in 18 days with this trend (slows down a bit)
------------------------------------------------------

[blacknail]

There is another reason that could explain this - there is a mutation that s causing a second target failure - this would explain why positive test results are being affected while they confirm what is going on with samples that only showed one target.

edit - this is just a hypothesis that I dreamt up - I have not seen any evidence

[gsgs]

---------------edit 2021-12-13------------------
backlog now. Yesterday's decline was not real.
Balloux deleted his thread, NICD apologizes, no comment by Moultrie yet.
It's still not exponential, more linear, but still growing

https://www.nicd.ac.za/latest-confirmed-cases-of-covid-19-in-south-africa-12-december-2021/

More backlogs expected

https://twitter.com/nicd_sa/status/1470128000746274820

------------------------------------------
IMO they should include estimates, what the real numbers are
in general
WHO,CDC,RKI,ECDC,
UN,.gov, - whatever
can be just one letter, if the estimate coincides with the given numbers
-----------------------------------------

[gsgs]

maybe older people are protected against omicron from multiple previous exposures to other cold-(corona) viruses
which were circulating decades ago ?!?
we saw that with flu
------------------------------------------
we could/should have created an omicron-like virus in the lab , more transmissable less virulent
maybe after this wave such strategies will be developed (H5N1)
But we must reach an international consensus and surveillance, because it could lead
to new manmade pandemics

[silylene]

https://www.theguardian.com/world/2021/dec/12/uk-has-omicron-covid-patients-in-hospital-government-confirms

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

People have been admitted to hospital with the Omicron variant in Britain, a government minister has confirmed, as a senior public health adviser said further curbs may be needed.

The education secretary, Nadhim Zahawi, said he could confirm there were “cases in hospital with Omicron”. “We’ve been able to test people who are in hospital over the past two weeks, and so there is a lag to hospitalisation,” he told Trevor Phillips on Sky News.


Speaking to the BBC, Susan Hopkins, the chief medical adviser of the UK Health Security Agency, said hospitals were diagnosing Omicron in an increasing number of people coming into emergency departments and that the numbers in hospital were expected to increase.

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.

[Pathfinder]

CDC Predicts U.S. COVID Deaths Will Rise As Britain Reports First Omicron Death

BY JENNI FINK ON 12/13/21 AT 10:53 AM EST
...
It's unclear what impact Omicron will have on hospitalizations and deaths, though. Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases (NIAID), told the Agence France-Presse the "best-case scenario" would be Omicron being highly transmissible but a variant that causes only mild disease.

Omicron causing mild disease could help the world avoid the surge in hospitalizations and deaths that Delta's fueling, according to Fauci.

However, Daniel Havlichek, former Chief of the College of Human Medicine's Infectious Diseases Division at Michigan State University, noted that if Omicron is 10 times more transmissible but only causes severe disease in one-tenth the people, there could be the same number of deaths by raw numbers. WHO COVID-19 technical lead Maria van Kerkhove also raised concerns about people getting complacent if Omicron is less severe than Delta.

Even if most people only have a mild illness, van Kerkhove told Face the Nation that a highly transmissible variant will increase the number of infections and as cases rise, so will hospitalizations because some people will get seriously ill.
...
https://www.newsweek.com/cdc-predict...-death-1658772

[silylene]

Danish Omicron case study just published. About 3,400 cases. Very interesting. Hospitalization rate is a bit greater than other variants. Primarily attacking 20-29 yr old category (unexpected!), and fewer cases among the 64+ yr old category (unexpected to me). Vaccine evasion is about twice the rate as other variants. Rapport om omikronvarianten https://t.co/ZstMAZZ2bd

[silylene]

The number hospitalized however is still small (n=14 in report). Maybe because of case time lag, more youthful case incidence, and protective effects of high vaccination levels? I think more hospitalization cases are needed before drawing any type of statistically firm conclusions.

[blacknail]

Yes, the number of cases is small, I was looking at table 6 that shows the cumulative Omicron cases as 28 (Tested positive prior or within
48 hrs after admission), or 0.8% of Omicron cases vs. 0.7% for other variants.

There are still many confounding factors though - perhaps people seek care more quickly when they are informed they have a novel strain; perhaps the omicron cases don't progress to higher levels of care; perhaps the younger age of the patients comes in to play.

[Emily]

Sounds like the same pattern that SA has. Nothing alarming if that is true.

[Emily]

https://twitter.com/tomhcalver/statu...64449773133824



Tom Calver @tomhcalver


South Africa's case fatality rate falls again to 0.5%. The theory that Omicron causes milder symptoms is becoming very hard to ignore...



12:06 PM · Dec 13, 2021·Twitter Web App

[Emily]

Video of interview with Dr Angelique Coetzee at link. Says it is generally mild for everyone, whether vaccinated or not, young or old.

https://twitter.com/statsjamie/statu...93515157819398


Jamie Jenkins
@statsjamie

Can we have Dr Angelique Coetzee on with Boris tonight at 8pm "There's no reason why you can't trust us when we say to you 'it's mild disease!'" Works for the South African Medical Association with details of the Omicron situation in the country

SA Medical Association head

From LBC

12:09 PM · Dec 12, 2021·Twitter for iPad

[sharon sanders]

Mia Malan

3 hours ago, 25 tweets, 8 min readRead on Twitter BREAKING [Thread]: 1. SA’s first real-world data on #Pfizer’s #COVID19 jab’s protection @ #Omicron infection + hospitalisation via @Discovery_SA + @MRCza

Note: This is data from the 1st 3 weeks of the outbreak, so it might change - regard it as preliminary real-world data

2. What data are findings based on?
1. @Discovery_SA = SA’s largest health insurer (3.7 mil members)
2. They used 211,000 positive #COVID19 PCR tests of adults (18+)
3. 41% of 211,000 + tests = received 2 doses of #Pfizer


3. Here is how #Omicron has progressed in SA:
#Omicron = now 90% of #COVID infections in SA


4. How effective is #Pfizer’s jab @ hospitalisation due 2 #Omicron?
1. 2 doses of #Pfizer’s jab makes vaccinated people 70% less likely 2 get hospitalised vs. unvaccinated people
2. This = lower than 93% protection the jab gave in SA’s #Delta wave (93% = @Discovery_SA data)

5. Protection of 2 doses of #Pfizer @ hospital admission due to #Omicron is maintained across all ages (18-79 years), but slightly lower for older age groups:
18-29: 92%
30-39: 75%
40-49: 82%
50-59: 74%
60-69: 67%
70-79: 59%

6. Important to note that the lower protection (down from 93% to 70%) against hospitalisation because of #Omicron could be because older people were vaccinated first in SA, so there has been a longer period for vaccine-derived immunity to wane than with younger age groups

7. 70% protection for vaccinated people @ hospital admission = still a high level of protection. WHO regards a #COVID19 vaccine effective if it provides 50% protection: bit.ly/325K60Y...

8. What about the risk of hospitalisation due to #Omicron infection compared to the variant (D614G) which dominated SA’s 1st #COVID wave?

Adults (18+) infected with #Omicron = 29% less likely to be hospitalised vs. infection with other variants

9. What are confounding factors for #Omicron real-life hospital admission data in SA?
High seroprevalence #SARS-CoV2 antibody levels in SA population (so antibodies due to previous #COVID19 infection) - in Gauteng = as high as 70% + of people

10. Hospital admissions (anecdotal data):
1. Most #Omicron admissions = unvaccinated people (16% of ICU admissions = vaccinated)
2. High % of incidental admissions (people going 2 hospital 4 things other than #COVID + test 4 admission + find out they have #COVID)

11. Out of hospital data (anecdotal):
1. @Discovery_SA is seeing milder illness with #Omicron (early data) with recoveries within 3 days
2. Higher reinfections (so people who've had #COVID19 get infected again) and breakthrough infections (vaccinated people getting infected)

12. #Omicron cases are growing much faster than during the #Delta wave, but hospitalisations slower. For the Omicron wave, SA has reached 60% of cases reached during the #Delta peak but we have reached only 20% of the hospital admissions of the Delta wave.

13. Children and #Omicron:
1. Main diagnoses 4 kids who get hospitalised = bronchiolitis and pneumonia, often with severe gastrointestinal symptoms + dehydration
2. Most kids = not hospitalised = mild symptoms (sore throat, nasal congestion, headache, fever, resolves in 3 days)

14.
1. Kids below 18 infected with #Omicron = 20% higher risk of admission 4 #COVID19 complications vs. 1st wave
2. This aligns with the 3rd #Delta wave (June-Sep 2021) when an increase in pediatric admissions (0-5 yrs) = also seen (so 4th wave risk = similar to 3rd wave risk)

15. To date, kids below 5 = higher admission risk than adults, but this could be driven by incidental admissions. This trend is starting to change: it looks like fewer children and more adults are starting to get admitted (@nicd_sa = similar findings).


16. NB data to point out re children:
1. The risk of kids testing + for #COVID19 because of #Omicron = 51% lower compared to adults
2. @nicd_sa/@MRCza data from Tswhane show most kids = admitted 2 hospital = incidental admissions


17. Vaccinated people = 33% less likely 2 get infected with #Omicron than unvaccinated people (this is a drop from 80% protection during the #Delta wave)

Here's how #Pfizer protection @ infection wanes 4 Omicron:
1. 2-4 wks after 2nd dose: 56%
2. 3-4 mnths after 2nd dose: 25%

18. What about the risk of reinfection?

1. People infected with #Delta = 40% relative risk of reinfection with #Omicron
2. People infected with Beta = 60% relative risk of infection with Omicron

19. More data on the reinfection risk with #Omicron:

@SACEMAdirector et al. in SA found the relative risk of reinfection with #Omicron for people who previously had #COVID and get exposed again = 3 times higher than for reinfection with #Delta/#Beta:



20. Two shots of #Pfizer continues to provide good protection @ hospitalisation, but protection has dropped from 93% with #Delta to 70% with #Omicron.

21. The protection @ hospitalisation that 2 shots of #Pfizer provide @ #Omicron infection for different ages:
- Highest protection = 18-29 yrs
- Lowest protection in 70-79 yrs
(Could be because 70-79 = vaccinated before 18-29, so = been more time for 70-79's immunity 2 wane)

22. This graph shows that #Omicron infection is associated with a 29% lower risk of hospital admission for adults compared to the 1st wave, but children have a 20% higher admission risk (but as mentioned previously, looks like it's starting to change).

23. Although excess deaths were high for the week of 28 Nov, it's still much lower than in previous #COVID19 waves (this correlates with lower #Omicron death rate data in hospitals, but it's early times)

24. How did @Discovery_SA obtain #PCR test data?
1. Results from @LancetLab_ZA [private lab] (45%)
2. Gauteng test results 55%
3. Results from hospital patients 8%

25. Summary:
1. Vaccination continues to provide significant protection @ falling seriously ill with #COVID (although reduced to 70%)
2. High nrs of breakthrough infections in vaccinated people (protection @ infections reduced from 80% to 33%)
3. Reinfection risk = increased

[sharon sanders]

bump this

[Pathfinder]

World Health Organization (WHO)
@WHO
·
33m

"77 countries have now reported cases of Omicron, and the reality is that Omicron is probably in most countries, even if it hasn’t been detected yet. Omicron is spreading at a rate we have not seen with any previous variant"-
@DrTedros
#COVID19
...
"We’re concerned that people are dismissing Omicron as mild.Surely, we have learned by now that we underestimate this virus at our peril. Even if Omicron does cause less severe disease, the sheer number of cases could once again overwhelm unprepared health systems"-
@DrTedros
...
"I need to be very clear: vaccines alone will not get any country out of this crisis.

Countries can – and must – prevent the spread of Omicron with measures that work today"-
@DrTedros
#COVID19
...
"It’s not vaccines instead of masks.

It’s not vaccines instead of distancing.

It’s not vaccines instead of ventilation or hand hygiene.

Do it all. Do it consistently. Do it well"-
@DrTedros
#COVID19

[gsgs]

WHO becomes less and less competent.
What is this based upon ? Are there any studies or is it just
Tedros' personal opinion ?
Who else says this ?

Most competent seems to be UK, currently (?) UKHSA,nhs.uk,gov.uk,SAGE,NERVTAG,
USA-CDC has lost some reputation recently too.
Maybe rely on ECDC ? RKI ? Macron ? #Topol,Balloux,Ward,Ding,Malan,Chise,...

So,vaccines, masks, distancing, ventilation, _and_ hand-hygiene

But countries do work_from_home, lockdown, 2g , vaccine passports, travel restrictions,
cancelling events, boosters.

[Emily]

UK?

https://www.breitbart.com/europe/2021/12/14/project-fear-number-uk-omicron-hospitalised-revised-250-10/

Project Fear: Number of UK Omicron Hospitalised Revised from 250 to 10

[sharon sanders]

bump this

[Pathfinder]

Omicron ‘probably the most significant threat’ since start of the pandemic, British health chief says

PUBLISHED WED, DEC 15 20211:27 PM EST
Matt Clinch

LONDON — Jenny Harries, CEO of the U.K. Health Security Agency, has given a stark warning of the threat that the new heavily mutated Covid-19 omicron variant poses to the country.
...
“I’m sure for example the numbers that we see on data over the next few days will be quite staggering compared to the rate of growth that we’ve seen in cases for previous variants,” she told a committee of British lawmakers on Wednesday.

“The real potential risk here — and I would underline that because we are still learning a lot about the variant — is in relation to its severity, clinical severity, and therefore whether those cases turn into severe disease, hospitalizations and deaths. We’re still at too early stage for that. In fact, the world probably is still at too early stage to be clear,” she added.
...
Harries also said Wednesday: “We don’t know what’s going to happen. But at the moment the indications are it could be as big or even bigger than the previous wave this time last year. So we’re preparing for that.”

https://www.cnbc.com/2021/12/15/omicron-probably-the-most-significant-threat-since-start-of-the-pandemic-british-health-chief-says.html

[Emily]

Delta must have missed the UK, then.

[Pathfinder]

Scientists see a ‘really, really tough winter’ with Omicron

Another major pandemic wave seems inevitable. The big question is how much severe disease it will bring

14 DEC 20214:05 PMBYKAI KUPFERSCHMIDT
...
Even if Omicron causes milder disease, as some scientists hope, the astronomical case projections mean the outlook is grim, warns Emma Hodcroft, a virologist at the University of Bern. “A lot of scientists thought Delta was already going to make this a really, really tough winter,” she says. “I’m not sure the message has gotten across to the people who make decisions, how much tougher Omicron is going to make this.”

...Harvard University epidemiologist William Hanage says the question of severity is still impossible to answer. ...By chance, many of the early cases in South Africa happened to be in younger people, who are less likely to develop severe disease. And even if the variant turns out to be inherently milder, the volume of cases will likely overwhelm health systems. “A colleague put it really well in one of our little depressing Slack channels,” Hanage says: “There’s not much that can spread this fast and be benign to a society that’s already got full hospitals without it.”

Scientists also worry Omicron—which represented a massive leap from known variants in genomic terms—may bring other, unpleasant evolutionary surprises. For instance, roughly one-tenth of Omicron genomes sequenced so far have an additional mutation in the spike protein called 346K that is predicted to make it even better at evading the immune system. “Omicron has most of the greatest hits for antibody escape already, so there aren’t a ton of additions that it could make, but 346K is one of them,” says Stephen Goldstein, a virologist at the University of Utah. “We have to keep an eye on it.”
...

https://www.science.org/content/article/scientists-see-really-really-tough-winter-omicron

[blacknail]

I don't see it as "by chance". People in their 20's are exactly the demographic that has less accountability than older demographics and less supervision than younger demographics.