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

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Christian Althaus

@C_Althaus
·
5h
Assuming the same generation time, the transmission advantage could act at two levels: 1) increase in transmissibility, 2) immune evasion. We recently developed a mathematical framework to relate differences in growth rates to these properties. 5/15

medrxiv.org
A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in...
Several SARS-CoV-2 variants of concern (VOC) are spreading rapidly in different regions of the world. The underlying mechanisms behind their transmission advantage remain unclear. We measured viral...
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56
Christian Althaus

@C_Althaus
·
5h
A potential increase in transmissibility can be expressed as ρD/R_w, where X is the estimated growth advantage (0.43 per day), D the generation time (5.2 days), and R_w the effective reproduction of the previous variant (~ 0.8 in RSA during October). 6/15 https://ibz-shiny.ethz.ch/covid-19-re-international/…
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Christian Althaus

@C_Althaus
·
5h
This would result in an increased transmissibility of 280% (95% CI: 98-468%). With Delta having an R_0 = 5-6 in the Northern Hemisphere during winter, the R_0 of Omicron would be around 10-30. Not impossible, but such a jump seems rather unlikely. 7/15
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Christian Althaus

@C_Althaus
·
5h
If the transmission advantage acted via immune evasion only, the level of immune evasion would be ρD(1-Ω)/(ΩR_w), with Ω being the proportion of the population that has fully protective immunity against infection with earlier variants. 8/15



Christian Althaus

@C_Althaus
·
5h
South Africa records an excess mortality of 230k during the pandemic, which corresponds to 0.39% of the overall population (https://github.com/dkobak/excess-mortality…). We earlier estimated the infection fatality ratio for the population of South Africa to be 0.35% (https://doi.org/10.1007/s10654-020-00649-w…). 9/15

github.com
GitHub - dkobak/excess-mortality: Excess mortality during COVID-19 pandemic
Excess mortality during COVID-19 pandemic. Contribute to dkobak/excess-mortality development by creating an account on GitHub.
3
42
Christian Althaus

@C_Althaus
·
5h
Hence, it is likely that almost everyone in South Africa has been infected with #SARSCoV2 and developed partial immunity against reinfection. In addition, 24% of the population have been fully vaccinated. 10/15

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Christian Althaus

@C_Althaus
·
5h
Thus, the proportion of the population that is fully protected (‘immune’) against infection and further transmission must be quite high. If we assume Ω = 75%, we get an immune evasion of 93% (95% CI: 32-100%), i.e., Omicron evades protective immunity in 93% of individuals. 11/15
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Christian Althaus

@C_Althaus
·
5h
For Ω = 90%, we obtain an immune evasion of 31% (95% CI: 11-52%) ‘only’. This clearly illustrates the current level of uncertainty about Omicron, and I want to emphasize again the preliminary character of these calculations. 12/15
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Christian Althaus

@C_Althaus
·
5h
Still, I do expect partial immune evasion to be the main driver of the observed dynamics, but increased transmissibility cannot be ruled out so far. 13/15
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Christian Althaus

@C_Althaus
·
5h
The developments in South Africa and observations from other countries during the coming days and weeks will allow us to shed more light on the properties of Omicron. 14/15
1
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Christian Althaus

@C_Althaus
·
5h
Finally, thanks for the amazing work from
@Tuliodna
,
@houzhou
,
@rjlessells
, and their colleagues in South Africa,
@firefoxx66
from
@ISPMBern
at
@unibern
for http://covariants.org,
@richardneher
and
@trvrb
for
@nextstrain
, and the many others working around the clock. 15/15

covariants.org
CoVariants
SARS-CoV-2 Mutations and Variants of Interest
5
7
99
 
Hospitalizations in Gauteng SA have tripled in the last 2 weeks (ICU + 'High Care'). Disease doesn't seem 'mild' at all. [reference: Dr. E. Feigl-Ding]
FFTcPdiXMAEZcGM?format=jpg&name=large.jpg
 
NICD-reports
daily hospitalisations, powerpoint
several weekly reports .pdf
https://www.nicd.ac.za/diseases-a-z...urveillance-reports/covid-19-special-reports/

NATIONAL COVID-19 DAILY REPORT
DAILY HOSPITAL SURVEILLANCE (DATCOV) REPORT
WEEKLY EPIDEMIOLOGICAL BRIEF
WEEKLY RESPIRATORY PATHOGENS SURVEILLANCE REPORT
WEEKLY TESTING SUMMARY
WEEKLY PRIVATE CONSULTATIONS EPIDEMIC THRESHOLD
WEEKLY HOSPITAL SURVEILLANCE (DATCOV) UPDATE
WASTEWATER-BASED EPIDEMIOLOGY FOR SARS-COV-2 IN SOUTH AFRICA
THE INITIAL AND DAILY COVID-19 EFFECTIVE REPRODUCTIVE NUMBER IN SOUTH AFRICA
PRIVATE CONSULTATIONS EXCESS RESPIRATORY ENCOUNTERS
SPECIAL PUBLIC HEALTH SURVEILLANCE BULLETIN
MODELLING CONSORTIUM (PROJECTIONS)
COVID-19 SPECIAL REPORTS
MONTHLY COVID-19 IN CHILDREN
 
Covid Omicron: No need to panic, South Africa minister says

Published1 hour ago
...
Government adviser and epidemiologist Salim Abdool Karim said he expected the number of cases to reach more than 10,000 a day by the end of the week, and for hospitals to come under pressure in the next two to three weeks.

Dr Phaahla said he wanted to "reiterate that there is absolutely no need to panic" because this "is no new territory for us".

"We are now more than 20 months' experienced in terms of Covid-19, various variants and waves," he added at a media briefing.
...
Health experts said that Gauteng, which includes Johannesburg, had entered a fourth wave, and most hospital admissions were of unvaccinated people.
...
https://www.bbc.com/news/world-africa-59463879
 
No media notice given on this prepared media event (Fauci standing next to President) - unless we were dropped off the list again....


President Biden:

do not to panic,
get vaccines and booster,
new vaccines are being developed if needed,
reminding on vaccines again,
US plan for winter does not include shut downs or lockdowns,
need to vaccinate the world,
US in better place in Dec. 2021 than Dec. 2020 because of vaccines,

Fauci briefly restates US entry policy.

Biden:

everyone should wear masks indoors unless eating or speaking at microphone,
urges vaccines and boosters again,
lockdowns off the table for now,
travel restrictions in place to give everyone a chance to get vaccines.

The end.
 
a new virus is created, presumably in an unknown South African immuno deficient patient
treated with antibodies.
it spreads quickly and pandemic waves around the world are expected with millions of deaths
and billions diseases and trillions of costs..
It has an unusual number of mutations not seen before and suggests that this may become
common now and will probably happen again.
And all that SA and WHO has to say is don't panic and complain about travel bans.
 
updated to 580. weekly hospiitalizations : 125,120,135,276,580,71 (last 2 weeks will be updated)
weekly positives : 593,547,426,737,2762 (expect an updated 10-20% increase for the last 2 weeks)
weekly positive rates 0.9%,0.9%,0.7%,1.1%,4.3%
promille increase yesterday in hospital admissions by age10group : 9,8,7,3,1,1,1,1,1,0
(all for Gauteng only)
{doesn't look milder than delta from these numbers}
 
--President Biden's update on Omicron to the public was announced yesterday --

Biden told it will take two weeks to have definitive data on Omicron variant

November 28, 20218:02 PM CST
Last Updated a day ago

By Susan Heavey

... Biden was due to update the public on the new variant and the U.S. response on Monday, the White House said. ...

https://www.reuters.com/world/us/us-...source=twitter
_________________________________________________

Biden to address nation on Omicron variant as travel restrictions take effect

November 29, 2021 9:32am

By Mark Moore

President Biden will update the nation on his administration’s response to the Omicron variant of COVID-19 on Monday, hours after travel restrictions targeting eight countries in southern Africa went into effect.

The president is scheduled to give remarks at 11:45 a.m. following a briefing with the White House pandemic response team, including chief medical adviser Dr. Anthony Fauci.

https://nypost.com/2021/11/29/biden-to-address-nation-on-omicron-variant-amid-restrictions/
 
-- Here it states the first detection of Omicron was on November 11th, 19 days ago --



— Trevor Bedford @trvrb

Here, I took the exact same approach using 77 available Omicron genomes from South Africa and Botswana. This yields a median estimate of a common ancestor at Oct 7 (95% CI between Sep 19 and Oct 21). This seems consistent with first detection in a sample from 11 Nov.

https://twitter.com/trvrb/status/1464353262119776258
 
Hat tip to https://twitter.com/BillyBostickson

https://twitter.com/Daoyu15/status/1464873865448808450
https://archive.md/dpuIq
Viret Seb
@SebViret

·
Nov 27
@stuartjdneil
, I’m would be interested to have your serious opinion on that. Seems yet another type of look for trouble experiment. And apparently useless wrt the one you described yesterday
Quote Tweet
Yuri Deigin
@ydeigin
· Nov 27
Oh and they actually were doing similar experiments in South Africa: https://pubmed.ncbi.nlm.nih.gov/33780970/
Show this thread

Viret Seb
@SebViret

·
Nov 27
Found one rational explanation actually
Quote Tweet
Moritz Gerstung
@MoritzGerstung
· Nov 26
Some thoughts about the punctuated evolution of variants of concern including B.1.1.529 in Southern Africa.
cleanpastedhtml
A shared characteristic of all known VOCs is that they appeared suddenly with a large number of mutations, many more than the incremental changes we see normally.
Show this thread


Daoyu
@Daoyu15

·
Nov 28
Or they are the result of experiments. MA experiments, VSV-spike experiments. BSL-3 containment is actually insufficient to contain SARS-CoV-2 and many directed evolution models are BSL-2.


Daoyu
@Daoyu15

·
Nov 28
Poor containment efficacy especially if the virus is used as an infectious cDNA clone, or recombination-prone large segments of the viral genome were used in a model that does not involve the full virus and therefore used in BSL-2


Daoyu
@Daoyu15
·
Nov 28

theaustralian.com.au
Beijing lab mishap ‘infected scientist’
A Beijing laboratory director was infected with Covid-19 in a lab accident in early 2020, explosive emails have revealed, showing an inadvertent leak of the highly contagious coronavirus is far from...


Daoyu
@Daoyu15
·
Nov 28
H655Y
Quote Tweet
notoriousFIL
@notoriousFIL
· Aug 14
I posited yesterday that perhaps the presence of H655Y in the Gamma variant could be understood as evidence of a laboratory acquired infection. It has been brought to my attention that a preprint specifically regarding properties of this mutation came out on August 5th. A
cleanpastedhtml
:
Show this thread


Daoyu
@Daoyu15

·
Nov 28
Also, HIV patients usually give line lengths that are about half this length. The line length lead to other VOCs were less than 1/4 that lead to 21K. Not likely a single patient can cause this. It takes more plasma selection using VSV-SARS-CoV-2 S to achieve this.


Daoyu
@Daoyu15

·
Nov 28
The length leading to other VOCs were less than half to about a quarter that of the 21K cluster. The S1 had twice as many mutations than all that have ever been accumulated before. Hard to make for a single patient, and would have required directed evolution (VSV-spike passages)


Daoyu
@Daoyu15

Replying to
@Daoyu15
and
@SebViret
In order for this to suddenly jump to twice the accumulated mutations of previous strains without leaving behind even a single sampled intermediate strain given the frequency of sampling globally and in ZA.
8:30 AM · Nov 28, 2021·Twitter for iPhone

8
Retweets

6
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23
Likes
 
Two doctors in Israel infected with suspected Omicron variant. Triple vaccinated (with Pfizer vaccine I assume since it is Israel). Presumably infected despite full PPE [*my assumption]


Omicron COVID variant: Two Sheba doctors confirmed infected

"Regarding the first doctor, the hospital said in a statement on Monday that “the doctor is vaccinated with three doses of the coronavirus vaccine, his condition is mild and he is improving,” adding that he does not need any medical attention."
"The second doctor, also a cardiologist, was likewise fully vaccinated." [*which means 3 shots in Israel]


https://www.jpost.com/health-and-we...est-positive-for-omicron-covid-variant-687412
 
Last edited by a moderator:
The 3D "shape" is illustrated in Alpha B.1.1.7, Delta B1.617.2, Beta B1.1.351 and Gamma: P.1.
In other words, the 3D "shape" is the same for all variants listed above.
 
Translation google


Omicron variant: the "light at the end of the tunnel" that will end the covid epidemic?

The new variant could sign the end of the epidemic.

Published on 11/30/2021 at 3:51 PM

Paradoxically enough, the appearance of the Omicron variant could be good news in the fight against the covid epidemic.

"In my opinion, this new variant is perhaps the light at the end of the tunnel," assures an Israeli immunologist on Tuesday on i24News .

Professor Zvika Granot of the Hebrew University of Jerusalem believes Omicron "is a very contagious variant, but perhaps not as aggressive as feared".

The doctor is basing his analysis on data from South Africa where this new variant was identified last week. The health authorities of the countries of southern Africa, particularly affected, indicate that the cases of Omicron rather suffer from benign symptoms less virulent than those of the Delta variant, which has become the majority in the world since this summer. People infected with this mutated virus seem to suffer much less from breathing difficulties in particular.

"Less and less aggressive"

"As the coronavirus evolves, it will be less and less aggressive," added Professor Granot. Omicron could therefore eventually supplant Delta with its high transmission capacity but at the same time drastically reduce the impact on the health system. According to the immunologist, the virus will probably still be present for many years, with new variants, less and less able to reach the status of a global pandemic.
...
Nicolas Monnet

https://www.i24news.tv/fr/actu/coro...iere-au-bout-du-tunnel-scientifique-a-i24news

-----------------------------------------------------------------------------------

#i24NEWS #i24NEWSDesk'

Maybe this new variant is the light at the end of the tunnel,' says immunologist


30 Nov 2021

 
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