Omicron

[ShortForBob]

Well it's got a name now.

Case numbers are still tiny and there's not much information about levels of illness or mortality.

Maybe this one will be friendlier (more transmissible, less deadly) 

We can hope.

(but we've only got ourselves to blame)

The World Health Organization (WHO) is calling for calm as the new Omicron coronavirus strain causes international borders to slam shut and global financial markets to plunge.


Key points:

• The WHO said it will take "a few weeks" to understand the full impact of Omicron
  
• Scientists fear current vaccines will not be effective against new strain
  
• Global stocks plummeted upon news of the Omicron variant 
  

Dozens of countries have closed their borders to South Africa and its neighbouring countries, where the variant was first found.

Scientists said it could take weeks to fully understand the variant's mutations and whether existing vaccines and treatments would work against it.

"Early analysis shows that this variant has a large number of mutations, that will require us to undergo further study," the WHO's Christian Lindmeier said.


"It will take a few weeks for us to understand what impact this variant has."

https://www.abc.net.au/news/2021-11-27/omicron-covid-19-borders-vaccines-mutant/100655742

 

[ShortForBob]

May as well start with WHO's news

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked to do the following:

• enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  
• submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  
• report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  
• where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.
  

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

A SARS-CoV-2 VOI is a SARS-CoV-2 variant:

• with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  
• that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. 
  

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

• increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  
• increase in virulence or change in clinical disease presentation; OR
  
• decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics
  

 



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[TheDragon]

Sucks, let's just hope it causes less serious disease. The rise in cases this week in South Africa is beyond exponential, from a couple hundred to a couple thousand and surely will skyrocket from there. Too soon to tell how serious disease it will cause, and since most South Africans remain unvaccinated, might take a while to tell if can infect vaccinated folk even more easily than Delta. But the data are telling that it (B.1.1.529 here) is already eliminating Delta, witness this graph of sequenced viral samples. In ten days it has gone from nothing to over 75%. I am scheduled to fly there Friday, and while Delta Airlines promises to continue service to Johannesburg from Atlanta, that might be hard to sustain after Monday when only US citizens and residents will be able to fly back to USA, so I'm trying to change my ticket to Wednesday or even Sunday.

 

[Zonker]

What is wrong with epsilon? Omnicron is hard to say

 

[NeedAClew]

@TheDragon be careful! Safe travels. 

 

[TheDragon]

Luckily this variant exhibit S-gene dropout in the standard PCR tests that amplify regions of the S gene and two other genes. As a result it can be easily tracked without having to do full genome sequencing, and already almost all cases in South Africa are this new Omicron variant by this criterion. I'm surprised other countries are not checking their PCR results to look for this feature, as this variant has surely already spread widely.

 

[Rain Man]

Luckily this variant exhibit S-gene dropout in the standard PCR tests that amplify regions of the S gene and two other genes. As a result it can be easily tracked without having to do full genome sequencing, and already almost all cases in South Africa are this new Omicron variant by this criterion. I'm surprised other countries are not checking their PCR results to look for this feature, as this variant has surely already spread widely.

Yes, it is surprising that countries are limiting entry from certain places.  That didn't work last year, and has almost no hope this year.  Small countries like New Zealand  with few entry points might benefit from such a strategy but most countries need not bother.

 

[SCARECROW]

Yes, it is surprising that countries are limiting entry from certain places.  That didn't work last year, and has almost no hope this year.  Small countries like New Zealand  with few entry points might benefit from such a strategy but most countries need not bother.

that was my first thought when reading the stories too.  Its already been dedicated in Europe, the Middle east and Asia.  Too late to close the barn door kids.

 

[IStream]

It buys time. Assuming it's not already here, this step could provide an extra month or two before it (inevitably) gets established here. With mRNA vaccines (that can be re-designed quickly), that extra time could be the difference between a manageable wave and a catastrophe.

 

[ShortForBob]

It buys time. Assuming it's not already here, this step could provide an extra month or two before it (inevitably) gets established here. With mRNA vaccines (that can be re-designed quickly), that extra time could be the difference between a manageable wave and a catastrophe.

Nah. We are all pretty fucked if this gets hold IMHO.

What bought us time was sensible people taking sensible precautions and sensible governments implementing harsh restrictions. We should have used that time vaccinating the world.

People are too weary of it all to go there again and Governments too fearful of smashing their economies and the polls.

Best we can hope is that the numerous vaccines provide some protection and that the mutations don't cause even nastier effects.

 

[ShortForBob]

I am scheduled to fly there Friday, and while Delta Airlines promises to continue service to Johannesburg from Atlanta, that might be hard to sustain after Monday when only US citizens and residents will be able to fly back to USA, so I'm trying to change my ticket to Wednesday or even Sunday.

Just hope your Gov doesn't opt for the Aussie option to buy time and lock you out. 

 

[phill_nz]

it's not known what this variant is yet

it can be any of 3

worse in that it's even more deadly ../  has the same as most others .. or /  a savior in that it does little else than further inoculate the infected against the others

sort of a vaccination for the anti vaxxers

if it's the last i would open the borders and welcome it in .. there will be that variant sooner or latter

 

[Rain Man]

it's not known what this variant is yet

it can be any of 3

worse in that it's even more deadly ../  has the same as most others .. or /  a savior in that it does little else than further inoculate the infected against the others

sort of a vaccination for the anti vaxxers

if it's the last i would open the borders and welcome it in .. there will be that variant sooner or latter

Yes, far too early to tell, but the rumour mill has already chosen the first.  I would expect the stock market to react quite violently on Monday. 

 

[weightless]

The rise in cases this week in South Africa is beyond exponential, from a couple hundred to a couple thousand and surely will skyrocket from there.

There's a fair bit of high frequency noise in their data.

 

[dogwatch]

What is wrong with epsilon? Omnicron is hard to say

Nothing but a variant was named "epsilon" back in July. https://www.independent.co.uk/news/health/epsilon-variant-covid-california-explainer-b1878909.html

The next Greek letter for allocation was "Nu". WHO decided not to use it as everyone confused it with "New".

 

[TheDragon]

And just to clarify it is spelled Omicron, even though Omnicron sounds more appropriate for a virus that might infect everyone on the planet, vaccinated or not.

 

[NeedAClew]

Just hope your Gov doesn't opt for the Aussie option to buy time and lock you out. 

I don't think we can bar entry to citizens and green card holders or their families. Not sure exactly why but none of the entry restrictions ever have applied to same. Hence ineffective. 

 

[ShortForBob]

I don't think we can bar entry to citizens and green card holders or their families. Not sure exactly why but none of the entry restrictions ever have applied to same. Hence ineffective. 

we didn't either.

Executive orders seem popular.

 

[NeedAClew]

we didn't either.

Executive orders seem popular.

But you had quarantine. We did that for Wuhan evacuees and maybe a cruise ship  iirc but not after the first month of covid. I think it's a Constitution thing here. EO on entry can't supercede that.