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Omicron variant

The home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
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This is the home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
pje16
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Re: Omicron variant

#461558

Postby pje16 » November 28th, 2021, 11:23 am

Re the OP
viewtopic.php?f=98&t=32279#p460956
UK Gov now loses Kudos for a delay
https://www.bbc.co.uk/news/uk-59449480
Why wasn't this done yesterday when Bo Jo addressed the nation :roll:

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Re: Omicron variant

#461560

Postby vagrantbrain » November 28th, 2021, 11:32 am

redsturgeon wrote:
We just need to be sensible.



And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.

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Re: Omicron variant

#461563

Postby redsturgeon » November 28th, 2021, 11:36 am

vagrantbrain wrote:
redsturgeon wrote:
We just need to be sensible.



And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...

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Re: Omicron variant

#461567

Postby vagrantbrain » November 28th, 2021, 11:52 am

redsturgeon wrote:
vagrantbrain wrote:
redsturgeon wrote:
We just need to be sensible.



And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...


I'm done. Take care

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Re: Omicron variant

#461568

Postby gryffron » November 28th, 2021, 11:54 am

Evidence SO FAR from SA is that omicron has high transmissibility but very mild symptoms. And yes, that's based on a fairly small number of positively identified cases. IF that holds up, it may itself prove to be a natural vaccine against its more dangerous cousins. I guess that's ultimately how pandemics die out.

Gryff

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Re: Omicron variant

#461571

Postby pje16 » November 28th, 2021, 11:55 am

redsturgeon wrote:
vagrantbrain wrote:
redsturgeon wrote:
We just need to be sensible.



And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...

The media is also to blame for overdoing "shortage of.." type headlines
Last month for example, if they hadn't reported the fact that a handful of BP stations could not get fuel delivered
there wouldn't have been a shortage so blame them if you had to sit is a queue

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Re: Omicron variant

#461576

Postby redsturgeon » November 28th, 2021, 12:09 pm

vagrantbrain wrote:
redsturgeon wrote:
vagrantbrain wrote:
And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...


I'm done. Take care


To ask the Sun to "wind it in a bit" is a bit like asking the sun not to rise tomorrow. The raison d'etre of the Sun is to produce headlines like these.

John

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Re: Omicron variant

#461577

Postby onthemove » November 28th, 2021, 12:13 pm

gryffron wrote:Evidence SO FAR from SA is that omicron has high transmissibility but very mild symptoms. And yes, that's based on a fairly small number of positively identified cases. IF that holds up, it may itself prove to be a natural vaccine against its more dangerous cousins. I guess that's ultimately how pandemics die out.

Gryff


Unless of course you take great pains to keep out that new variant and prevent it circulating.

(I guess this is where you got your info ... "the South African doctor who first spotted the new Covid variant Omicron, says the patients seen so far have had "extremely mild symptoms"" https://www.bbc.co.uk/news/av/uk-59450988 )

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Re: Omicron variant

#461579

Postby Julian » November 28th, 2021, 12:16 pm

redsturgeon wrote:Watching the Marr show this morning to try to get a calm overview of where we are this is my take.

South African doctor reports new variant a few days ago that seems highly transmissible and gives rise to a slightly different set of mild symptoms in those patients seen. (NB "mild" just means not needing hospitalisation)

This new variant is found to contain an very large number of mutations and thus could evade the current vaccines.

In the light of this, measures are swiftly taken to limit spread.

A renewed push on vaccines is in place.

Vaccine companies are already looking to prepare new vaccines available in a few months.

In the meantime we may find that best case scenario is that the Omicron variant, though highly contagious is relatively mild and the measures put in place have been an over reaction. We should know more in two weeks.

Worst case scenario is that Omicron evades the vaccine and takes hold in our elderly and vulnerable population and causes a new peak in hospitalisations and deaths but at least we acted quickly to mitigate the worst impacts though more restrictions may be necessary.

We just need to be sensible.

No need to panic or get angry...

John

Thanks for the summary John. I watched another what I would call "calm overview" of the situation. I suspect that it's way more technical than the Andrew Marr coverage, it's a video from a doctor who has been doing various in-depth videos on aspects of SARS-CoV-2/Covid-19 and just posted one on Omicron - https://www.youtube.com/watch?v=LLsMqC7WxTc

The things I took away from the video were ...

1 - The fact that the PCR tests still work for Omicron, although with one "widely used PCR test" (https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern) failing to detect the S gene (and S gene dropout has been seen in other variants e.g. Alpha so it's not new), gives Dr Syed (the author/presenter of the video) some confidence that even if there is some level of immune escape it will not be catastrophic/total such that it takes us back to square one. If tests can still detect the virus then at least infection-acquired immunity should still recognise it quite well. Maybe the situation is less certain on vaccine-induced immunity since it does focus on the spike protein but so far on the S gene dropout they are only taking about one type of PCR test as opposed to all. [ Do you (John) have any inside knowledge about how many different variants of the PCR test there are and has any internal chatter amongst the testing community started discussing in more detail which tests show S gene dropout on Omicron and which (if any) don't? ] Regardless of that, as mentioned S gene dropout was also seen in Alpha and other variants and vaccine immunity even against mild symptomatic disease still held up pretty well and against severe disease still remained very strong so it's by no means a clear indication of vaccine-induced immune escape.

2 - Yes there are a lot of mutations in Omicron but that might also make the virus unstable and there is still a possibility that like the Beta variant it could fizzle out either due to instability or because it isn't sufficiently fitter than Delta to outcompete it. That latter reason was what did for the Beta variant that actually had more immune escape from the vaccines than Delta has(*). Even though graphs of growth rates look alarming the actual number of cases is still very low even in South Africa. Yes of course it is infectious and could displace Delta but it is still too early to know that for sure based on actual observed cases rather than theoretical concerns about spike mutations. Delta might still prevail.

3 - There has been much focus on the spike mutations possibly making it more infections but the spike is also suspected to be responsible for various mechanisms that cause damage to various systems in the body, i.e. increase the severity of disease in some people. If the spike is changed significantly that not only raises the possibility of increased transmissibility but also the possibility of a reduction in disease severity due to that mutated spike protein no longer being able to cause some of those damaging effects.

4 - It's too early to know for sure about disease severity vs Delta because the identification of this variant is so recent that people infected haven't had time to progress to severe disease if that is the way it is going. I didn't see the data source Dr Syed was referencing but he did say that there were early indications that the incubation period for Omicron might be longer than that of Delta. At first glance that might seem alarming, people walking around for longer spreading it asymptomatically, but the other side of that coin is that if the virus is taking longer to cause sufficient damage for symptoms to arise that could be an indication that it is milder than other strains in terms of overall disease severity; slower effect gives the immune system longer to fight it off. That might even be a big win if Omicron turned out to be fit enough to out-compete Delta but significantly less severe such that a surge in hospitalisations doesn't happen and ultimately hospitalisations decrease.

So I agree with your take John, and with a few subsequent comments on this thread about the media getting a bit hysterical about all of this and potentially whipping up public panic. Yes of course it could go badly, Omicron might out-compete Delta and have sufficiently higher vaccine escape to noticeably blunt the benefits of the current vaccines, but at the other end of the spectrum it could end up replacing Delta with a variant that is far less likely to land even the unvaccinated in hospital and us oldies (and the vulnerable) who have been double-jabbed and boosted might retain really solid 90+% protection against hospitalisation. Just maybe this could be the final act of it turning from a pandemic to a not-too-troubling endemic virus.

- Julian (ever the optimist!)

(*) South Africa actually sold off it's stock of the Oxford/AZ vaccine without rolling it out because an in-country trial (albeit a small one) showed effectively 0% efficacy against mild/moderate symptomatic disease at the time when the Beta variant was the dominant variant in SA.

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Re: Omicron variant

#461582

Postby Hallucigenia » November 28th, 2021, 12:24 pm

redsturgeon wrote:
vagrantbrain wrote:
redsturgeon wrote:
We just need to be sensible.



And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...


To that end, might I suggest that this thread be renamed "New Omicron variant"?

There's no great evidence it originated in South Africa, and "super-variant" is not particularly helpful. It seems unfair to attribute it to South Africa when it's only because the HIV epidemic has given them some of the best virus surveillance capabilities in the world, and they're next to a load of countries where healthcare can be rudimentary. A variant could arise almost anywhere in sub-Saharan Africa and it would probably be detected first in South Africa. Compare with "Spanish flu" in 1918, which was a USian virus exported to Flanders and had nothing to do with Spain other than as a neutral country in WWI Spain felt free to report bad stuff in a way that those at war could not.

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Re: Omicron variant

#461590

Postby Julian » November 28th, 2021, 12:46 pm

Hallucigenia wrote:
redsturgeon wrote:
vagrantbrain wrote:
And the media need to wind it in a bit. Headlines like "UK battles to save christmas" last night on the Suns website won't help.


The Sun...


To that end, might I suggest that this thread be renamed "New Omicron variant"?

There's no great evidence it originated in South Africa, and "super-variant" is not particularly helpful. It seems unfair to attribute it to South Africa when it's only because the HIV epidemic has given them some of the best virus surveillance capabilities in the world, and they're next to a load of countries where healthcare can be rudimentary. A variant could arise almost anywhere in sub-Saharan Africa and it would probably be detected first in South Africa. Compare with "Spanish flu" in 1918, which was a USian virus exported to Flanders and had nothing to do with Spain other than as a neutral country in WWI Spain felt free to report bad stuff in a way that those at war could not.

Well said! In fact that video I just linked to quotes the first identified case as coming from a sample collected on 9th November from an HIV patient in Botswana.

If the "dream scenario" was to emerge, Omicron fitter than Delta but causing appreciably less severe disease with no or minor extra immune escape vs Delta, I wonder how quickly the UK Government would change policy? If that dream scenario did happen then my lay-person's take would be that it would then be actively in our interest to open up borders so that we could import Omicron, displace the more severe Delta variant, and thus reduce hospital admissions and speed up (due to Omicron being fitter) the roll-out of natural immunity to the unvaccinated.

- Julian

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Re: Omicron variant

#461597

Postby Mike4 » November 28th, 2021, 1:05 pm

Julian wrote:
Hallucigenia wrote:
redsturgeon wrote:
The Sun...


To that end, might I suggest that this thread be renamed "New Omicron variant"?

There's no great evidence it originated in South Africa, and "super-variant" is not particularly helpful. It seems unfair to attribute it to South Africa when it's only because the HIV epidemic has given them some of the best virus surveillance capabilities in the world, and they're next to a load of countries where healthcare can be rudimentary. A variant could arise almost anywhere in sub-Saharan Africa and it would probably be detected first in South Africa. Compare with "Spanish flu" in 1918, which was a USian virus exported to Flanders and had nothing to do with Spain other than as a neutral country in WWI Spain felt free to report bad stuff in a way that those at war could not.

Well said! In fact that video I just linked to quotes the first identified case as coming from a sample collected on 9th November from an HIV patient in Botswana.

If the "dream scenario" was to emerge, Omicron fitter than Delta but causing appreciably less severe disease with no or minor extra immune escape vs Delta, I wonder how quickly the UK Government would change policy? If that dream scenario did happen then my lay-person's take would be that it would then be actively in our interest to open up borders so that we could import Omicron, displace the more severe Delta variant, and thus reduce hospital admissions and speed up (due to Omicron being fitter) the roll-out of natural immunity to the unvaccinated.

- Julian


And seconded. The thread title is very inappropriate.

Dr Campbell talks about the Belgium case having arrived in Belgium on 11/11/21, but not developing any symptoms prompting testing until 24th Nov. (IIRC, might have the dates a day wrong.) This means either the incubation period has stretched out to nearly two weeks, or they contracted it in Belgium. Neither is a particularly encouraging possibility.

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Re: Omicron variant

#461607

Postby dealtn » November 28th, 2021, 1:51 pm

Julian wrote:
If the "dream scenario" was to emerge, Omicron fitter than Delta but causing appreciably less severe disease with no or minor extra immune escape vs Delta, I wonder how quickly the UK Government would change policy? If that dream scenario did happen then my lay-person's take would be that it would then be actively in our interest to open up borders so that we could import Omicron, displace the more severe Delta variant, and thus reduce hospital admissions and speed up (due to Omicron being fitter) the roll-out of natural immunity to the unvaccinated.

- Julian


I agree that would be genuinely interesting to see how the, generally, less informed public, would be "sold" that this is the most appropriate response.

Many think the "let it spread in a controlled way" opening up in the summer was a way of ensuring growing natural immunity through infection at an advantageous time of the year. But the authorities couldn't vocalise such a policy for fear of being attacked for acting inappropriately. If true I suspect little credit is given for the relative lack of a surge in cases currently compared to other nations.

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Re: Omicron variant

#461618

Postby redsturgeon » November 28th, 2021, 2:51 pm

Julian wrote:
1 - [ Do you (John) have any inside knowledge about how many different variants of the PCR test there are and has any internal chatter amongst the testing community started discussing in more detail which tests show S gene dropout on Omicron and which (if any) don't? ]

2 - Yes of course it is infectious and could displace Delta but it is still too early to know that for sure based on actual observed cases rather than theoretical concerns about spike mutations. Delta might still prevail.

3 - There has been much focus on the spike mutations possibly making it more infections but the spike is also suspected to be responsible for various mechanisms that cause damage to various systems in the body, i.e. increase the severity of disease in some people. If the spike is changed significantly that not only raises the possibility of increased transmissibility but also the possibility of a reduction in disease severity due to that mutated spike protein no longer being able to cause some of those damaging effects.

4 - I didn't see the data source Dr Syed was referencing but he did say that there were early indications that the incubation period for Omicron might be longer than that of Delta.



My responses as follows

1. Yes certainly at least two different types of PCR testing that we use. One express test only looks at one gene rather than three.

2. My understanding was that it has rapidly displaced Delta already in SA.

3.Time will tell if omicron causes more severe illness than other variants.

4. The Belgium case suggested perhaps a 2 week incubation period.

John

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Re: Omicron variant

#461639

Postby redsturgeon » November 28th, 2021, 4:30 pm

Latest from John Campbell includes summary of latest from SA. Conflicting news on how bad omicron might be.

https://www.youtube.com/watch?v=cdkCVeWc1pQ

John

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Re: Omicron variant

#461642

Postby 9873210 » November 28th, 2021, 4:39 pm

Julian wrote:
2 - Yes there are a lot of mutations in Omicron but that might also make the virus unstable and there is still a possibility that like the Beta variant it could fizzle out either due to instability or because it isn't sufficiently fitter than Delta to outcompete it.


I really don't like the way you phrase that, it's pretty incompatible with the theory of evolution and the mathematics of virus spread. It's possible that Omicron isn't really a thing, rather a part of the normal range of the virus or a series of unlikely random events that happened to blip the detection network. Your phrasing could be interpreted to match one of those, but it does not describe them.

For Omicron to be a real strain and to persist it has to be able stable enough to survive somewhere and it has to outcompete delta somewhere.

Omicron could persist at a low level alongside Delta in a number of cases.
1) Omicron is continually arising by spontaneous mutations from Delta.
2) Omicron has a non-human host and continually crosses between species.
3) Omicron can out compete Delta in a particular environment (For example over 30C and 100% humidity, or in people with a particular gene).
4) Omicron is not competing with Delta, a dread twin pandemic.
5) probably others, but Omicron evolved some mutations that allowed it to outcompete delta and then evolved more mutations that made it fall apart is not one of them.

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Re: Omicron variant

#461689

Postby look » November 28th, 2021, 8:01 pm

https://www.reuters.com/world/africa/sa ... 021-11-28/

mild symptoms, can be treated at home.

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Re: Omicron variant

#461705

Postby gryffron » November 28th, 2021, 9:46 pm

look wrote:https://www.reuters.com/world/africa/safrican-doctor-says-patients-with-omicron-variant-have-very-mild-symptoms-2021-11-28/
mild symptoms, can be treated at home.

Yeah it's quoting the same doctor as the I did and the BBC link onthemove provided above. But she was/is working from a very small sample size. It'd be nice. But by no means conclusive yet.

Gryff

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Re: Omicron variant

#462188

Postby Sorcery » November 30th, 2021, 10:13 pm

gryffron wrote:
look wrote:https://www.reuters.com/world/africa/safrican-doctor-says-patients-with-omicron-variant-have-very-mild-symptoms-2021-11-28/
mild symptoms, can be treated at home.

Yeah it's quoting the same doctor as the I did and the BBC link onthemove provided above. But she was/is working from a very small sample size. It'd be nice. But by no means conclusive yet.

Gryff


The omicron variant seems quite infectious : https://www.telegraph.co.uk/global-heal ... nfections/

“It is very early days, we will have to wait and see in the next week or two. This appears to be very, very infectious, we are inundated with patients.”

“We don’t know what is happening going forward, so this is so stressful – the sheer number,” said Dr Cohen.

Hatzollah, a private ambulance service run by members of the city's Jewish community, has kept meticulous records of Covid-19 infections since the pandemic began.

They say there has been a staggering surge of infections in the last two and half weeks. They have gone from receiving no calls about Covid-19 to more than 60 a day.

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Re: Omicron variant

#462190

Postby XFool » November 30th, 2021, 10:25 pm

look wrote:https://www.reuters.com/world/africa/safrican-doctor-says-patients-with-omicron-variant-have-very-mild-symptoms-2021-11-28/

mild symptoms, can be treated at home.

Time to get the garlic out again?


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