Omicron news

[Aladdin]

None of this sounds good to me...
If Omicron can spread rapidly and mutates further as it spreads, how fucked are we? "We" being those most vulnerable like the elderly and immunocompromised?

 

[xenon]

But if antibodies against Omicron aren't (strongly) effective against Delta (and why would they be, if the reverse isn't true?), the fact that somebody has had Omicron doesn't stop them carrying on getting Delta. In that case, Omicron is no more a limiting factor against the spread of Delta than the 'flu is. What you're saying only works in the one-way situation in which Omicron antibodies stop Delta but Delta antibodies don't stop Omicron.

But we're not starting from 0. There's already a defence against delta. The defence needed to fight omicron might not work against it but it's too late for delta.

I mean in a perfect lab scenario. There'll always be pockets of unprotected population obviously.

 

[kabbes]

But we're not starting from 0. There's already a defence against delta. The defence needed to fight omicron might not work against it but it's too late for delta.

I mean in a perfect lab scenario. There'll always be pockets of unprotected population obviously.

I'm really not seeing much evidence that Delta is done. 50,000+ infections a day in this country alone would tend to argue against that scenario.

 

[xenon]

Actually I wonder can you have both variants at the same time.

 

[kabbes]

Actually I wonder can you have both variants at the same time.

Yes, this is what I am wondering. If not, why not? Although I am aware that understanding the impact of multiple pathologies in the same individual is another level of complexity again. You also need to consider all the other pathogens and other microbial thingies that are present too -- bacteria, fungi, other viruses etc. Not straightforward!

 

[xenon]

I'm really not seeing much evidence that Delta is done. 50,000+ infections a day in this country alone would tend to argue against that scenario.

Sure, but over the medium term. Mind you, there could be the Pi varient by then.

 

[zahir]

Thread

 

[xenon]

Musst admit I've tended to figuratively picture it like lots of blue dots swarming around. Blue being delta.
Once everything's turned blue, Red (omicron) comes along, swarms much quicker and in wider dispersal patterns and blue gets taken over.

Not sure if that helps anyone else though...

 

[StoneRoad]

Actually I wonder can you have both variants at the same time.

There were several cases of "orginal" and "delta" in the same individual.

I'm now worrying that we'll have a large omicron wave this winter that is largely uncontrolled by the vaccines.
If omicron evades the vaccines, then the boffins need to be doing the required tweaking asap.

 

[elbows]

I think (iirc from listening to an interview with an immunologist recently) then the bit I highlighted is actually possible - quick re-infection and possibly concurrent infections with both.

The rest just makes my head feel like it's going to explode.

The way I think about it is by not focussing so much on whether that can happen in some instances, but rather how often it happens, whether it makes up a large part of the picture or is just a sideshow.

There is much that I do not claim to know, and I treat assumptions as mere placeholders that I will only make use of where there would otherwise be a complete void.

I dont like to make assumptions about whether a strain will dominate until the signs are much clearer in real data. But so far I tend to think about momentum - dominant strains gain a hell of a lot of momentum in order to get to that position, they outcompete other strains in ways that have not been subtle so far.

I understand the logic of kabbes questions about this and I dont have many answers, other than to think about that momentum and not to consider immunity in a simplistic way. There are multiple levels of immune defense and probably some overlap which should not be ignored, even when variants are quite different. The overlap may not be enough to prevent a nasty new wave and lots of health care pressure, but it can still be enough to allow the new strain to dominate at the expense of previous strains.

Consider the story of flu for the first two thirds of the 20th century. H2N2 was different enough from H1N1 to cause a new pandemic, and yet it also dominated and caused the previous strain to dissapear. Likewise H3N2s arrival led to the demise of H2N2. The story loses its simplicity after that because H1N1 came back in the 1970's (quite possibly due to human error) and we've had two major strains of influenza A co-existing ever since, but if people look for explanations about the story of flu strains in the 20th century then maybe it will still help with the current questions.

 

[elbows]

Thread

Thanks for that. I did read that hospital report last night and would describe it as a familiar scene - some good news that should be tempered by the fact its still too early in that wave to draw safe conclusions, and that a small percentage of a very large number can still be incredibly bad news.

 

[Supine]

I think you're not grasping what I'm saying. Or possibly vice versa.

If antibodies don't mutually "work" to eliminate both variants then from our point of view, these are essentially two different diseases. Omicron won't replace Delta because somebody who has already had Omicron can still get Delta. This is fundamentally different to Alpha and Delta, whereby somebody who has had Delta now (basically) can't get Alpha. In the latter case, Delta outcompeted Alpha and Alpha disappeared. However, in the former case, there is nothing to stop Omicron and Delta co-existing.

Now, if antibodies do mutually "work" to eliminate both variants then fine, the competition happens and only one variant wins. But this seems to be far from certain right now. The hope is there, but not the sure knowledge.

And sure, you get an interesting non-linear dynamic system akin to a multiple predator-prey model where the antibodies are partially mutually effective. In this case, my expectation is that there is no stationary point to the system, and each will see flare ups over time. But if this happens, we are effectively looking at a long-term two-variant system, not a system in which one variant replaces the other.

I think I get what your saying but to get to the answer you need to get into the next level of complexity regarding immune systems. Not my area of expertise but I’ll give it a bash! Bored on a train so why not.

Its too simplistic to talk about antibodies for a particular strain of covid. The immune system recognises lots of little bits of covid. You could have 2, 10, 100 bits of the covid shape which are recognised and antibodies created. When covid mutates some of these shapes will disappear and therefore the memory of what they look like is redundant.

This is why you sometimes hear talk of a broader immune response post natural infection because the immune system will be recognising shapes in the main protein and not just the spike. Current vaccines only use the spike shape to train the immune system. Some of the newer vaccines will be using inactivated whole covid to train the immune system so it will be interesting to see how well they do.

Back to the race, if your body recognises 39 bits of covid and omicron comes along with shape changes you might get a reduction in recognised shapes from 39 down to 19 or 10 or 6. Who knows! The point is that the less shapes recognised the less efficient the immune response would be. So far the spike hasnt changed enough to stop vaccines working efficiently. Omricon has people worried because of the number of shape differences. It will naturally start to become the dominant type because it has a competitive advantage. Also need to remember that omicron isnt a fixed mutation and is already changing as mistakes happen during replication all the time. There is already a family branch of omicron that does not have the s gene dropout. That appears to be something that comes and goes over time.

So yeah, its not a one variant scenario or two types living side by side. Its a constantly changing outlook and when the next significant changes occur it will be designated Pi variant. We all need to accept annual jabs, with the latest variants encoded to fine tune the immune response over time.

Not sure that answers all of your questions but maybe a start?

 

[elbows]

Plus there is plenty of theory that is only being put to the test properly by this pandemic. I believe some experts think there is a risk of trying to be too clever for our own good when it comes to tweaking the vaccines to act against specific new strains, due to the complexities of the immune system and some counter-intuitive possibilities.

Original antigenic sin is just one example and only time will truly demonstrate whether that idea is actually applicable to this virus and whether our response has the potential to make things worse.

Plus one of the many reasons I have to wait to see what happens elsewhere with Omicron is due to differences in previous wave variants in South Africa compared to a country like the UK. They had a beta wave in the past, we didnt.

 

[kabbes]

Thanks both. That does make sense, and I guess we’ll see over time what the dominant features are of the particular circumstances we are in that determine else happens on this occasion.

 

[Supine]

Just on the subject of on-going changing here is the current ‘family tree’ for the omicron clade. As you can see it is evolving in multiple ways already (most being insignificant luckily). I recommend the nextstrain. org website if you want to get into the detail of mutations.

 

[elbows]

Other things to keep in mind include that studies into immunity and SARS-CoV-2 are inevitably biased towards using the aspects of our immune system that they find reasonably easy to measure. Hence the emphasis on antibody levels in the blood, which is far from the whole immune system story.

As far as I know there are still plenty of outstanding questions when it comes to immune response to even more disparate viruses. For example there are some studies which imply there may be some cross-reactive antibodies generated from either the pandemic virus or a bunch of the other human coronaviruses that were around long before this pandemic. I dont think they've found strong evidence that recent infection with one of the other coronaviruses confers protection against infection or severe disease of the Covid-19 variety, but it could still be the case, especially if the phenomenon is somewhat brief and transient. Indeed that possibility was on the list of possible explanations for why some countries did not suffer as great a healthcare burden in the first wave, if they had had a large wave of a normal human coronavirus with just the right pre-pandemic timing that a chunk of their population ended up with better, but temporary, defences against the arrival of the pandemic.

The transient nature of some of this stuff is also worth consuidering when seeking explanations for why a new strain can dominate at the expense of the previously dominant strain - the momentum of the new strain and the huge numbers affected could massively rob the previous strain of opportunities for a time, and during that time the old strain runs out of sufficient hosts.

But then again I would caution that the transient nature of the immune response may receive an undue degree of attention because that waning form of immunity is most strongly associated with the aspects of our immune response that are easiest to measure (eg via the blood), and the longer-lasting forms of protection are much harder to measure and obtain masses of data about.

 

[_Russ_]

Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction

 

[Supine]

Slightly mind bending thread on transmission advantage

 

[Aladdin]

Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction

And he probably has no immune issues or underlying health problems.

 

[teuchter]

Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction

So basically information which is of no use to anyone.

 

[gentlegreen]

Fairly standard for John Invermectin Campbell

 

[_Russ_]

So basically information which is of no use to anyone.

Oh you speak for everyone?
The abundance of comments that add fuck all to the discussion is getting a bit boring

 

[kabbes]

Slightly mind bending thread on transmission advantage

That really puts the advantage of omicron over delta into perspective. Over five days, based on current immunity levels, they think it likely grows about 4 times faster.

 

[elbows]

That really puts the advantage of omicron over delta into perspective. Over five days, based on current immunity levels, they think it likely grows about 4 times faster.

Although they expect the existing immunity picture in each country to make quite a difference, so I'll be waiting for UK-specific data to firm up in the next week or two before I judge the extent to which the shit will hit the fan here.

My default assumption is that it will be grim and will necessitate the imposition of strong measures, but I'm always ready to change my tune on that.

 

[elbows]

I'm not a big fan of the headline framing of this article, because unlike the arrival of previous variants, this time the government have not pretended that we are actually trying to contain this variant, and have been more honest that these measures are only to slow its spread. And buying time for more boosters is a sensibe thing to do, its just a shame they didnt bother doing more on the domestic measures front too.

Covid: Travel changes too late to halt potential new wave - scientist

The return of pre-departure Covid tests for travellers to the UK will come into force on Tuesday.

www.bbc.co.uk

 

[kabbes]

Although they expect the existing immunity picture in each country to make quite a difference, so I'll be waiting for UK-specific data to firm up in the next week or two before I judge the extent to which the shit will hit the fan here.

My default assumption is that it will be grim and will necessitate the imposition of strong measures, but I'm always ready to change my tune on that.

It's highly uncertain at the moment, but one of the estimates in that thread did try to take account of the existing immunity context of the UK. If I remember rightly, it was a slightly lower estimate (but with a huge range of uncertainty)

 

[teuchter]

Oh you speak for everyone?
The abundance of comments that add fuck all to the discussion is getting a bit boring

In my view your post containing that video falls into this category but you are free to explain how you think it is a useful contribution.

 

[elbows]

It's highly uncertain at the moment, but one of the estimates in that thread did try to take account of the existing immunity context of the UK. If I remember rightly, it was a slightly lower estimate (but with a huge range of uncertainty)

Yes, I'm waiting for more of that S-gene dropout data from the UK to emerge before I put weight in the number deduced by that means.

 

[2hats]

Very early UK (and EU) sequencing data might suggest a <3-day doubling rate (in a population with delta dominant and relatively high vaccine-induced immunity). However, one should bear in mind there could be a sequence over-sampling bias. Equally there could be under-sampling as non-SGTF omicron 'family' (sub-)variants are definitely out there.

 

[ska invita]

In my view your post containing that video falls into this category but you are free to explain how you think it is a useful contribution.

Russ is a troll, should be banned long ago