Covid 19 #43: Oh Omicron, oh Omicron, how numerous are thy spike proteins.

[Larry of the Lawn]

19 minutes ago, The Anti-Targ said:

Yes, you could get a super infection with both delta and omicron, especially since they seem to be targeting different parts of the respiratory tract to invade they are not really directly competing for "food". Delta focuses on the alveoli of the lungs, omicron on the bronchi. But omicron produces more virus and has a shorter incubation period which makes it spread faster, and earlier, and you will get sick sooner and (hopefully) limit your social contact before delta has as much of a chance to spread. So, even if you are infected with delta and omicron at the same time you will give omicron to more people than you will delta. Omicron will spread through a population sooner and faster and delta might try to follow, but omicron will generate an immune response in its wake that stops delta in its tracks.

Is that really true about being able to get both because they compete for different areas of the body?  Is getting both at the same time actually worse or even possible?

[mormont]

AFAIK it's always been possible to get two COVID variants at the same time. But it's unlikely because your immune system should be activated. IIRC there is some evidence that even getting an unrelated virus like 'flu or a cold can provide limited protection against catching COVID variants.

On the other hand if you do manage to catch two COVID variants or COVID plus 'flu, you're likely to be in real trouble. 

[rotting sea cow]

2 hours ago, Filippa Eilhart said:

I still don’t really get how one variant outcompetes others. Shouldn’t they all just be in circulation? If I get omicron it doesn’t magically mean I’m immediately immune to Delta? 

There are different factors at play. If there is no enough cross-immunity, it's perfectly possible to have co-circulating strains. Variants were displaced mostly because there was enough cross-immunity and they were competing for the same hosts. That might not be the case with Delta vs Omicron. This twitter thread explain it better than I could.

Now. Trevor Bedford is overlooking here that all our actions to contain Omicron will hurt Delta circulation more than the first strain. Vaccines are more effective against Delta than against Omicron and any restriction will hurt the less dominant and less contagious strain. I think we should try to do it because reducing the genetic diversity of SARS-CoV-2 should be a goal in its own. Specially if it's proven correct that Omicron is less virulent.

[rotting sea cow]

Regarding variants. There has been a lot of regional differences on the variants dominance.

For example. Alpha rocket in the Northern Hemisphere, but was never at high circulation levels in S. America nor Africa.

Beta never caused havoc outside Southern Africa.

Gamma and Lambda hammered South America but caused little trouble outside

Delta was catastrophic in India and other countries, but for many countries the wave was comparatively mild. In S. America is the dominant strain right now but the waves have been mild to non-existent.

Nu caused a wave of infections in Colombia and I suppose in Central America, but not much outside.

I think it is an interesting behavior.

We'll see how it goes with Omicron.

[Iskaral Pust]

Positive home tests, e.g. rapid antigen tests, don’t get reported anywhere and are not included in the published case count.  Only PCR tests processed by official testing facilities are counted.  So while the case count was probably understated early in the pandemic due to lack of testing, it’s probably understated again now due to having home tests available.

With this omicron surge, people have to wait in line for well over an hour to get a PCR test.  All of the people I know are just relying on multiple home tests over a few days and then self-isolate.

[rotting sea cow]

58 minutes ago, mormont said:

On the other hand if you do manage to catch two COVID variants or COVID plus 'flu, you're likely to be in real trouble. 

Actually there are some interesting things of viral interference. I'd need to look for the sources but from what I remember

1) Rhinoviruses shut the cell doors and do not allow entry of other viruses. They also enhance the interferon responses and mucous production, so they really protect you against influenza and coronaviruses.

2) Influenza A enhances ACE2 expression and possibly makes any COVID infection worse.

[Mr. Chatywin et al.]

5 hours ago, BigFatCoward said:

To be honest I'm not as worried about the football, compared to the darts at Alexander Palace, which has the potential to be the biggest superspreader event in history. 

My favorite sports podcast has two members on it who couldn't stop talking about going to the darts this years over the last few weeks, but now it sounds like they've had to cancel the trip. Is it really all they're making it out to be?

Anyways, called into work for the second straight day. Yesterday I had terrible diarrhea, and this morning when I took my temp it was at 99.8 (I typically run in the low to mid 97s), so now I'm in the protocol and need to get one of these hard to find tests to be cleared to return to work. 

[Zorral]

6 hours ago, BigFatCoward said:

To be honest I'm not as worried about the football, compared to the darts at Alexander Palace, which has the potential to be the biggest superspreader event in history.

Like the Anime Con Nov. 18 - 20th that brought Omicron, not just to NYC but spread it throughout the country, like the Sturgis Motorcycle rallies do in July. Your Darts Championship goes on a lot longer than the Anime Con did, so ya, you all are in for it all right.

[Kalbear]

On getting both, you're missing the whole transmission vector. 

Omicron is more able to get around vaccine resistances. Presumably a person hasn't changed their behavior that much. So before, when a person might have interacted with 10 people, one of which had delta but was asymptomatic and not spreading much and 7 of the others were vaccinated - now those 7 are far more likely to spread it. 

And that's why omicron is catching fire- because there is a shit ton of fuel of vaccinated people it can spread through, and a bunch more who had previously caught covid and are being reinfected with omicron. 

And while it's possible for someone to get delta and omicron it is really unlikely - you would have to be around two spreaders of two different variants about the exact same time and catch it from both right then. Anything else would mean your immune system would already be fighting it and make it much harder for the other to get a foothold.

[Iskaral Pust]

It seems very likely that omicron is displacing delta.  The NYT reported today that 75% of new cases in the US are omicron.

Co-infection is possible but pretty improbable: exposure vectors, immune response already triggered, self-isolating once you know of an infection reduces the opportunity for a second exposure.

[Impmk2]

6 hours ago, rotting sea cow said:

Now. Trevor Bedford is overlooking here that all our actions to contain Omicron will hurt Delta circulation more than the first strain. Vaccines are more effective against Delta than against Omicron and any restriction will hurt the less dominant and less contagious strain. I think we should try to do it because reducing the genetic diversity of SARS-CoV-2 should be a goal in its own. Specially if it's proven correct that Omicron is less virulent.

Starting to be some indications that Omicron may be more suseptible to NPIs than Delta - has generally slowed / fallen off far faster than expected as restrictions have been brought / populations have modified behaviour across quite a few European cities. Currently Omicron growth is falling faster than Delta in London.

Could be consistant with Omicron's growth advantage being through a shorter generation time + immune evasion, with Delta still being more inherently transmissible and a bit of a slower burner. If this occupation of seperate transmission niches holds, along with their antigenic dissimilarity, I wouldn't take cocircluation off the table. Certainly the UKHSA is modelling cocirculation for the next couple months in the UK.

[Zorral]

https://www.defenseone.com/technology/2021/12/us-army-creates-single-vaccine-effective-against-all-covid-sars-variants/360089/

[The Anti-Targ]

17 hours ago, Lermo T.I. Krrrammpus said:

Is that really true about being able to get both because they compete for different areas of the body?  Is getting both at the same time actually worse or even possible?

An immune response will be reasonably quick, in most cases with viruses the reason you get sick, seriously ill and die is because of the immune response, not the direct damage of the virus (some viruses fuck you up directly). The immune response typically begins before you get sick. For some viruses, by the time you start feeling like shit the virus has almost been wiped out (not sure about the 'Rona), but I'm pretty sure you clear the virus before you get better with COVID-19, and I think long COVID is not about chronic active infection with the virus but your immune system continuing to remain on high alert well beyond the presence of any danger. So to be unlucky enough to catch two variants you would need to be exposed at almost the same time. And it would really only be during a period when two variants are circulating pretty evenly within a population that simultaneous exposure is possible.

In the case of omicron and delta the targeting different parts of the respiratory tract means they are not directly competing for hijacking the same cells to there isn't competitive inhibition happening. But if omicron gets in first and gets an immune response going before delta gets past the lag phase, then it will be the immune response the stops delta getting a foot hold, so it would still require more or less simultaneous exposure.

[rotting sea cow]

11 hours ago, Impmk2 said:

Starting to be some indications that Omicron may be more suseptible to NPIs than Delta - has generally slowed / fallen off far faster than expected as restrictions have been brought / populations have modified behaviour across quite a few European cities. Currently Omicron growth is falling faster than Delta in London.

Could be consistant with Omicron's growth advantage being through a shorter generation time + immune evasion, with Delta still being more inherently transmissible and a bit of a slower burner. If this occupation of seperate transmission niches holds, along with their antigenic dissimilarity, I wouldn't take cocircluation off the table. Certainly the UKHSA is modelling cocirculation for the next couple months in the UK.

Well. I'm not sure of that because neither UK nor S. Africa have implemented any important NPI. I agree that the shorter incubation time might produce a faster burnout, so the falling cases in S. Africa and London. But I'd think that instead of big waves, we could have short explosive bursts. We'll see in the coming weeks. Nevertheless, vaccination and boosting will certainly affect Delta circulation more than Omicron's.

Granted, co-circulation cannot be dismissed. I remember reading that even Beta is still circulating at very low levels in Europe, so annihilating Delta might not be as easy as it sounds. The question is whether it will be circulating at epidemiological important levels.

Regarding intrinsic transmission rates. Some people are putting Omicron R0 at frigging 10!

https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(21)00559-2/fulltext

 

[rotting sea cow]

3 hours ago, Zorral said:

https://www.defenseone.com/technology/2021/12/us-army-creates-single-vaccine-effective-against-all-covid-sars-variants/360089/

Very interesting. Thanks!

This was another failing of 2021. While in 2020 there was a big push to develop vaccines, very little was done in 2021 or certainly not with any sense of urgency. Why? We had vaccines and there were excellent! Now, it's coming to bite us in the back as we may need better ones and little priority was given to them (where the seven hells are intranasal vaccines?). As the article detail, even testing them is complicated due to previous immunity.

 

[Maithanet]

Don't love that.

 

[Week]

Probably good that we cancelled our weekend in DC over XMas... 

[Fragile Bird]

Worldcon had such excellent timing, lol!

I see Israel has announced 4th shots.

Here in Canada provinces are hitting new records, the country has hit record daily case levels, crossing 10,000 cases a day.

[Filippa Eilhart]

2 hours ago, Fragile Bird said:

I see Israel has announced 4th shots

are they basing it on any kind of science?

[Deadlines? What Deadlines?]

3 hours ago, Fragile Bird said:

Worldcon had such excellent timing, lol!

I see Israel has announced 4th shots.

Here in Canada provinces are hitting new records, the country has hit record daily case levels, crossing 10,000 cases a day.

Israel still needs to work on first and second shots. Their vaccination rate is barely better than the US.

Here in Alberta they just opened boosters to 18+ with a 5+ month interval since the 2nd dose. This means I'm eligible. Positivity rates here have taken a massive U-turn, mostly Omicron.

We've been vaccinating 5-11 year olds for about a month and hit 33% 1st doses yesterday. That's ~130k jabs.