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

[Fragile Bird]

Ok. That says a lot. Damn it.

[Week]

"a small percentage of a large number can still be a large number."

[Impmk2]

New UKHSA report. Summation:

 

I find these summarys to be pretty accessible and a pretty accurate reflection of where things stand. The UK has excellent surveillence so is good to keep an eye on.

Good news: The UKHSA analysis backs up the previous reports on severity. They predict a 50-70% lower hospitalisation rate. This reduction now being mirrored across the world.*

Bad news: The boosters are waning fast against Omicron. Drops to 50% (or lower) efficacy after a couple months. We will need to update the vaccines.

 

 

*Data from here (Australia) reported yesterday was also showing this reduction, and that's in a basically vaccine only background.

[Filippa Eilhart]

1 hour ago, Impmk2 said:

: The boosters are waning fast against Omicron. Drops to 50% (or lower) efficacy after a couple months

we’ve not had a couple of months with Omicron yet…

eta

oh never mind, couple of months after booster, not after omicron. Lol.

 

I think we need to give up on the idea of protecting against symptoms and concentrate on protecting against severe disease.

[The Anti-Targ]

1 hour ago, Impmk2 said:

New UKHSA report. Summation:

 

I find these summarys to be pretty accessible and a pretty accurate reflection of where things stand. The UK has excellent surveillence so is good to keep an eye on.

Good news: The UKHSA analysis backs up the previous reports on severity. They predict a 50-70% lower hospitalisation rate. This reduction now being mirrored across the world.*

Bad news: The boosters are waning fast against Omicron. Drops to 50% (or lower) efficacy after a couple months. We will need to update the vaccines.

 

 

*Data from here (Australia) reported yesterday was also showing this reduction, and that's in a basically vaccine only background.

So if delta hospitalisation is 10/1000 of test positive cases then omicron will be 3-5/1000. If Delta peak is 60,000/day and omicron peak is 200,000/day then at peak delta you are getting 600 hospitalisations/day and with omicron you are getting 600-1000 hospitalisations/day. And if death rate is similarly proportioned then daily deaths in an uncontrolled omicron wave aren't going to look pretty either.

The only thing saving any country from unmitigated disaster from omicron is vaccination / previous infection with an earlier strain.

[Raja]

3 hours ago, Impmk2 said:

I find these summarys to be pretty accessible and a pretty accurate reflection of where things stand. The UK has excellent surveillence so is good to keep an eye on.

Agreed. The caveat here is that their confidence on of infection severity being lower is 'low', there are plenty of uncertainties at the moment and it is difficult to determine severity due to a couple of things, something the report states explicitly here

Quote

There is insufficient data to comment on severity of illness once in hospital or mortality.

Available data suggests that the observed reduction in risk in the UK is likely to be partly a reduction in intrinsic severity of the virus and partly to protection provided by prior infection. We cannot confidently quantify the relative contributions of these 2 factors at present. Even at the reduced hospitalisation risk observed, the combined growth advantage and immune evasion properties of Omicron have the potential to lead to very high numbers of admissions to hospital.

In addition, the case to hospitalization ratio for Omicron will *likely* always be lower than Delta, something Natalie Dean gets into here - this is particularly true if Omicron's rate of reinfection is high, see the thread below

Lastly, to distill down some of the hospital admissions stuff in London, we are currently at 75% of admissions with the primary cause being COVID, the FT charts are net change, which is an important point to highlight.

I know I said lastly, but we're clearly breaking rules here. There are two flavours of 'incidental covid' - one would be someone being admitted for something else, say a broken femur and then on admission we find out they also have COVID. Now this makes the admission complicated because they need a covid ward/ bed and also surgery on their broken bone. This involves two sets of doctors ( Medicine/ Resp for the covid bit) and Orthopedics ( the bone doctors) to look after them, and in this case, it would also be unlikely anyone would even touch the bone if the person becomes unwell with COVID. I doubt they would even operate on a covid positive patient.

The second flavour of 'incidental covid' would be hospital acquired covid, and this is not good at all - patients that are in the hospital for something else entirely, say a coronary angiogram for a heart attack ( a life saving procedure), now they get their operation and will usually leave on that day or the next day - now a way this person gets covid is that the ward they are on has an outbreak of covid (  something that happened in all of the waves that have happened in the UK) or one of the staff tests positive given that there is significant community spread in the UK - we now have a patient that has had a significant health issue who will now be dealing with another one - now vaccination should help a lot with this kind of thing, but outbreaks in hospitals are difficult to avoid when there is significant community transmission.

There's more on the hospital acquired covid bit here and here

Quote

During the first wave, it was estimated that 20% of hospital cases were acquired in hospital – defined as cases diagnosed more than a week after admission. A similar proportion of hospital cases were acquired in hospital between 1 September and 14 November: the proportion has grown with the number of cases, from 10% in September to 19% in the first two weeks of November

Quote

Last month the Guardian reported that, since March 2020, “Up to 8700 patients died after catching covid-19 in English hospitals.”1 The question is whether any of these cases could have been avoided and what we need to do better in future, rather than just seeking to apportion blame.

The story was based on freedom of information requests sent to all 126 acute hospital trusts, with 81 replying. A total of 32 307 patients admitted with other conditions had contracted covid-19 while in hospital, and 8747 (27%) died within 28 days, showed figures supplied by the trusts themselves.

 

[A True Kaniggit]

1 hour ago, The Anti-Targ said:

The only thing saving any country from unmitigated disaster from omicron is vaccination / previous infection with an earlier strain.

And improved treatments I suppose.

Aren’t the current treatments far superior than when it initially hit?

[Which Tyler]

4 hours ago, Clueless Northman said:

Where would that be? Northern US and Europe definitely had a seasonal effect. Seasonal viruses have that pattern where seasons actually apply. It's very different in hot climates with plenty of AC (peak during summer because people gather indoor due to heat waves), and it's very different in hot climates without AC (lower infections all year round).

2nd wave in Fall 2020 in Europe was the definitive proof: it went up the roof as soon as temps dropped by 10+ degrees in a couple of weeks and weather turned to shit clouds and rains.

I repeat - 'Source please"

Repeated assertion doesn't make a source.

A single datum (Europe's second wave) doesn't make definitive, especially when directly contradicted by another single datum (Europe's third wave)

[Padraig]

5 hours ago, Mlle. Zabzie said:

Is it just that it takes about the amount of time between peaks for people's immunity to wane and behavior to change?  Point is, we know more about the virus than we did two years ago, but we certainly don't know everything, including whether it is "seasonal."  

I don't really disagree.  I think there is a seasonality factor involved but there are a lot of factors, and nothing has been proved yet.  Like, they are now reporting a higher rate of people getting COVID a second time.  Omicron is being blamed but obviously the population of people with prior COVID is now higher and the average time since initial illness keeps going up (and thus, immunity is declining).  So yes, Omicron is probably more evasive but i'm not sure do topline figures show how much.

Getting a firm picture of COVID is challenging.  But I do think seasonality is a factor.  Enough countries point in that direction (e.g. Germany).  But other countries, less so, because of countervailing factors (e.g. Delta).

4 hours ago, Clueless Northman said:

If Omicron is really a bad nasty cold for the more or less "immune" people - who already got covid or got at least 2 doses -, then is it that necessary that everybody gets a 4th dose taylored for Omicron?

But we don't know this.  That's the point.  Israel is talking about a 4th dose because it seems fool hardy to assume that Omicron is a bad cold.  If it is, yay, but if it isn't?  I don't see the evidence to be sure that only the unvaccinated are at risk.  At most, it seems that Omicron reduces the likelihood of having a bad illness but since Omicron effects more people, we could easily end up with many deaths still.

You are deriding governments for making bad decisions but you seem to be quite happy to jump to conclusions yourself?

Yes, there could have been more work at improving vaccines but again, was there a huge uproar in the scientific community to improve the vaccines?  They had proved robust against previous variants.  Seems like hindsight is creating 20/20 vision.

4 hours ago, Clueless Northman said:

The Spanish flu would also have been dealt with with at most a 3-dose vaccines, considering current flu are dealt with with a 1-dose vaccine that has some efficiency over the next 4-6 months.

Comparing a mild disease with a deadly one?  That doesn't sound particularly scientific at all.

[Impmk2]

Great twitter thread about transmission dynamics in Omicron. A lot of the nitty gritty of the modelling goes over my head, but I believe someone was asking for the evidence of reduced generation / transmission time yesterday. This lays it out how that assumption would fit the current observations in growth across various countries at the moment.

 

If this is correct we're in for very short sharp peaks which really stess the hospital system, but burns through inside 1-2 months.

[Clueless Northman]

5 hours ago, Impmk2 said:

Bad news: The boosters are waning fast against Omicron. Drops to 50% (or lower) efficacy after a couple months. We will need to update the vaccines.

At some point, we'll have to see how bad Omicron actually is for people who already got 2 or 3 doses, because it's definitely not going to be similar to vanilla covid or Delta hitting people with 0 immunity. I honestly think a lot of people just won't care if it's a bad cold to them with basically no risk this gets worse than a mild flu, and there'll be no point to pushing them to take boosters every few months. Besides, every passing week means more and more people vaccinated or exposed to one variant or another.

Last but not least, we'll soon see to which extent SA observations stand up in Europe and America - the hospitalizations figures seems reasonably accurate, so we'll see if the 75% drop in ICU stays and the 85% drop in deaths stand. Those are the main factors that can make sure hospitals don't collapse under the weight of Omicron patients. I'm actually more worried about temporary shortage of health staff due to covid "mild" cases that will still put them in quarantine and about the potentially numerous cases of covid caught in hospital that Raja mentions.

 

2 hours ago, Which Tyler said:

A single datum (Europe's second wave) doesn't make definitive, especially when directly contradicted by another single datum (Europe's third wave)

You mean the main current Delta wave, which actually began later in 2021 than last year's 2nd wave because weather was okayish for a bit longer? Yeah, definitely no seasonal effect here. Granted, that's for continental Europe. There's something very strange going on with UK since the massive Delta wave has been ongoing since Summer - maybe some Brexit "UK does it its own way" thing going on. Maybe is it that UK has been testing way way more than EU during most of 2021 and caught plenty of cases all year long, yet covid cases are mostly very mild during Summer and begin to get rougher in Fall, so more EU people noticed and got tested since October?

 

2 hours ago, Padraig said:

But we don't know this.  That's the point.  Israel is talking about a 4th dose because it seems fool hardy to assume that Omicron is a bad cold.  If it is, yay, but if it isn't?  I don't see the evidence to be sure that only the unvaccinated are at risk.  At most, it seems that Omicron reduces the likelihood of having a bad illness but since Omicron effects more people, we could easily end up with many deaths still.

Many deaths amidst the unvaccinated, yup, possible. I don't see why I should care nor why people as a whole should care. The vast majority opted for vaccines. If we're serious about democracy, we should stop worrying about the minority who decided to go its own stupid way and make sure the majority of people can live their lifes as freely as possible, specially when said majority proved to be the solidarity-minded one who followed the rules. Time to take measures to ensure the unvaccinated stop jeopardizing the healthcare network (meaning mandatory vaccines if governments had any sense).

About protection, vaccines aren't always able or designed to offer 100% protection against all infections, specially in the long run. Even when antibodies decrease, the key protection is still there. Heck, at this point even Drosten and Fauci are basically stating that vaccines don't provide absolute immunity but are there to ensure no bad outcomes and only mild disease, yet they're fully aware that people will get covid sooner or later, just like people have colds or even, rarely hopefully, the flu. If eradication isn't possible anymore, there's no point to vaccinate everybody every few months, though it might be important for immunocompromised people. After a few doses, we're going to hit a brickwall of diminishing returns.

[The Anti-Targ]

4 hours ago, A True Kaniggit said:

And improved treatments I suppose.

Aren’t the current treatments far superior than when it initially hit?

The really good ones are very expensive and limited in supply. So that's not helping too much on a population basis.

Unless you mean ivermectin.

[Raja]

43 minutes ago, The Anti-Targ said:

The really good ones are very expensive and limited in supply.

Tociluzimab, maybe. But dexamethasone is cheaply available and has many steroid alternatives, such as prednisolone. And Dex is given to more patients than Toci + Remdesivir + the monoclonals I mention below given that the indication for it is much wider than Tociluzimab and Remdesivir, the latter makes no difference in mortality in hospitalized patients.

Casirivimab + Imdevimab are the monoclonal stuff that is more expensive, but have their own indication ( seronagative patients) - I need to read up the quality of evidence this is based on as I haven't had a look, but this is the more expensive stuff among the hospitalized patients, but it's for a subset of patients based on indication & recovery trial results - would hesitate to call them 'really good ones'

[The Anti-Targ]

1 hour ago, Raja said:

Tociluzimab, maybe. But dexamethasone is cheaply available and has many steroid alternatives, such as prednisolone. And Dex is given to more patients than Toci + Remdesivir + the monoclonals I mention below given that the indication for it is much wider than Tociluzimab and Remdesivir, the latter makes no difference in mortality in hospitalized patients.

Casirivimab + Imdevimab are the monoclonal stuff that is more expensive, but have their own indication ( seronagative patients) - I need to read up the quality of evidence this is based on as I haven't had a look, but this is the more expensive stuff among the hospitalized patients, but it's for a subset of patients based on indication & recovery trial results - would hesitate to call them 'really good ones'

Steroids have been used since very early on in the pandemic, as they have been in use for various viral diseases for decades. So it's not a difference maker between early pandemic and late pandemic severity and hospitalisation, which was the point I was responding to, i.e. medicines available now that were not available or in use in 2020 / early 2021.

[Which Tyler]

7 hours ago, Clueless Northman said:

You mean the main current Delta wave, which actually began later in 2021 than last year's 2nd wave because weather was okayish for a bit longer? Yeah, definitely no seasonal effect here. Granted, that's for continental Europe. There's something very strange going on with UK since the massive Delta wave has been ongoing since Summer - maybe some Brexit "UK does it its own way" thing going on. Maybe is it that UK has been testing way way more than EU during most of 2021 and caught plenty of cases all year long, yet covid cases are mostly very mild during Summer and begin to get rougher in Fall, so more EU people noticed and got tested since October?

I take it that you still don't have a source for your definitive and inarguable statement that April-May; June-September, and December-February are all the same season.

[Spockydog]

Bollocks to all this. For the next forty-eight hours at least, I'm sucking up all the optimism. Om nomi Omicron.

[Padraig]

***delete double post somehow***

[Padraig]

12 hours ago, Raja said:

...

Hopefully the new Pfizer drug will make a big difference.  Its almost 90% effective (although it was tested on unvaccinated people with pre existing conditions, somewhat niche.  It's now being tested on a wider range of people).  I believe it has recently been approved in the US, EU and UK (?) for emergency use.

13 hours ago, Clueless Northman said:

 I honestly think a lot of people just won't care if it's a bad cold to them with basically no risk this gets worse than a mild flu, and there'll be no point to pushing them to take boosters every few months.

This was always the case though.  Most people under 50 are going to be fine.  The question is, whether for those over 70, will the vast majority be ok?   Vaccination was always more about protecting the vulnerable than ourselves.  Although, there is always a risk that a younger person will get a bad dose for some reason.  They may not die but can still be significantly ill.

So yes, there may be diminishing returns in vaccination (e.g. you can see the drop in vaccines in Israel on dose number 3).  But I can see governments continuing to encourage it if they see a major danger.  Especially as Omicron seems to be able to evade vaccines much more than previous variants.

At the same time, there probably is too much focus on antibody derived immunity.  And the hope is that other generators of immunity will ensure we avoid shocking number of deaths.

Most countries are still seeing significant levels of fatalities.  I'm not sure how much of that is vaccinated v unvaccinated.  Even in countries with relatively low vaccination rates, the older age group is generally much more likely to be vaccinated.  So you might still find that the percentage of deaths is still significant in the vaccinated cohort, simply because the vulnerable group will always be the most vulnerable.   I'd certainly want hard data on deaths before I shrug my shoulders at it.  (For example, Ireland has a very high vaccination rate but too many people are still dying.  I imagine most of those are vaccinated.  It can only do so much when COVID is so prevalent.  Spain and Sweden have kept fatalities down but that may change with the latest wave).

The 75%/85% reductions already seem to be on the optimistic side when it comes to European countries.

14 hours ago, Clueless Northman said:

If eradication isn't possible anymore, there's no point to vaccinate everybody every few months, though it might be important for immunocompromised people. After a few doses, we're going to hit a brickwall of diminishing returns.

What is this fear regarding vaccination?  I don't like injections but if it saves lives, sure, why not?

As long as COVID doesn't generate another super-variant, we probably wouldn't need endless vaccination anyhow.  There will eventually be a second generation of vaccines.  Or a multivalent.

[mormont]

16 hours ago, Clueless Northman said:

Many deaths amidst the unvaccinated, yup, possible. I don't see why I should care nor why people as a whole should care.

I don't mean to be rude about this, but y'know, people will die. Why do you think people need a reason to care about that?

I can be quite impatient with some of the anti-vax crowd, I'm seen some appalling behaviour from them and they are putting vulnerable people at risk. But I don't want them to die.

 

 

[Raja]

2 hours ago, Padraig said:

Hopefully the new Pfizer drug will make a big difference.  Its almost 90% effective (although it was tested on unvaccinated people with pre existing conditions, somewhat niche.  It's now being tested on a wider range of people).  I believe it has recently been approved in the US, EU and UK (?) for emergency use.

Had a look at Paxlovid and I dunno - there's a lot of things that need to go right for it to make a big difference, off the top of my head

1. As you mention, trial included patients that were not vaccinated so it's not really a drug we are using for the majority of the population 

2. Has to be given within 5 days of symptom onset - this means one needs to have a robust testing system that allows people to easily access to PCR tests and decent turn around times. 5 days of PCR test would have been easy, but symptom onset makes it tough

3. It's not for hospitalized patients - so probably something I'm never going to prescribe myself, but hopefully it prevents hospitalization to the extent that the study reports.

4. It has some contraindications - so if one looks at the FDA release for health professionals, it's contraindicated in patients that take statins, which is a significant number of people. Out of the drugs listed, the statins are the most common but also included are anti-psychotics, anti-anginal drugs 

5. Availability - as with a lot of these drugs, stockpiled by some countries, not available in the majority