B.1.1.529 Omicron variant

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OffTheRock
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Re: B.1.1.529 Omicron variant

Post by OffTheRock » Tue Jan 04, 2022 7:35 pm

That article says it will start to be included from the end of this month although I thought I'd read middle of Jan somewhere last month.

I know it shouldn't surprise me that it's taken omicron to speed them up on this, but it does. I dread to think how many cases we might have over the 218k reported today.

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Re: B.1.1.529 Omicron variant

Post by monkey » Tue Jan 04, 2022 8:39 pm

Quick question, because my google Fu is failing me and I'm sure someone here knows. It might also have been discussed, but I can't find the answer with the search.

What's the typical length of time between exposure and hospitalisation for omicron?

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sTeamTraen
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Re: B.1.1.529 Omicron variant

Post by sTeamTraen » Wed Jan 05, 2022 12:52 am

lpm wrote:
Fri Dec 31, 2021 6:22 pm
Volume of cases is massively understated. I think this will throw all shpalman equations out. There simply isn't the data.

Hospitalisations are rising as expected. Christmas Day infections will start to arrive in hospitals in about another week.
Does anyone know why the UK hospital admission numbers haven't been updated in more than a week?

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Something something hammer something something nail

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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Wed Jan 05, 2022 6:49 am

sTeamTraen wrote:
Wed Jan 05, 2022 12:52 am
lpm wrote:
Fri Dec 31, 2021 6:22 pm
Volume of cases is massively understated. I think this will throw all shpalman equations out. There simply isn't the data.

Hospitalisations are rising as expected. Christmas Day infections will start to arrive in hospitals in about another week.
Does anyone know why the UK hospital admission numbers haven't been updated in more than a week?
Because Scotland hasn't supplied figures since the 27th.
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jimbob
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Re: B.1.1.529 Omicron variant

Post by jimbob » Wed Jan 05, 2022 10:06 am

sTeamTraen wrote:
Wed Jan 05, 2022 12:52 am
lpm wrote:
Fri Dec 31, 2021 6:22 pm
Volume of cases is massively understated. I think this will throw all shpalman equations out. There simply isn't the data.

Hospitalisations are rising as expected. Christmas Day infections will start to arrive in hospitals in about another week.
Does anyone know why the UK hospital admission numbers haven't been updated in more than a week?


Untitled.png
This is what it looks like for England upto 3rd Jan

Image

I use 7day rolling totals for hospital admissions and cases because they're easier to explain what they mean, as opposed to new cases and average numbers in hospital.
Have you considered stupidity as an explanation

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lpm
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Re: B.1.1.529 Omicron variant

Post by lpm » Wed Jan 05, 2022 10:34 am

...and yet we still see "decoupled" and "vaccines have broken the link" wandering about the discourse like unkillable zombies.

Clearly Omicron is another change to the gearing. But the pathway is guaranteed.
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sTeamTraen
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Re: B.1.1.529 Omicron variant

Post by sTeamTraen » Wed Jan 05, 2022 4:08 pm

jimbob wrote:
Wed Jan 05, 2022 10:06 am
This is what it looks like for England upto 3rd Jan
What is going on with the loopy bits of the left-hand plot?
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lpm
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Re: B.1.1.529 Omicron variant

Post by lpm » Wed Jan 05, 2022 4:16 pm

The minor oscillations during the long plateau of July to Nov 2021.
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jimbob
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Re: B.1.1.529 Omicron variant

Post by jimbob » Wed Jan 05, 2022 8:31 pm

lpm wrote:
Wed Jan 05, 2022 4:16 pm
The minor oscillations during the long plateau of July to Nov 2021.
Yup

Here's June-November, each dot is one day.

Forget about the annotations, I just CBA to fix them
Screenshot 2022-01-05 203054.png
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Bird on a Fire
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Wed Jan 05, 2022 9:29 pm

I saw this kind of phase plot in a really cool paper on bird demography recently. Really effective visualisation IMHO.
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Grumble
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Re: B.1.1.529 Omicron variant

Post by Grumble » Fri Jan 07, 2022 7:05 am

Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
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jimbob
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Re: B.1.1.529 Omicron variant

Post by jimbob » Fri Jan 07, 2022 8:19 am

Grumble wrote:
Fri Jan 07, 2022 7:05 am
Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
Yes, but the advantage is that I can say "this is the rolling sum of the last 7 days" for both axes. Rather than describing a rolling average

Of course, if more of the cases are in the vaccinated, you'd really hope that the hospitalisations per case for Omicron would be lower
Have you considered stupidity as an explanation

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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 8:34 am

jimbob wrote:
Fri Jan 07, 2022 8:19 am
Grumble wrote:
Fri Jan 07, 2022 7:05 am
Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
Yes, but the advantage is that I can say "this is the rolling sum of the last 7 days" for both axes. Rather than describing a rolling average.
The rolling average would be the rolling sum of the last 7 days, divided by 7.

(I prefer to use the 7-day either-side average; it doesn't change the number, just which date it's assigned to.)
Grumble wrote:
Fri Jan 07, 2022 7:05 am
Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
jimbob wrote:
Fri Jan 07, 2022 8:19 am
Of course, if more of the cases are in the vaccinated, you'd really hope that the hospitalisations per case for Omicron would be lower.
This is why I also follow the occupancy, since we don't have figures for numbers discharged per day.
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Re: B.1.1.529 Omicron variant

Post by jimbob » Fri Jan 07, 2022 9:18 am

shpalman wrote:
Fri Jan 07, 2022 8:34 am
jimbob wrote:
Fri Jan 07, 2022 8:19 am
Grumble wrote:
Fri Jan 07, 2022 7:05 am
Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
Yes, but the advantage is that I can say "this is the rolling sum of the last 7 days" for both axes. Rather than describing a rolling average.
The rolling average would be the rolling sum of the last 7 days, divided by 7.

(I prefer to use the 7-day either-side average; it doesn't change the number, just which date it's assigned to.)
Grumble wrote:
Fri Jan 07, 2022 7:05 am
Doesn’t the relevance of a 7-day rolling admission change when the average length of stay changes?
jimbob wrote:
Fri Jan 07, 2022 8:19 am
Of course, if more of the cases are in the vaccinated, you'd really hope that the hospitalisations per case for Omicron would be lower.
This is why I also follow the occupancy, since we don't have figures for numbers discharged per day.
They show different things. Hospital admissions are going to be more tightly coupled to actual cases (as in one-time incidents) than actual hospital occupancy, as the lag will be more spready.
Have you considered stupidity as an explanation

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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 9:27 am

jimbob wrote:
Fri Jan 07, 2022 9:18 am
They show different things.
Yes, that's why I follow both of them.
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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 12:15 pm

Nearly 40% of Covid hospital cases in England now patients primarily being treated for something else, latest figures show

Is that a lot? Is it more than before? Less than before?
NHS England has this morning published its latest “primary diagnosis” supplement. This is a dataset that shows how many of the daily Covid hospital cases are patients being treated in hospital for Covid, and how many are patients with Covid being treated primary for something else.

The hospital figures that are published daily do not make this distinction

The latest figure is for Tuesday 4 January and it shows that in England 13,045 patients were in hospital with Covid on that day, but only 8,200 for Covid. That means only 63% of Covid cases were in hospital primary because of Covid.

This figures has been drifting down. The equivalent figure for the previous Tuesday, when total Covid cases were 8,321, was 67%, and the Tuesday before that, when overall cases were 6,245, 71% of them were people being treated primary for Covid.

The figures cover acute hospital admissions only.
So that 40% (well done for giving a figure in the headline and then talking about one minus it in the rest of the text) is a number which has been "drifting" up, but then the numbers in hospital (with+for) overall have been going up.

How about we always visualization the data:
Primary-Diagnosis-Supplement-20220106.png
Primary-Diagnosis-Supplement-20220106.png (33.68 KiB) Viewed 319 times
From the beginning of October (when this data starts) until mid December it was roughly constant at around 25%, now it's come up to around 40%.
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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 12:28 pm

Not sure whether to interpret that as patients who were already in hospital for something else are catching covid while they're in there, or that covid is now worse in people with pre-existing conditions.

Or that there's an epidemic of pre-existing conditions f.ck should I know.
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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 12:47 pm

... or that the same number of people are needing to go to hospital for acute reasons and when they covid-test them on arrival an increasing number of them turn out to be positive - that's probably it.

Only having the data since October means I can't really compare this to previous waves.
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Woodchopper
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Fri Jan 07, 2022 12:52 pm

shpalman wrote:
Fri Jan 07, 2022 12:47 pm
... or that the same number of people are needing to go to hospital for acute reasons and when they covid-test them on arrival an increasing number of them turn out to be positive - that's probably it.

I expect its a combination of that and picking up an infection in hospital.

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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 1:30 pm

molto tricky

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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 1:45 pm

Woodchopper wrote:
Fri Jan 07, 2022 12:52 pm
shpalman wrote:
Fri Jan 07, 2022 12:47 pm
... or that the same number of people are needing to go to hospital for acute reasons and when they covid-test them on arrival an increasing number of them turn out to be positive - that's probably it.

I expect its a combination of that and picking up an infection in hospital.
Sooner or later every ward becomes a covid ward.
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shpalman
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Jan 07, 2022 5:10 pm

Well it's interesting how hospital occupancy is going up, and deaths are going up (so you're hitting your target of 1000 deaths per week with quite a margin to spare, well done) but MV bed occupancy isn't.

Of course we can't see if that's because there are lots of short-stay* admissions to the MV beds, or if the doctors have realized that some patients are just going to die anyway so there's no point.


* - and of course we don't know in what state patients are leaving them.
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Re: B.1.1.529 Omicron variant

Post by dyqik » Fri Jan 07, 2022 6:05 pm

Here I think there's fewer on ICU beds on ventilators, but more on low level oxygen through a cannula, on general wards

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Re: B.1.1.529 Omicron variant

Post by Herainestold » Fri Jan 07, 2022 6:06 pm

shpalman wrote:
Fri Jan 07, 2022 5:10 pm
Well it's interesting how hospital occupancy is going up, and deaths are going up (so you're hitting your target of 1000 deaths per week with quite a margin to spare, well done) but MV bed occupancy isn't.

Of course we can't see if that's because there are lots of short-stay* admissions to the MV beds, or if the doctors have realized that some patients are just going to die anyway so there's no point.


* - and of course we don't know in what state patients are leaving them.
When all is said and done, Omicron is going to prove to be deadlier than Delta.
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Re: B.1.1.529 Omicron variant

Post by jimbob » Fri Jan 07, 2022 6:32 pm

shpalman wrote:
Fri Jan 07, 2022 5:10 pm
Well it's interesting how hospital occupancy is going up, and deaths are going up (so you're hitting your target of 1000 deaths per week with quite a margin to spare, well done) but MV bed occupancy isn't.

Of course we can't see if that's because there are lots of short-stay* admissions to the MV beds, or if the doctors have realized that some patients are just going to die anyway so there's no point.


* - and of course we don't know in what state patients are leaving them.

dyqik wrote:
Fri Jan 07, 2022 6:05 pm
Here I think there's fewer on ICU beds on ventilators, but more on low level oxygen through a cannula, on general wards
There are questions whether it's worse for blood clotting
Have you considered stupidity as an explanation

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