COVID-19

Covid-19 discussion, bring your own statistics
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shpalman
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Re: COVID-19

Post by shpalman » Thu May 27, 2021 5:28 pm

I also tried moving the lower limit of the y-axis down a bit on the log scale to check the effect wasn't an optical illusion. Now the data occupy roughly the same amount of graph on this scale as they do on the linear plot I made (which starts at zero).
mec-vent-UK-data_2021-May-26.jpg
mec-vent-UK-data_2021-May-26.jpg (54.65 KiB) Viewed 677 times
Here's the previous linear plot:

Image
molto tricky

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Sciolus
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Re: COVID-19

Post by Sciolus » Thu May 27, 2021 6:59 pm

Thanks KAJ et al, and apologies for contributing to the derail -- I genuinely found the original hard to read, but it's all very clear now.

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Re: COVID-19

Post by bolo » Thu May 27, 2021 9:38 pm

These graphs are, I think, the current number of patients in ventilation beds, not the number of new patients placed into that status each day. So I'm not sure how much to worry about the leveling off unless someone has other data on how long the patients in question stay on ventilation.

For example, if there 120 patients in the UK who for some reason have all been on ventilation for months, and will stay that way for the foreseeable, then that sucks for them, but essentially no new patients are requiring ventilation, which is great.

Whereas, if each day half the patients on ventilation in the UK come off it, one way or the other, and are replaced by new patients who didn't previously need ventilation, then the flattening means things have stopped getting better, which is bad.

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Re: COVID-19

Post by KAJ » Fri May 28, 2021 7:33 am

bolo wrote:
Thu May 27, 2021 9:38 pm
These graphs are, I think, the current number of patients in ventilation beds, not the number of new patients placed into that status each day. So I'm not sure how much to worry about the leveling off unless someone has other data on how long the patients in question stay on ventilation.

For example, if there 120 patients in the UK who for some reason have all been on ventilation for months, and will stay that way for the foreseeable, then that sucks for them, but essentially no new patients are requiring ventilation, which is great.

Whereas, if each day half the patients on ventilation in the UK come off it, one way or the other, and are replaced by new patients who didn't previously need ventilation, then the flattening means things have stopped getting better, which is bad.
lpm made a somewhat similar point, and added that the criteria for entering or staying in MV beds may be relaxed as more beds are available. That possibility is supported by the fact that the "... figures are the numbers of patients in beds which are capable of delivering mechanical ventilation..." (emphasis added), not necessarily those needing MV. Similar arguments would apply to number of inpatients, but not I think to numbers of admissions - constrained by the non-Covid backlog. I gave that data earlier and here's a chart
Admits.png
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It's much "noisier" (doesn't seem to be a day-of-week effect) but I think there may, perhaps, possibly, be a suggestion of a plateau. But my eyes are becoming tired from too much entrail gazing, I suppose we'll know one way or the other in a few weeks.

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Re: COVID-19

Post by raven » Fri May 28, 2021 1:03 pm

lpm wrote:
Thu May 27, 2021 1:56 pm
What we need is England excluding all towns beginning with B, and the towns beginning with B separately.

Nearly all the country has weeks before it needs to worry about intensive care beds and hospital admissions. A few places will be seeing worrying rises now. The vaccine seems to work just fine against 167-variant hospitalisation so it remains a pretty desperate race to keep ahead.
You can look at hospitalisations in, say, Bolton NHS trust on the gov.uk dashboard. linky Small numbers but definite rises in admissions & MVbeds.

Then you could look by regions that don't have the towns beginning with B, like the SW or SE.linky for SE Admissions & MVbeds flatlining.

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Re: COVID-19

Post by Woodchopper » Sun Jun 06, 2021 9:41 pm


Prelminary Analysis of Excess Mortality Suggests That Over 1.7 Million May Have Perished in Relation to the Covid-19 Pandemic in India More Than in Any Other Country

Based on excess mortality rates, the pandemic-related mortality through the first 19 weeks of 2021 in 6 Indian regions was 131.5 to 181.8 per 100,000 population. If these rates apply to India as a whole, then between 1.78 to 2.46 million people may have perished in India as a result of the Covid-19 pandemic by the 19th week of 2021. This mortality exceeds the known mortality in every other country in the world.
https://www.researchgate.net/publicatio ... er_Country

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Re: COVID-19

Post by shpalman » Mon Jun 07, 2021 6:51 am

Woodchopper wrote:
Sun Jun 06, 2021 9:41 pm

Prelminary Analysis of Excess Mortality Suggests That Over 1.7 Million May Have Perished in Relation to the Covid-19 Pandemic in India More Than in Any Other Country

Based on excess mortality rates, the pandemic-related mortality through the first 19 weeks of 2021 in 6 Indian regions was 131.5 to 181.8 per 100,000 population. If these rates apply to India as a whole, then between 1.78 to 2.46 million people may have perished in India as a result of the Covid-19 pandemic by the 19th week of 2021. This mortality exceeds the known mortality in every other country in the world.
https://www.researchgate.net/publicatio ... er_Country
Lombardy had an official covid death toll of 250.5 per 100,000 at the beginning of 2021, and is now at 334.6 per 100,000. But in the first wave, i.e. up until the beginning of June 2020, the official death toll was 160 per 100,000 and that for sure was an underestimate.

"This mortality exceeds the known mortality in every other country in the world" because the population of India exceeds almost every other country in the world.
molto tricky

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Re: COVID-19

Post by Woodchopper » Mon Jun 07, 2021 7:04 am

Yes, from the paper it’s clear that they mean absolute mortality.

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Re: COVID-19

Post by Woodchopper » Mon Jun 07, 2021 7:39 pm

Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2

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Re: COVID-19

Post by jimbob » Mon Jun 07, 2021 9:35 pm

Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Indeed.

I mentioned it about this time last year on ISF and got this reply.
We've got a saying around here, working around hazardous materials, hazardous equipment and often at hazardous heights. 'What doesn't kill you just screws you up really, really bad for a very, very long time.'
Have you considered stupidity as an explanation

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shpalman
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Re: COVID-19

Post by shpalman » Wed Jun 09, 2021 5:40 pm

Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Well don't worry, cases and deaths are going up too.
uk-cases-and-deaths-log.png
uk-cases-and-deaths-log.png (39.38 KiB) Viewed 309 times
molto tricky

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Re: COVID-19

Post by Herainestold » Wed Jun 09, 2021 7:37 pm

shpalman wrote:
Wed Jun 09, 2021 5:40 pm
Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Well don't worry, cases and deaths are going up too.

uk-cases-and-deaths-log.png
I hope the NHS has been stocking up on oxygen.

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Re: COVID-19

Post by KAJ » Wed Jun 09, 2021 8:05 pm

shpalman wrote:
Wed Jun 09, 2021 5:40 pm
Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Well don't worry, cases and deaths are going up too.

uk-cases-and-deaths-log.png
And numbers in mechanical ventilation beds. Apologies for the chart - it's really intended for my personal consumption. It shows a quadratic in black and a loess fit (## `geom_smooth()` using method = 'loess' and formula 'y ~ x') in blue. Could certainly be improved, but I think it's reasonably clear.
MVBeds.png
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Re: COVID-19

Post by jimbob » Wed Jun 09, 2021 8:39 pm

KAJ wrote:
Wed Jun 09, 2021 8:05 pm
shpalman wrote:
Wed Jun 09, 2021 5:40 pm
Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Well don't worry, cases and deaths are going up too.

uk-cases-and-deaths-log.png
And numbers in mechanical ventilation beds. Apologies for the chart - it's really intended for my personal consumption. It shows a quadratic in black and a loess fit (## `geom_smooth()` using method = 'loess' and formula 'y ~ x') in blue. Could certainly be improved, but I think it's reasonably clear.
MVBeds.png

Do the same for the NW and the signal is very clear
Have you considered stupidity as an explanation

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Re: COVID-19

Post by sTeamTraen » Wed Jun 09, 2021 8:45 pm

shpalman wrote:
Wed Jun 09, 2021 5:40 pm
Well don't worry, cases and deaths are going up too.
The UK's 14-day case rate is now 99 (total cases in the last 14 days per 100K people), making a complete joke of Spain's decision to adjust the threshold for "safe country" status from 25 to 75 so as to include the UK three weeks ago when the rate was around 45. They evaluate the number every two weeks and when they looked last Friday is was 72.5 ("Hey, still below 75") and still rising.
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Re: COVID-19

Post by Herainestold » Wed Jun 09, 2021 10:30 pm

KAJ wrote:
Wed Jun 09, 2021 8:05 pm
shpalman wrote:
Wed Jun 09, 2021 5:40 pm
Woodchopper wrote:
Mon Jun 07, 2021 7:39 pm
Count the cost of disability caused by COVID-19
Focusing only on cases and deaths hides the pandemic’s lasting health burden on people, societies and economies
https://www.nature.com/articles/d41586-021-01392-2
Well don't worry, cases and deaths are going up too.

uk-cases-and-deaths-log.png
And numbers in mechanical ventilation beds. Apologies for the chart - it's really intended for my personal consumption. It shows a quadratic in black and a loess fit (## `geom_smooth()` using method = 'loess' and formula 'y ~ x') in blue. Could certainly be improved, but I think it's reasonably clear.
MVBeds.png
We watched in awe last year as Italy went down in flames, and then it happened here. This year we observed the disaster in India, we sat on our hands, failed to seal the border, secure that our vaccine roll out made us impregnable, and now we are seeing the same thing happen again.

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Re: COVID-19

Post by Woodchopper » Thu Jun 10, 2021 4:46 am


Highlights


Performed detailed molecular and spatial analysis of the COVID-19 brain immune response

Pathognomonic microglial nodules and T cell infiltration are present in COVID-19 brains

Altered microglia-T cell interactions correlate with systemic measures of inflammation

Vascular leakage is linked with immune activation, ACE2 expression and viral antigen
Abstract

COVID-19 can cause severe neurological symptoms, but the underlying pathophysiological mechanisms are unclear. Here, we interrogated the brain stem and olfactory bulb in COVID-19 patients postmortem using imaging mass cytometry to understand the local immune response at a spatially resolved, high-dimensional single-cell level and compared their immune map to non-COVID respiratory failure, multiple sclerosis and control patients. We observed substantial immune activation in the central nervous system with pronounced neuropathology (astrocytosis, axonal damage, blood-brain-barrier leakage) and detected viral antigen in ACE2 receptor-positive cells enriched in the vascular compartment. Microglial nodules and the perivascular compartment represented COVID-19-specific microanatomic immune niches with context-specific cellular interactions enriched for activated CD8+ T cells. Altered brain T cell–microglial interactions were linked to clinical measures of systemic inflammation and disturbed hemostasis.

This study identifies profound neuroinflammation with activation of innate and adaptive immune cells as correlates of COVID-19 neuropathology, with implications for potential therapeutic strategies.
https://www.cell.com/immunity/fulltext/ ... 21)00246-6

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Re: COVID-19

Post by Herainestold » Thu Jun 10, 2021 5:04 am

Woodchopper wrote:
Thu Jun 10, 2021 4:46 am

Highlights


Performed detailed molecular and spatial analysis of the COVID-19 brain immune response

Pathognomonic microglial nodules and T cell infiltration are present in COVID-19 brains

Altered microglia-T cell interactions correlate with systemic measures of inflammation

Vascular leakage is linked with immune activation, ACE2 expression and viral antigen
Abstract

COVID-19 can cause severe neurological symptoms, but the underlying pathophysiological mechanisms are unclear. Here, we interrogated the brain stem and olfactory bulb in COVID-19 patients postmortem using imaging mass cytometry to understand the local immune response at a spatially resolved, high-dimensional single-cell level and compared their immune map to non-COVID respiratory failure, multiple sclerosis and control patients. We observed substantial immune activation in the central nervous system with pronounced neuropathology (astrocytosis, axonal damage, blood-brain-barrier leakage) and detected viral antigen in ACE2 receptor-positive cells enriched in the vascular compartment. Microglial nodules and the perivascular compartment represented COVID-19-specific microanatomic immune niches with context-specific cellular interactions enriched for activated CD8+ T cells. Altered brain T cell–microglial interactions were linked to clinical measures of systemic inflammation and disturbed hemostasis.

This study identifies profound neuroinflammation with activation of innate and adaptive immune cells as correlates of COVID-19 neuropathology, with implications for potential therapeutic strategies.
https://www.cell.com/immunity/fulltext/ ... 21)00246-6
Its pretty nasty. Is that the original wild type covid, or the new Delta variant? The virus seems to have mutated and pivoted to younger people, as wellas being more transmissible and deadlier.

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shpalman
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Re: COVID-19

Post by shpalman » Thu Jun 10, 2021 10:05 am

This year's "four weeks behind Italy" is going to be "link between Covid cases and deaths has been broken" isn't it?

It obviously hasn't. Even if the CFR has been reduced by an order of magnitude, it's still there.

Note that my graph is scaled for a 2% mortality rate which was about right for the 2nd-wave peak at the beginning of this year. The minimum in cases (a month ago) was about 2000 a day and the minimum in deaths was around 7 a day a couple of weeks after that.* Ok, that's not very many, but it's still 0.35% [spurious precision alert].

Image

* - better than Italy though, we still have ten times more deaths per day than that despite cases now having fallen to 2000 a day; a month ago we still had 10000 cases per day.
molto tricky

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Re: COVID-19

Post by sTeamTraen » Thu Jun 10, 2021 1:49 pm

shpalman wrote:
Thu Jun 10, 2021 10:05 am
This year's "four weeks behind Italy" is going to be "link between Covid cases and deaths has been broken" isn't it?

It obviously hasn't. Even if the CFR has been reduced by an order of magnitude, it's still there.
IIRC, "Four weeks behind Italy" (I remember it as "two weeks") was used more as "This is where you'll be in four weeks if you don't do anything", rather than as a complacent "Ha, look at the Italians with their terrible numbers, no way that will happen to us with our four-week cushion".

I think it may be too early to tell, and will vary by country depending on vaccine take-up and how it's distributed around the age cohorts. Here are three countries where deaths uncoupled from cases pretty spectacularly, quite early after the vaccination campaign started. Of course at some point deaths will be proportional to cases (it would be weird if they weren't), but if that's at 0.03% of the base CFR (i.e., actually like flu) then there will come a point at which it's actually reasonable to unlock a bit.

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Something something hammer something something nail

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shpalman
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Re: COVID-19

Post by shpalman » Thu Jun 10, 2021 1:59 pm

sTeamTraen wrote:
Thu Jun 10, 2021 1:49 pm
shpalman wrote:
Thu Jun 10, 2021 10:05 am
This year's "four weeks behind Italy" is going to be "link between Covid cases and deaths has been broken" isn't it?

It obviously hasn't. Even if the CFR has been reduced by an order of magnitude, it's still there.
IIRC, "Four weeks behind Italy" (I remember it as "two weeks") was used more as "This is where you'll be in four weeks if you don't do anything", rather than as a complacent "Ha, look at the Italians with their terrible numbers, no way that will happen to us with our four-week cushion".
https://www.bbc.com/news/uk-51858987
sTeamTraen wrote:
Thu Jun 10, 2021 1:49 pm
I think it may be too early to tell, and will vary by country depending on vaccine take-up and how it's distributed around the age cohorts. Here are three countries where deaths uncoupled from cases pretty spectacularly, quite early after the vaccination campaign started. Of course at some point deaths will be proportional to cases (it would be weird if they weren't), but if that's at 0.03% of the base CFR (i.e., actually like flu) then there will come a point at which it's actually reasonable to unlock a bit.
True, but right now it looks ten times higher than that in the UK.
molto tricky

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Re: COVID-19

Post by sTeamTraen » Thu Jun 10, 2021 9:15 pm

shpalman wrote:
Thu Jun 10, 2021 1:59 pm
sTeamTraen wrote:
Thu Jun 10, 2021 1:49 pm
I think it may be too early to tell, and will vary by country depending on vaccine take-up and how it's distributed around the age cohorts. Here are three countries where deaths uncoupled from cases pretty spectacularly, quite early after the vaccination campaign started. Of course at some point deaths will be proportional to cases (it would be weird if they weren't), but if that's at 0.03% of the base CFR (i.e., actually like flu) then there will come a point at which it's actually reasonable to unlock a bit.
True, but right now it looks ten times higher than that in the UK.
Agreed. As I noted here we still have a way to go everywhere before the vaccines get to enough people to make an order of magnitude difference, and we may still hit Christian Drosten's nightmare scenario of the virus ripping through the younger less-old population in larger numbers than last year and overwhelming the hospitals with a CFR of one-sixth of last year's. But at some point we will have to start living with Covid as part of the long-term landscape.
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Re: COVID-19

Post by lpm » Thu Jun 10, 2021 9:37 pm

Hospitalization/deaths of young people will be swamped by >80s who are unvaccinated or >80s in the vaccine fail percentage.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: COVID-19

Post by shpalman » Fri Jun 11, 2021 6:49 am

lpm wrote:
Thu Jun 10, 2021 9:37 pm
Hospitalization/deaths of young people will be swamped by >80s who are unvaccinated or >80s in the vaccine fail percentage.
“What [hospital] chief executives are consistently telling us is that it is a much younger population that is coming in, they are less clinically vulnerable, they are less in need of critical care...
(Still from here)

I mean, I get why he's considering it a good thing that it's younger people ending up in hospital now, but it's also a bad thing (however young and healthy they are [or were] they are still bad enough that they need the hospital), unless the absolute numbers are also very low. (You want the average age to be lower because the older people just aren't there, not that the numbers are the same but the age range has shifted.) But if you've got young people in the hospital then you must have a lot of infections among young people. It will actually be a good thing if the only people in hospital with covid end up being a few of the oldest and/or most fragile.
molto tricky

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Re: COVID-19

Post by lpm » Fri Jun 11, 2021 7:16 am

Delta is still heading up the heat map. We've been here before - fires at the bottom with school age and <30, slow spread upwards over many weeks. We've seen twice that you can't shield the vulnerable when cases are very high in the young.

The vulnerable now are the 2 million unvaccinated over 50s, rather than the 25 million unvaccinated young. A tenth of the size, but anything from 30x to 300x higher fatality rates.

Plus another 2 million where we can assume the vaccine only partially works, hospitalising instead of killing.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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