COVID-19

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Re: COVID-19

Post by shpalman » Mon Jun 14, 2021 7:17 pm

Concerns grow in St Ives over Covid cases linked to G7 summit
Andrew George, who speaks for the Liberal Democrats in Cornwall on health, said he was concerned about the cases.

He said he did not believe the leaders were “vectors” for Covid. “But other people associated with G7 – security staff, police, media have been intermixing.”
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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 8:10 am

What's this about then? Some paper saying the 3rd wave will kill 43,500 people (31,000 to 63,000).

https://twitter.com/Dr_D_Robertson/stat ... 5291531268

My little model was only a guess, but it was an order of magnitude lower. This sort of scale would require the entire unvaccinated population to catch it, plus 10% of the vaccinated. I can't come up with any scenario that kills this many - except one where two vaccine doses only give 50% protection or something. We already know that's not the case.

Why the f.ck are serious people spewing out Herainestold style b.llsh.t?
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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 8:35 am

Oh ffs.

Dug into it, and Imperial College are assuming reduction in symptomatic disease is:

1st dose AZ 33% (pessimistic case 20%)
2nd dose AZ 55% (pessmistic case 30%)

1st dose Pfizer 33% (pessimistic case 20%)
2nd dose Pfizer 85% (pessmistic case 78%)

With corresponding low rates for cuts in transmission, hospitalisations and deaths

No wonder their model churns out a spectacularly high death toll from a massive 3rd wave. Surprised it isn't even higher.

It's been a year and a quarter and still modellers put their heads down into complicated computer programs, running scenarios and checking the maths, and never coming back out to check their original assumptions against reality. They seem to have the attitude that their maths is correct, therefore their model is correct. A complete disconnect with the real world has never bothered them - as per last year when they confidently announced R numbers <1 with precise confidence intervals, even while other statistics showed a well established rise in cases.
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Re: COVID-19

Post by jimbob » Tue Jun 15, 2021 8:42 am

lpm wrote:
Tue Jun 15, 2021 8:10 am
What's this about then? Some paper saying the 3rd wave will kill 43,500 people (31,000 to 63,000).

https://twitter.com/Dr_D_Robertson/stat ... 5291531268

My little model was only a guess, but it was an order of magnitude lower. This sort of scale would require the entire unvaccinated population to catch it, plus 10% of the vaccinated. I can't come up with any scenario that kills this many - except one where two vaccine doses only give 50% protection or something. We already know that's not the case.

Why the f.ck are serious people spewing out Herainestold style b.llsh.t?
Covid Zoe blogpost about this from 10th June

https://covid.joinzoe.com/post/cases-ri ... ccinations
Current risk of new daily COVID infection

in the unvaccinated: 1 in 2,908
after 1 vaccine dose: 1 in 7,091
after 2 vaccine doses : 1 in 22,455
Have you considered stupidity as an explanation

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Re: COVID-19

Post by shpalman » Tue Jun 15, 2021 8:55 am

Looking at the minima in cases per day and deaths per day, maybe the CFR will be ten times lower than it was during the last wave (which was over 500 deaths per day for 3 months or so) but that doesn't actually mean deaths will be ten times lower in the next wave; maybe they'll let case rates get ten times higher.* You're at more than 7000 cases per day on a 10-14 day doubling time with a government which at best could only be persuaded not to unlockdown any more, let alone put back any lockdown measures. But with only 10 deaths a day at the moment, people won't care about cases until the deaths start getting serious again.

* - well, maybe not ten times, but if 50,000 cases per day only causes 100 deaths per day I can imagine people not really caring.
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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 9:05 am

Those 100 deaths per day will be (a) very old/vulnerable who were imperfectly vaccinated, and (b) people who didn't take up the offer of the vaccine.

(a) We probably have to "not care" as a society, like not caring about flu. Respiratory diseases kill the elderly. It might well be that we get a few years of low flu mortality in partial compensation.

(b) I'm really not sure how to view the deaths of vaccine refusers. Anyone got any idea about the proportion who are genuine "can't haves", compared to the conspiracy theorists and the can't-be-arseds? There will be people whose deliberate actions to ignore their health will lead to them occupying a hospital bed and crowding out other NHS users.
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Re: COVID-19

Post by Grumble » Tue Jun 15, 2021 9:16 am

lpm wrote:
Tue Jun 15, 2021 9:05 am
Those 100 deaths per day will be (a) very old/vulnerable who were imperfectly vaccinated, and (b) people who didn't take up the offer of the vaccine.

(a) We probably have to "not care" as a society, like not caring about flu. Respiratory diseases kill the elderly. It might well be that we get a few years of low flu mortality in partial compensation.

(b) I'm really not sure how to view the deaths of vaccine refusers. Anyone got any idea about the proportion who are genuine "can't haves", compared to the conspiracy theorists and the can't-be-arseds? There will be people whose deliberate actions to ignore their health will lead to them occupying a hospital bed and crowding out other NHS users.
On the subject of vaccine hesitancy, ordinary people can easily get confused or given bad advice from sources they trust. I suspect they are a bigger number than the proper conspiracy theorists, at least for normal vaccines. There has been so much publicity about the covid vaccines that this probably isn’t true on this occasion, but there will be some.
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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 9:18 am

lpm wrote:
Tue Jun 15, 2021 8:35 am
Oh ffs.

Dug into it, and Imperial College are assuming reduction in symptomatic disease is:

1st dose AZ 33% (pessimistic case 20%)
2nd dose AZ 55% (pessmistic case 30%)

1st dose Pfizer 33% (pessimistic case 20%)
2nd dose Pfizer 85% (pessmistic case 78%)

With corresponding low rates for cuts in transmission, hospitalisations and deaths

No wonder their model churns out a spectacularly high death toll from a massive 3rd wave. Surprised it isn't even higher.

It's been a year and a quarter and still modellers put their heads down into complicated computer programs, running scenarios and checking the maths, and never coming back out to check their original assumptions against reality. They seem to have the attitude that their maths is correct, therefore their model is correct. A complete disconnect with the real world has never bothered them - as per last year when they confidently announced R numbers <1 with precise confidence intervals, even while other statistics showed a well established rise in cases.
Those AZ and Pfizer numbers against Delta are low but not bonkers, see: https://www.thelancet.com/journals/lanc ... 1/fulltext

Though one issue is the extent to which AZ will protect against death and hospital admission among people who are infected with Delta.

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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 9:20 am

Grumble wrote:
Tue Jun 15, 2021 9:16 am
lpm wrote:
Tue Jun 15, 2021 9:05 am
Those 100 deaths per day will be (a) very old/vulnerable who were imperfectly vaccinated, and (b) people who didn't take up the offer of the vaccine.

(a) We probably have to "not care" as a society, like not caring about flu. Respiratory diseases kill the elderly. It might well be that we get a few years of low flu mortality in partial compensation.

(b) I'm really not sure how to view the deaths of vaccine refusers. Anyone got any idea about the proportion who are genuine "can't haves", compared to the conspiracy theorists and the can't-be-arseds? There will be people whose deliberate actions to ignore their health will lead to them occupying a hospital bed and crowding out other NHS users.
On the subject of vaccine hesitancy, ordinary people can easily get confused or given bad advice from sources they trust. I suspect they are a bigger number than the proper conspiracy theorists, at least for normal vaccines. There has been so much publicity about the covid vaccines that this probably isn’t true on this occasion, but there will be some.
I agree that its best to view most vaccine refusers as people who've been duped rather than active conspiracy theorists. We only see the latter on social media etc.

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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 9:22 am

Those AZ and Pfizer numbers against Delta are low but not bonkers, see: https://www.thelancet.com/journals/lanc ... 1/fulltext
They are bonkers. It's pretty clear two doses of AZ gives in the region of 80% - 90% protection.
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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 9:28 am

Woodchopper wrote:
Tue Jun 15, 2021 9:20 am
I agree that its best to view most vaccine refusers as people who've been duped rather than active conspiracy theorists. We only see the latter on social media etc.
Can I edit that to "adults who've been duped..." please.

We need to live in a world of personal responsibility. Personally I am happy to accept limits on my freedom to protect the vulnerable or due to the stupidity of children. But I refuse to accept limits on my freedom due to the stupidity of adults. Current government controls over my life are inherently wrong and there needs to be a high bar for them to be imposed.

I appreciate the history and the racial element and the rest, but at some point you've got to leave adults to go off and take their own chances.
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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 10:07 am

lpm wrote:
Tue Jun 15, 2021 9:22 am
Those AZ and Pfizer numbers against Delta are low but not bonkers, see: https://www.thelancet.com/journals/lanc ... 1/fulltext
They are bonkers. It's pretty clear two doses of AZ gives in the region of 80% - 90% protection.
That's the protection AZ was giving against Alpha. As per the above link, AZ doesn't appear to be doing nearly so well against Delta. When the new variant becomes dominant you gotta revise your assumptions.

ETA, see here from Public Health England
the Pfizer-BioNTech vaccine was 88% effective against symptomatic disease from the B.1.617.2 variant 2 weeks after the second dose, compared to 93% effectiveness against the B.1.1.7 variant
2 doses of the AstraZeneca vaccine were 60% effective against symptomatic disease from the B.1.617.2 variant compared to 66% effectiveness against the B.1.1.7 variant
both vaccines were 33% effective against symptomatic disease from B.1.617.2, 3 weeks after the first dose compared to around 50% effectiveness against the B.1.1.7 variant
https://www.gov.uk/government/news/vacc ... er-2-doses

See the new variant thread for more.

Delta is bad news, especially for those with an AZ vaccine.

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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 10:22 am

Woodchopper wrote:
Tue Jun 15, 2021 9:18 am
Though one issue is the extent to which AZ will protect against death and hospital admission among people who are infected with Delta.
Looked that up, AZ and Pfizer still giving over 90% protection against hospitalization.
https://khub.net/web/phe-national/publi ... F479607266

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Re: COVID-19

Post by jimbob » Tue Jun 15, 2021 10:23 am

https://www.pharmatimes.com/news/az,_pf ... nt_1371652
The new data, published as a pre-print, demonstrated that two doses of AZ’s COVID-19 vaccine are 92% effective against hospitalisation caused by the Delta variant, with no deaths observed among vaccinated individuals.
However, the data also showed that the vaccine is less effective against milder symptomatic COVID-19 disease.

The vaccine was 74% effective against symptomatic disease caused by the Alpha variant and 64% effective against the Delta variant.

Meanwhile, the Pfizer/BioNTech vaccine was found to be 96% effective against the Delta variant after two doses.
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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 10:24 am

jimbob wrote:
Tue Jun 15, 2021 10:23 am
https://www.pharmatimes.com/news/az,_pf ... nt_1371652
The new data, published as a pre-print, demonstrated that two doses of AZ’s COVID-19 vaccine are 92% effective against hospitalisation caused by the Delta variant, with no deaths observed among vaccinated individuals.
However, the data also showed that the vaccine is less effective against milder symptomatic COVID-19 disease.

The vaccine was 74% effective against symptomatic disease caused by the Alpha variant and 64% effective against the Delta variant.

Meanwhile, the Pfizer/BioNTech vaccine was found to be 96% effective against the Delta variant after two doses.
Yes, looks like we both got there.

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Re: COVID-19

Post by wilsontown » Tue Jun 15, 2021 11:27 am

It's all about AZ and Pfizer, but what about those of us who are on team Moderna?
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Re: COVID-19

Post by El Pollo Diablo » Tue Jun 15, 2021 1:28 pm

Had a positive lateral flow test result today (had my first pfizer jab at the end of May). Current symptoms are headache, runny nose, sinusitis, sore throat. Thought it was a cold, someone else suggested hay fever, and only bothered to request some LFTs yesterday because I saw this BBC article.

Went off to get a PCR at lunchtime. But I'm holed up now for a wee while.
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Re: COVID-19

Post by Sciolus » Tue Jun 15, 2021 1:37 pm

lpm wrote:
Tue Jun 15, 2021 9:05 am
(b) I'm really not sure how to view the deaths of vaccine refusers. Anyone got any idea about the proportion who are genuine "can't haves", compared to the conspiracy theorists and the can't-be-arseds? There will be people whose deliberate actions to ignore their health will lead to them occupying a hospital bed and crowding out other NHS users.
The only medical contraindications are those at risk of thrombosis and thrombocytopenia, and a tiny, tiny number of people with known allergies to vaccine ingredients. Pregnancy is considered to be fine. Things like immunodeficiency are not contraindications. So genuine can't haves are very few indeed.

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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 1:39 pm

Woodchopper wrote:
Tue Jun 15, 2021 10:24 am
jimbob wrote:
Tue Jun 15, 2021 10:23 am
https://www.pharmatimes.com/news/az,_pf ... nt_1371652
The new data, published as a pre-print, demonstrated that two doses of AZ’s COVID-19 vaccine are 92% effective against hospitalisation caused by the Delta variant, with no deaths observed among vaccinated individuals.
However, the data also showed that the vaccine is less effective against milder symptomatic COVID-19 disease.

The vaccine was 74% effective against symptomatic disease caused by the Alpha variant and 64% effective against the Delta variant.

Meanwhile, the Pfizer/BioNTech vaccine was found to be 96% effective against the Delta variant after two doses.
Yes, looks like we both got there.
The Guardian has a handy summary:

The Covid Delta variant: how effective are the vaccines?
https://www.theguardian.com/world/2021/ ... e-vaccines

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Re: COVID-19

Post by jimbob » Tue Jun 15, 2021 5:19 pm

Rolling Case rate by age in NW England heatmap with colour boundaries every factor of 2 from end of Feb (bottom) to Jun 10th (top)

0-4 on L 85-89 on R

Image
And plotted since 1st Nov

Image
Have you considered stupidity as an explanation

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Re: COVID-19

Post by Woodchopper » Tue Jun 15, 2021 5:31 pm

lpm wrote:
Tue Jun 15, 2021 8:35 am
Oh ffs.

Dug into it, and Imperial College are assuming reduction in symptomatic disease is:

1st dose AZ 33% (pessimistic case 20%)
2nd dose AZ 55% (pessmistic case 30%)

1st dose Pfizer 33% (pessimistic case 20%)
2nd dose Pfizer 85% (pessmistic case 78%)

With corresponding low rates for cuts in transmission, hospitalisations and deaths

No wonder their model churns out a spectacularly high death toll from a massive 3rd wave. Surprised it isn't even higher.

It's been a year and a quarter and still modellers put their heads down into complicated computer programs, running scenarios and checking the maths, and never coming back out to check their original assumptions against reality. They seem to have the attitude that their maths is correct, therefore their model is correct. A complete disconnect with the real world has never bothered them - as per last year when they confidently announced R numbers <1 with precise confidence intervals, even while other statistics showed a well established rise in cases.
The actual projections from here https://assets.publishing.service.gov.u ... step_4.pdf
Projections.jpg
Projections.jpg (302.32 KiB) Viewed 2246 times
The Imperial estimates for transmission appear to be pessimistic but not bonkers.

The estimates for AZ and hospitalization (one dose 73% second dose 85%) appear to be a little optimistic for one dose (PHE has it at 71%) and pessimistic but not bonkers for second dose (PHE has it at 92%).

Biggest issue for the AZ vaccine is the transmission effectiveness. Lots of people who got the AZ vaccine are going to be getting asymptomatic infections or infections with mild symptoms. So they are presumably going to be passing it on (though I hope for a shorter period than people who get seriously ill).

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Re: COVID-19

Post by Herainestold » Tue Jun 15, 2021 5:34 pm

Woodchopper wrote:
Tue Jun 15, 2021 5:31 pm


The Imperial estimates for transmission appear to be pessimistic but not bonkers.

The estimates for AZ and hospitalization (one dose 73% second dose 85%) appear to be a little optimistic for one dose (PHE has it at 71%) and pessimistic but not bonkers for second dose (PHE has it at 92%).

Biggest issue for the AZ vaccine is the transmission effectiveness. Lots of people who got the AZ vaccine are going to be getting asymptomatic infections or infections with mild symptoms. So they are presumably going to be passing it on (though I hope for a shorter period than people who get seriously ill).
The problem is that the vaccines don't stop transmission, especially of Delta variant.Vaccinated people get infected, most don't get very sick, although the frail, the obese, those with co-morbidities like diabetes and hypertension may well die. The virus will travel through the vaccinated population and when it encounters the unvaccinated it is like a smouldering flame reaching dry tinder. Watch out.

It would have been encouraging in the government had re-impoised at least some restrictions like indoor dining, but either they dont believe their own modelling or they simply dont care.

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Re: COVID-19

Post by lpm » Tue Jun 15, 2021 5:58 pm

jimbob wrote:
Tue Jun 15, 2021 5:19 pm
Rolling Case rate by age in NW England heatmap with colour boundaries every factor of 2 from end of Feb (bottom) to Jun 10th (top)

0-4 on L 85-89 on R
Are you able to easily change population sizes for this heat map?

E.g. create an imaginary country called "NW Unvaccinatia" with a total population of loads of 0-30 year olds, some 30-40, only a handful of >50s?

Just take England's vaccination % for each cohort and multiply by cohort population? Instead of 20,000 people over 80, pretend there are 1,000 people?

Otherwise it will never ever show spread towards the right. Too few cases per large vaccinated population. But if adjusted it might show spread of a few cases into the small unvaccinated population.
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Re: COVID-19

Post by jimbob » Tue Jun 15, 2021 6:42 pm

lpm wrote:
Tue Jun 15, 2021 5:58 pm
jimbob wrote:
Tue Jun 15, 2021 5:19 pm
Rolling Case rate by age in NW England heatmap with colour boundaries every factor of 2 from end of Feb (bottom) to Jun 10th (top)

0-4 on L 85-89 on R
Are you able to easily change population sizes for this heat map?

E.g. create an imaginary country called "NW Unvaccinatia" with a total population of loads of 0-30 year olds, some 30-40, only a handful of >50s?

Just take England's vaccination % for each cohort and multiply by cohort population? Instead of 20,000 people over 80, pretend there are 1,000 people?

Otherwise it will never ever show spread towards the right. Too few cases per large vaccinated population. But if adjusted it might show spread of a few cases into the small unvaccinated population.
There are raw case numbers in https://coronavirus.data.gov.uk/details ... mographics

When you download the CSV, you need to still separate by comma and colon (and remove closing curly bracket from some datatypes) to get it into a decent format.

I could possibly look at this data

https://coronavirus.data.gov.uk/details ... mographics and divide by the percent unvaccinated for that day.

The vaccination data has 334 columns, which I haven't yet worked out what the fields for each age range are

But as it's an excel array, it is actually fairly trivial to get the data into both matrices once I've worked that out
Have you considered stupidity as an explanation

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Re: COVID-19

Post by Grumble » Tue Jun 15, 2021 8:36 pm

El Pollo Diablo wrote:
Tue Jun 15, 2021 1:28 pm
Had a positive lateral flow test result today (had my first pfizer jab at the end of May). Current symptoms are headache, runny nose, sinusitis, sore throat. Thought it was a cold, someone else suggested hay fever, and only bothered to request some LFTs yesterday because I saw this BBC article.

Went off to get a PCR at lunchtime. But I'm holed up now for a wee while.
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