COVID-19

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

Post by Sciolus » Sun Mar 21, 2021 9:06 pm

Grumble wrote:
Sun Mar 21, 2021 8:38 pm
Thanks KAJ. I like this graph from the Guardian which shows the incidence for 3 age ranges. It’s only going up for the under 20’s, which must mean that the increase in testing for school kids is picking up previously undetected cases - which is what we want I think.
Or opening schools is increasing cases in under-20s, which is what we don't want. The ONS survey shows a continuing fall, but that's only for the first week of schools returning in England, so it's still too early to tell.
(NInjad while looking up ONS stuff.)

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Re: COVID-19

Post by Herainestold » Sun Mar 21, 2021 11:54 pm

Can't wait to get back to normal?

If all restrictions are lifted in early 2022, we can still expect 20 000 deaths.
If we wait until January, 2022, to completely lift all restrictions, such that the entire adult population have been offered two doses of vaccine, we still generally predict a substantial outbreak upon relaxation with a large number of associated deaths (appendix p 11 shows the associated dynamics over time; figure 2D, table 2). Even with 85% protection against infection, the sudden release of all restrictions is predicted to generate an infection wave leading to 21 400 deaths (95% CI 1480–57 600).
We really need to stay locked down hard.

https://www.thelancet.com/journals/lani ... 2/fulltext

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Re: COVID-19

Post by shpalman » Mon Mar 22, 2021 8:37 am

Herainestold wrote:
Sun Mar 21, 2021 11:54 pm
Can't wait to get back to normal?

If all restrictions are lifted in early 2022, we can still expect 20 000 deaths.
If we wait until January, 2022, to completely lift all restrictions, such that the entire adult population have been offered two doses of vaccine, we still generally predict a substantial outbreak upon relaxation with a large number of associated deaths (appendix p 11 shows the associated dynamics over time; figure 2D, table 2). Even with 85% protection against infection, the sudden release of all restrictions is predicted to generate an infection wave leading to 21 400 deaths (95% CI 1480–57 600).
We really need to stay locked down hard.

https://www.thelancet.com/journals/lani ... 2/fulltext
Well that's an argument for a zero-covid strategy...
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lpm
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Re: COVID-19

Post by lpm » Mon Mar 22, 2021 8:52 am

It's also an argument for the flu strategy.

In fact, 20,000 Covid deaths in 2022 might easily matched by the saving of 20,000 flu deaths - if there's basic masks + social distancing + big flu vaccine program.
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Re: COVID-19

Post by badger » Mon Mar 22, 2021 11:37 am

Apparently earlier does not necessarily mean better, when it comes to UK lockdown (because earlier first spring lockdown equals bigger second waves around winter, which, erm, could be prevented by, erm, earlier lockdowns?) Odd piece, seems to be no paper behind it:

Argues Cambridge Epidemiologist
...by effectively delaying part of the first wave from the spring until the second wave in the winter, this meant that many countries had a higher proportion of the population still susceptible to infection, and so led to even higher death tolls as health systems struggled to cope.

And this would have been even worse in the UK with one of the lowest numbers of hospital and ICU beds per head in Europe – which would have led to even higher excess deaths – both from Covid-19 and other causes as capacity was overwhelmed.

Of course, looking at just Covid-19 mortality doesn’t give the full picture as different counties code deaths in different ways and so we need to look at excess mortality, which is the best comparative measure. However, that will have to wait until the end of the second/third wave in the summer.

But based on current trends, it seems likely that many of these countries that we thought were doing well due to their early lockdowns and small first waves will end up having higher excess mortality than the UK, including Czechia, Poland, Portugal, and many others.

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Re: COVID-19

Post by jimbob » Mon Mar 22, 2021 12:09 pm

badger wrote:
Mon Mar 22, 2021 11:37 am
Apparently earlier does not necessarily mean better, when it comes to UK lockdown (because earlier first spring lockdown equals bigger second waves around winter, which, erm, could be prevented by, erm, earlier lockdowns?) Odd piece, seems to be no paper behind it:

Argues Cambridge Epidemiologist
...by effectively delaying part of the first wave from the spring until the second wave in the winter, this meant that many countries had a higher proportion of the population still susceptible to infection, and so led to even higher death tolls as health systems struggled to cope.

And this would have been even worse in the UK with one of the lowest numbers of hospital and ICU beds per head in Europe – which would have led to even higher excess deaths – both from Covid-19 and other causes as capacity was overwhelmed.

Of course, looking at just Covid-19 mortality doesn’t give the full picture as different counties code deaths in different ways and so we need to look at excess mortality, which is the best comparative measure. However, that will have to wait until the end of the second/third wave in the summer.

But based on current trends, it seems likely that many of these countries that we thought were doing well due to their early lockdowns and small first waves will end up having higher excess mortality than the UK, including Czechia, Poland, Portugal, and many others.
Sweden, Denmark, Norway say that's bollocks.

And look at London in the first and second waves too
Have you considered stupidity as an explanation

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Re: COVID-19

Post by shpalman » Mon Mar 22, 2021 12:20 pm

"many countries had a higher proportion of the population still susceptible to infection" is basically nonsense, when you consider we're anyway talking about 5-10% of the population at most, which makes for very little difference between R_0 and R_t.

Wot I reckon is more along the lines of countries/regions which didn't have a bad first wave, because they locked down properly and early, didn't take the second wave very seriously.
molto tricky

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Re: COVID-19

Post by jimbob » Mon Mar 22, 2021 12:41 pm

dup
Have you considered stupidity as an explanation

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Re: COVID-19

Post by jimbob » Mon Mar 22, 2021 12:43 pm

shpalman wrote:
Mon Mar 22, 2021 12:20 pm
"many countries had a higher proportion of the population still susceptible to infection" is basically nonsense, when you consider we're anyway talking about 5-10% of the population at most, which makes for very little difference between R_0 and R_t.

Wot I reckon is more along the lines of countries/regions which didn't have a bad first wave, because they locked down properly and early, didn't take the second wave very seriously.
Yup.

And you can extend that further. East Asia had a bad SARS outbreak, and they took SARS-COV-2 seriously from the start - including masks.

Europe didn't and didn't
Have you considered stupidity as an explanation

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Re: COVID-19

Post by badger » Mon Mar 22, 2021 2:21 pm

jimbob wrote:
Mon Mar 22, 2021 12:09 pm
badger wrote:
Mon Mar 22, 2021 11:37 am
Apparently earlier does not necessarily mean better, when it comes to UK lockdown (because earlier first spring lockdown equals bigger second waves around winter, which, erm, could be prevented by, erm, earlier lockdowns?) Odd piece, seems to be no paper behind it:

Argues Cambridge Epidemiologist
...by effectively delaying part of the first wave from the spring until the second wave in the winter, this meant that many countries had a higher proportion of the population still susceptible to infection, and so led to even higher death tolls as health systems struggled to cope.

And this would have been even worse in the UK with one of the lowest numbers of hospital and ICU beds per head in Europe – which would have led to even higher excess deaths – both from Covid-19 and other causes as capacity was overwhelmed.

Of course, looking at just Covid-19 mortality doesn’t give the full picture as different counties code deaths in different ways and so we need to look at excess mortality, which is the best comparative measure. However, that will have to wait until the end of the second/third wave in the summer.

But based on current trends, it seems likely that many of these countries that we thought were doing well due to their early lockdowns and small first waves will end up having higher excess mortality than the UK, including Czechia, Poland, Portugal, and many others.
Sweden, Denmark, Norway say that's bollocks.

And look at London in the first and second waves too
In the article he gives specific reasons for not using Den/Nor and non-Euro as comparators (mainly because of amount of international travel and/or climate), and am happy to go with that for the sake of argument and see what turns up...

London - yep, that seems to run counter to his argument. Sweden, am not so sure - as I see it they had a slightly higher peak of excess death in second wave, so to me that also undoes his position, but he's really talking about countries which did well first, then didn't.

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Re: COVID-19

Post by badger » Mon Mar 22, 2021 2:35 pm

jimbob wrote:
Mon Mar 22, 2021 12:43 pm
shpalman wrote:
Mon Mar 22, 2021 12:20 pm
"many countries had a higher proportion of the population still susceptible to infection" is basically nonsense, when you consider we're anyway talking about 5-10% of the population at most, which makes for very little difference between R_0 and R_t.

Wot I reckon is more along the lines of countries/regions which didn't have a bad first wave, because they locked down properly and early, didn't take the second wave very seriously.
Yup.

And you can extend that further. East Asia had a bad SARS outbreak, and they took SARS-COV-2 seriously from the start - including masks.

Europe didn't and didn't
Yes, I think worse second waves might be more due to (lack of) observance of NPIs than the speed of first lockdown, but then he says as much in his article:
And this has happened despite second and third lockdowns in many of these countries as people understandably struggled to maintain compliance with restrictions for months on end. (The degree of compliance also closely tracks fear of the virus/high death tolls, and so is lower when fear/deaths are lower, and so earlier lockdowns are not as effective, as we saw here in November.)

Such an outcome was both predictable, and predicted. Lockdowns in the absence of vaccines could only postpone – not prevent – infections, hospital admissions and deaths.
But yes, the 'proportion of population infected argument' is curious coming from an epidemiologist. Would like to see more justification for that one!

Am also a little confused as to why he felt the need to publish his great theory in a short broadsheet article (at this point I wander into a pro-Boris conspiracy, which is a shame, as I think there's merit in trying to look at unintended effects of lockdown, and that when the waves occur is an interesting factor. If only we had an inquiry, eh? Oh.)

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Re: COVID-19

Post by Herainestold » Mon Mar 22, 2021 4:27 pm

shpalman wrote:
Mon Mar 22, 2021 8:37 am
Herainestold wrote:
Sun Mar 21, 2021 11:54 pm
Can't wait to get back to normal?

If all restrictions are lifted in early 2022, we can still expect 20 000 deaths.
If we wait until January, 2022, to completely lift all restrictions, such that the entire adult population have been offered two doses of vaccine, we still generally predict a substantial outbreak upon relaxation with a large number of associated deaths (appendix p 11 shows the associated dynamics over time; figure 2D, table 2). Even with 85% protection against infection, the sudden release of all restrictions is predicted to generate an infection wave leading to 21 400 deaths (95% CI 1480–57 600).
We really need to stay locked down hard.

https://www.thelancet.com/journals/lani ... 2/fulltext
Well that's an argument for a zero-covid strategy...
Zero Covid works for China, South Korea, Taiwan, Japan, Australia and New Zealand.
It could work for the UK too, as we are an Island nation. We do have another opportunity to implement it, thanks to the apparent success of our vaccine strategy of hoovering up all of Europe's vaccine supply.
Some of the things we would need to do for Zero Covid, would also help us in the fight against climate change, restrictions on travel, movement and reduced commercial activity all help to reduce our carbon footprint.

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Re: COVID-19

Post by Bird on a Fire » Mon Mar 22, 2021 4:44 pm

shpalman wrote:
Mon Mar 22, 2021 12:20 pm
"many countries had a higher proportion of the population still susceptible to infection" is basically nonsense, when you consider we're anyway talking about 5-10% of the population at most, which makes for very little difference between R_0 and R_t.

Wot I reckon is more along the lines of countries/regions which didn't have a bad first wave, because they locked down properly and early, didn't take the second wave very seriously.
Your Wot I Reckon is also wot I reckon happened here in Portugal. There basically wasn't a first wave at all, strict lockdown maintained all through summer, with gradual relaxations through the autumn even after schools went back and extra breaks at Christmas and New Year, resulting in a second wave and third tsunami that's meant they basically might as well not have bothered.
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Re: COVID-19

Post by headshot » Mon Mar 22, 2021 5:25 pm

It was Christmas wot did it.

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Re: COVID-19

Post by Bird on a Fire » Mon Mar 22, 2021 5:32 pm

Normal Christmas: see too much of your family, want to kill them

2020 Christmas: see very little of your family, actually kill them
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Re: COVID-19

Post by shpalman » Mon Mar 22, 2021 5:38 pm

If you base your next fortnight's strategy on a calculation of the R which takes a week or two to come through then you'll always be trying to ride an unstable system.

If you base your next fortnight's strategy on how deaths or hospitalizations are going then you've got another two weeks' delay and it's even more unstable.

I have the feeling that Italy let things get so bad in October because at the time while cases were obviously going up, deaths and hospitalizations "weren't too bad". And of course by the time they're bad it's too late to stop them getting really bad.

I never expected everyone to be so stupid after the first wave.

Maybe the increased testing and the feeling of only having picked up a small fraction of cases during the first wave gave people a false sense of security, that the fatality rate would be a lot less the second time.
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Re: COVID-19

Post by jimbob » Mon Mar 22, 2021 6:20 pm

shpalman wrote:
Mon Mar 22, 2021 5:38 pm
If you base your next fortnight's strategy on a calculation of the R which takes a week or two to come through then you'll always be trying to ride an unstable system.

If you base your next fortnight's strategy on how deaths or hospitalizations are going then you've got another two weeks' delay and it's even more unstable.

I have the feeling that Italy let things get so bad in October because at the time while cases were obviously going up, deaths and hospitalizations "weren't too bad". And of course by the time they're bad it's too late to stop them getting really bad.

I never expected everyone to be so stupid after the first wave.

Maybe the increased testing and the feeling of only having picked up a small fraction of cases during the first wave gave people a false sense of security, that the fatality rate would be a lot less the second time.
Exactly.

And whilst R is moderately* useful for modelling, and a shortcut sometimes (If vaccination reduces transmission by 79% that reduces R by 79%) it is far too slow for actually controlling the outbreak - where all you need to know is that if numbers are growing, we have a problem. If numbers are supposedly stable, but nonzero, we will have a problem as that's not actually a stable situation.



*moderately, because we know that Covid is particularly prone to superspreaders, so you really need a measure of clumps - and probably a full Monte Carlo type analysis to get much beyond a very simplistic approach.
Have you considered stupidity as an explanation

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Re: COVID-19

Post by lpm » Mon Mar 22, 2021 6:47 pm

The best way to use R is not as a properly modelled epidemiology number.

Instead R is best seen as a measure of lockdownness. R becomes a shorthand for whether you are locked down enough or too little.

- UK was locked down at approx 1.4 in December 2020. i.e. 1.4 is a measure how inadequately the UK was locked down
- 5 Jan to 8 Mar lockdown was approx 0.7, i.e. sufficient to get cases halving every two weeks
- With schools now open, lockdownness = approx 1.0, so cases flat

Lockdownness is a dynamic thing, responding to the lockdown measures + the spread of the English variant + the level of vaccination. The only control dial a country has is lockdownness - and we now have really good information on what sort of R a country gets for each lockdown level. There's really no excuse. It looks like the UK judged its lockdown pretty well for Jan to March, is OK now with the 8 March unlockdown step, but the planned 12 April unlockdown currently looks a bit risky. It all depends on how the vaccination program dampens the response to the control dial in the next couple of weeks.
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Re: COVID-19

Post by headshot » Mon Mar 22, 2021 7:31 pm

Except the strategy isn’t for reduce infections per se. It’s for reduce hospitalisations and deaths.

They’ve already stated they assume Covid will become an endemic disease managed by vaccination.

Infections rates will go up. The Govt will be happy with this as long as serious cases, resulting in hospitalisation and death, are avoided.

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Re: COVID-19

Post by sTeamTraen » Mon Mar 22, 2021 11:01 pm

shpalman wrote:
Mon Mar 22, 2021 5:38 pm
If you base your next fortnight's strategy on a calculation of the R which takes a week or two to come through then you'll always be trying to ride an unstable system.

If you base your next fortnight's strategy on how deaths or hospitalizations are going then you've got another two weeks' delay and it's even more unstable.

I have the feeling that Italy let things get so bad in October because at the time while cases were obviously going up, deaths and hospitalizations "weren't too bad". And of course by the time they're bad it's too late to stop them getting really bad.

I never expected everyone to be so stupid after the first wave.

Maybe the increased testing and the feeling of only having picked up a small fraction of cases during the first wave gave people a false sense of security, that the fatality rate would be a lot less the second time.
Three weeks ago our rate in the Balearics got below 30/100k/7 days (having been 15x that at the peak in January) and the regional government cautiously opened the terraces, then a couple of weeks later they added limited indoor service (30% capacity) in restaurants. The rate dipped below 20 briefly, but is now back up to 26 as of today, and there is already talk of closing indoor service again. So hopefully the lessons have been learned. To be fair we have managed to keep schools open since September, with constant indoor mask wearing.

There will also be a sigh of relief in some quarters if Germany re-imposes quarantine and arrival testing, for example by reducing the case threshold in the area from which people are returning to zero. Spain has never imposed any sort of arrival quarantine nor blocked EU free movement throughout the whole pandemic, but there is now an optically bad situation whereby you can come to Mallorca for Easter from Germany, but not from Madrid (because of a ban on outgoing travel from the latter, not on landing on the islands). In practice I think that's not a bad compromise since with the curfew the tourists will be walking on the beach in the day and having an early night whereas Spanish families will be staying on camp beds in small apartments and hugging granny at regular intervals, but it is a hard sell.
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Re: COVID-19

Post by jimbob » Tue Mar 23, 2021 9:39 am

So the UK is having a minute's silence on the anniversary of the start of the first lockdown.

I find this pretty offensive. Johnson spent the time up to this downplaying the situation, undermining his own government's guidelines (boasting about shaking hands with Covid patients, for example). He is the person most responsible for the UK's terrible death toll in the first wave, and repeated many of his mistakes in the second.

He now pretends to care, as if it was an inevitable disaster rather than one he made maybe 9x worse than it should have been.
Have you considered stupidity as an explanation

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Re: COVID-19

Post by bagpuss » Tue Mar 23, 2021 10:02 am

jimbob wrote:
Tue Mar 23, 2021 9:39 am
So the UK is having a minute's silence on the anniversary of the start of the first lockdown.

I find this pretty offensive. Johnson spent the time up to this downplaying the situation, undermining his own government's guidelines (boasting about shaking hands with Covid patients, for example). He is the person most responsible for the UK's terrible death toll in the first wave, and repeated many of his mistakes in the second.

He now pretends to care, as if it was an inevitable disaster rather than one he made maybe 9x worse than it should have been.
I've been feeling much the same. While I have no issue with a minute's silence for remembering the victims, I'd much prefer to be spending that minute venting my anger at Johnson and all his cronies.

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Re: COVID-19

Post by wilsontown » Tue Mar 23, 2021 12:17 pm

Grumble wrote:
Sun Mar 21, 2021 6:45 pm
Any chance of updated graphs wilsontown? Today’s reported deaths are 33, lowest since last September.
Your wish is my command...

Here's the rate of change in cases - all over the shop, but broadly flat:
Case_rate_change.png
Case_rate_change.png (42.62 KiB) Viewed 253 times
Rate of change in deaths also has a lot of variability but seems to be accelerating, which is good news. I am using deaths by date of death, so the last few points are spurious as the numbers are incomplete:
Death_rate_change.png
Death_rate_change.png (35.32 KiB) Viewed 253 times
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Re: COVID-19

Post by jimbob » Tue Mar 23, 2021 12:50 pm

This is a nightingale plot for England and Wales all-deaths data from wk31, 1999 to wk10, 2021. Year running from wk31-wk30.

Image
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Re: COVID-19

Post by Bird on a Fire » Tue Mar 23, 2021 1:03 pm

There was an anti-lockdown protest in Lisbon yesterday, with about 3000 people in attendance.

According to Twitter one of the organisers already has covid.
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