COVID-19

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Re: COVID-19

Post by Woodchopper » Mon Jul 26, 2021 8:22 am

lpm wrote:
Sun Jul 25, 2021 10:00 pm

One solution to the puzzle would be if Delta has a dual nature - very contagious for a portion of the population, with high R, but same as other strains for the rest of the population. So it rips through the susceptible portion then fizzles when trying to spread wider.
As far as I’m aware we don’t know much about why some people are super spreaders and others not, though the environment they’re in plays a major role.

But hypothesising a dual Delta seems to be to over complicate things. We should first rule out the simpler explanation that the fall in cases is due to changes in behaviour and increasing numbers of people with antibodies.

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Re: COVID-19

Post by lpm » Mon Jul 26, 2021 8:29 am

bob sterman wrote:
Mon Jul 26, 2021 7:16 am
Yes but the only reporting 1st positives issue only rules out 4.5 million people from being recorded as cases in this wave (official previous cases).

It leaves over 90% of the population free to be recorded as a case if they test positive now. So it wouldn't be a big enough effect to fully account for the drop.

... and we're looking at week-on-week movements. The variation between this week's reinfections and last week's reinfections must be, what, five cases? Ten?

Mad policy though.
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Re: COVID-19

Post by shpalman » Mon Jul 26, 2021 8:34 am

Looking at the England data, the case rate in the 20-24 age range peaked at nearly 1300/100,000/week (which is more than the peak in January, which was about 1000). What do we think the actual case rate could have been, taking into account mild/asymptomatic cases and also those who don't want to have to self-isolate, or who can't afford to self-isolate, so avoid getting tested?
Woodchopper wrote:
Sun Jul 25, 2021 2:48 am
... 3. If it does turn out to be a trend:

- perhaps there was a football effect (with messy data).
- people have noticed the case numbers and are reacting by being more careful.
- there are now very few adults left without antibodies. A combination of antibodies plus some social distancing and mask wearing is enough to keep r down.
- wait for the influence of freedom day.
There could be herd immunity "very few adults left without antibodies" now in the 20-24 range which was previously driving growth, i.e. the covid got to them faster than the vaccine did and deaths will peak in 2-3 weeks time and then, well, you're golden until you breed another f.cking variant which comes to kill us all.
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Re: COVID-19

Post by lpm » Mon Jul 26, 2021 9:04 am

But India. What explains India? Vaccination stats are 7% second dosed, 18% one dose.

There can't possibly be herd immunity "very few adults left without antibodies" in India. No way are they anywhere near the 85% required by the maths, yet cases are down from 283 per million to 28 per million (official cases obviously). Delta went into reverse with only modest lockdowniness and little vaccination.

Today India - which looked totally f.cked by raging Delta - has lower (official) cases than the relative newcomers to Delta like Italy, France, Spain etc.
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Re: COVID-19

Post by lpm » Mon Jul 26, 2021 10:55 am

A good thread from the weekend:

https://twitter.com/jburnmurdoch/status ... 6244478977

I particularly liked this chart. Look at the y-axis for the huge risk gradient between a 30 year old and 80 year old. It shows in picture form why unlocking when 18-30s had only one dose was fine as a policy - all that matters is that over 50s are double dosed - and why the UK's strict vaccinations by descending age cohorts saved so many lives.

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Re: COVID-19

Post by headshot » Mon Jul 26, 2021 11:40 am

Is it possible that Delta is symptomatic earlier in the infection cycle?

I see that Zoe is detailing new and different symptoms for Delta compared to Alpha or the original variants.

If earlier variants meant one was infectious for 10 days before being symptomatic, is it possible that Delta's symptoms are apparent within a shorter period...meaning infectious people are circulating less before they isolate?

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Re: COVID-19

Post by Martin Y » Mon Jul 26, 2021 1:22 pm

Would that sort of difference explain what changed to make the UK wave peak and peak first in Scotland?

Scottish schools break up earlier; could there be something about delta that makes kids a particularly important vector? Also as LPM remarked what did India suddenly start doing right? Their huge delta wave peaked when they only had about 10% first jabs and dropped to a steadyish low level despite the number of tests not declining. Was that a social behaviour change or something odd about delta?

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Re: COVID-19

Post by tom p » Mon Jul 26, 2021 1:31 pm

lpm wrote:
Mon Jul 26, 2021 9:04 am
But India. What explains India? Vaccination stats are 7% second dosed, 18% one dose.

There can't possibly be herd immunity "very few adults left without antibodies" in India. No way are they anywhere near the 85% required by the maths, yet cases are down from 283 per million to 28 per million (official cases obviously). Delta went into reverse with only modest lockdowniness and little vaccination.

Today India - which looked totally f.cked by raging Delta - has lower (official) cases than the relative newcomers to Delta like Italy, France, Spain etc.
My Indian friends and colleagues say there has been strict lockdowns in India & everyone has been obeying them.
working from home is still the norm.
kids still not at school
lots of flooding in some cities meaning people staying indoors more than usual
plus, the 283 per million could have been a peak post Kumbh Mela and other superspreader events which are now not happening (e.g. the cricket 20:20 world cup has moved from India, whereas a few months ago they were playing matches to crowds of >100k people at the Narendra Modi stadium)

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Re: COVID-19

Post by WFJ » Mon Jul 26, 2021 1:48 pm

lpm wrote:
Mon Jul 26, 2021 9:04 am
But India. What explains India? Vaccination stats are 7% second dosed, 18% one dose.

There can't possibly be herd immunity "very few adults left without antibodies" in India. No way are they anywhere near the 85% required by the maths, yet cases are down from 283 per million to 28 per million (official cases obviously). Delta went into reverse with only modest lockdowniness and little vaccination.

Today India - which looked totally f.cked by raging Delta - has lower (official) cases than the relative newcomers to Delta like Italy, France, Spain etc.
Why couldn't India be close to herd immunity, at least within cities? It was reported last week that excess deaths in India were over 4M in the last year, which could suggest the official figures of COVID deaths are only a tenth of the actual numbers. If deaths are underreported to such an extent, it's not hard to believe that only a much smaller fraction of cases have been reported.

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Re: COVID-19

Post by bob sterman » Mon Jul 26, 2021 3:34 pm

bob sterman wrote:
Sun Jul 25, 2021 8:57 pm
So for the past 3 days new reported cases have been down 30-40% on the same day 7 days previously.
Today - 24,950 new cases reported vs 39,950 last Monday. Another drop over 7 days of nearly 40%.

This is weird :?

Is Occam's razor sharp enough to explain it????

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Re: COVID-19

Post by shpalman » Mon Jul 26, 2021 3:49 pm

f.cked if I know. I'd have been predicting 60-70,000 by now. Oh well, let's hope it's a real trend, it's much happier about being wrong in this direction than the alternative.
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Re: COVID-19

Post by Woodchopper » Mon Jul 26, 2021 4:03 pm

WFJ wrote:
Mon Jul 26, 2021 1:48 pm
lpm wrote:
Mon Jul 26, 2021 9:04 am
But India. What explains India? Vaccination stats are 7% second dosed, 18% one dose.

There can't possibly be herd immunity "very few adults left without antibodies" in India. No way are they anywhere near the 85% required by the maths, yet cases are down from 283 per million to 28 per million (official cases obviously). Delta went into reverse with only modest lockdowniness and little vaccination.

Today India - which looked totally f.cked by raging Delta - has lower (official) cases than the relative newcomers to Delta like Italy, France, Spain etc.
Why couldn't India be close to herd immunity, at least within cities? It was reported last week that excess deaths in India were over 4M in the last year, which could suggest the official figures of COVID deaths are only a tenth of the actual numbers. If deaths are underreported to such an extent, it's not hard to believe that only a much smaller fraction of cases have been reported.
Indeed.

I haven’t seen an analysis of India’s Delta wave. But:

Combining waves 1 and 2, as of May 15, while India reported a total of nearly 25 million cases and 270 thousand deaths, the estimated number of infections and deaths stand at 491 million (36% of the population) and 1.21 million respectively, yielding an estimated (combined) infection fatality rate of 0.25%.
https://www.medrxiv.org/content/10.1101 ... 21257823v1

An IFR of 0.25 is much lower than in the UK. But India has a much younger population and it’s been suggested that outside the middle and upper classes daily exposure to pathogens may provide some protection. So 0.25 looks plausible.

If we take the lower estimate of 3.4 million excess deaths (see post in the other thread), with an IFR of 25% we get to 1.36 billion people having been infected.That’s very close to the 1.39 billion population of India.

This is all very back of the envelope. But it suggests that India having reached herd immunity isn’t a bonkers explanation.

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Re: COVID-19

Post by Bird on a Fire » Mon Jul 26, 2021 8:02 pm

That's very interesting, thanks Woodchopper.

I know cases have been reported in people who've been vaccinated, as well as reinfections, but if they're mostly not leading to deaths or hospitalisations then we should expect to see the UK figures for those (more important) variables trending downwards in a week or so. That would be excellent news.

There's also just a teeny tiny part of me that doesn't trust the UK's official figures, so it'll be nice to see what happens elsewhere. Portugal's cases are still trending up, for instance, despite having second highest vaccine coverage in Europe (51% fully done, 67% at least with first dose).

ETA although latest estimates suggest Rt is down to 1.04, so could be turning there too. Still <10% of the population with confirmed infections ever, which would make herd antibody-having 77% at most (but definitely less).
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Re: COVID-19

Post by Bird on a Fire » Mon Jul 26, 2021 8:12 pm

The next job is for someone to do similar back of envelope calculations for the UK (preferably with a range of assumptions about case ascertainment rate).
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Re: COVID-19

Post by Woodchopper » Mon Jul 26, 2021 8:59 pm

Bird on a Fire wrote:
Mon Jul 26, 2021 8:12 pm
The next job is for someone to do similar back of envelope calculations for the UK (preferably with a range of assumptions about case ascertainment rate).
@Jamesward73 @bristoliver @jamesannan are doing that sort of thing on Twitter.

There was also a good discussion on the last episode of More or Less.

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Re: COVID-19

Post by Woodchopper » Mon Jul 26, 2021 9:03 pm

And just to reiterate, if there has been a real decline in cases it looks like herd immunity among adults plus summer behaviour is enough to get R to a bit below 1.

Wait for another wave in the autumn when the holidays are over and people want to stay indoors. Immunity may be waning by then as well.

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Re: COVID-19

Post by lpm » Mon Jul 26, 2021 9:24 pm

Bird on a Fire wrote:
Mon Jul 26, 2021 8:02 pm
That's very interesting, thanks Woodchopper.

I know cases have been reported in people who've been vaccinated, as well as reinfections, but if they're mostly not leading to deaths or hospitalisations then we should expect to see the UK figures for those (more important) variables trending downwards in a week or so. That would be excellent news.

There's also just a teeny tiny part of me that doesn't trust the UK's official figures, so it'll be nice to see what happens elsewhere. Portugal's cases are still trending up, for instance, despite having second highest vaccine coverage in Europe (51% fully done, 67% at least with first dose).

ETA although latest estimates suggest Rt is down to 1.04, so could be turning there too. Still <10% of the population with confirmed infections ever, which would make herd antibody-having 77% at most (but definitely less).
Netherlands is another country with a Delta surge, followed by falls. But they relockdowned.
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Re: COVID-19

Post by Herainestold » Mon Jul 26, 2021 9:31 pm

Woodchopper wrote:
Mon Jul 26, 2021 9:03 pm
And just to reiterate, if there has been a real decline in cases it looks like herd immunity among adults plus summer behaviour is enough to get R to a bit below 1.

Wait for another wave in the autumn when the holidays are over and people want to stay indoors. Immunity may be waning by then as well.
Yes. This is a false dawn. There will be a massive autumn wave, especially as vaccination rate is slowing.
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Re: COVID-19

Post by Bird on a Fire » Mon Jul 26, 2021 11:59 pm

lpm wrote:
Mon Jul 26, 2021 9:24 pm
Bird on a Fire wrote:
Mon Jul 26, 2021 8:02 pm
That's very interesting, thanks Woodchopper.

I know cases have been reported in people who've been vaccinated, as well as reinfections, but if they're mostly not leading to deaths or hospitalisations then we should expect to see the UK figures for those (more important) variables trending downwards in a week or so. That would be excellent news.

There's also just a teeny tiny part of me that doesn't trust the UK's official figures, so it'll be nice to see what happens elsewhere. Portugal's cases are still trending up, for instance, despite having second highest vaccine coverage in Europe (51% fully done, 67% at least with first dose).

ETA although latest estimates suggest Rt is down to 1.04, so could be turning there too. Still <10% of the population with confirmed infections ever, which would make herd antibody-having 77% at most (but definitely less).
Netherlands is another country with a Delta surge, followed by falls. But they relockdowned.
So far, Portugal is just doing that salami thing - vaccine passports necessary to dine inside at the weekend, things closing early in some municipalities, etc. And while there is the summer behaviour of wanting to be outside, in some places it'll be pushing 40°C for the next month causing people to want to retreat to cooler interiors.

Delta is here in Iceland too, causing more cases than ever and a change to entry policy. But so far it's still masks off everywhere and no restrictions once you're out of 5 days' quarantine plus negative PCRs.

We shall see.
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Re: COVID-19

Post by jdc » Tue Jul 27, 2021 1:28 am

Woodchopper wrote:
Mon Jul 26, 2021 9:03 pm
And just to reiterate, if there has been a real decline in cases it looks like herd immunity among adults plus summer behaviour is enough to get R to a bit below 1.

Wait for another wave in the autumn when the holidays are over and people want to stay indoors. Immunity may be waning by then as well.
Booster planned for September-December alongside flu vaccination apparently. If you're vulnerable or over 50 that is. Purchase news here: https://www.ft.com/content/7ca875ec-e80 ... 40c80ea2c5 and JCVI plans here: https://www.gov.uk/government/publicati ... 21-to-2022

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Re: COVID-19

Post by Herainestold » Tue Jul 27, 2021 2:34 am

Bird on a Fire wrote:
Mon Jul 26, 2021 11:59 pm
lpm wrote:
Mon Jul 26, 2021 9:24 pm
Bird on a Fire wrote:
Mon Jul 26, 2021 8:02 pm
That's very interesting, thanks Woodchopper.

I know cases have been reported in people who've been vaccinated, as well as reinfections, but if they're mostly not leading to deaths or hospitalisations then we should expect to see the UK figures for those (more important) variables trending downwards in a week or so. That would be excellent news.

There's also just a teeny tiny part of me that doesn't trust the UK's official figures, so it'll be nice to see what happens elsewhere. Portugal's cases are still trending up, for instance, despite having second highest vaccine coverage in Europe (51% fully done, 67% at least with first dose).

ETA although latest estimates suggest Rt is down to 1.04, so could be turning there too. Still <10% of the population with confirmed infections ever, which would make herd antibody-having 77% at most (but definitely less).
Netherlands is another country with a Delta surge, followed by falls. But they relockdowned.
So far, Portugal is just doing that salami thing - vaccine passports necessary to dine inside at the weekend, things closing early in some municipalities, etc. And while there is the summer behaviour of wanting to be outside, in some places it'll be pushing 40°C for the next month causing people to want to retreat to cooler interiors.

Delta is here in Iceland too, causing more cases than ever and a change to entry policy. But so far it's still masks off everywhere and no restrictions once you're out of 5 days' quarantine plus negative PCRs.

We shall see.
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Iceland has a very high vax level but their cases are exponential. Hope it doesnt interfere with your field work.
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Re: COVID-19

Post by Woodchopper » Tue Jul 27, 2021 8:19 am

jdc wrote:
Tue Jul 27, 2021 1:28 am
Woodchopper wrote:
Mon Jul 26, 2021 9:03 pm
And just to reiterate, if there has been a real decline in cases it looks like herd immunity among adults plus summer behaviour is enough to get R to a bit below 1.

Wait for another wave in the autumn when the holidays are over and people want to stay indoors. Immunity may be waning by then as well.
Booster planned for September-December alongside flu vaccination apparently. If you're vulnerable or over 50 that is. Purchase news here: https://www.ft.com/content/7ca875ec-e80 ... 40c80ea2c5 and JCVI plans here: https://www.gov.uk/government/publicati ... 21-to-2022
Good news for vulnerable people in Britain. But not good for our attempt to vaccinate the world if many people will need three doses.

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Re: COVID-19

Post by lpm » Tue Jul 27, 2021 8:52 am

My latest highly sophisticated theory total guess: vaccine eagerness among 18-30s tipped the equation, despite relatively low overall percentage take up and first dose only. The UK rollout basically finished on 11 July but the eager young got their first doses a lot earlier.

The UK "Glastonbury rush" to book vaccine appointments was on Tues 8 June, when 25 to 29 opened.

There was then a 23-25 stage and finally appointments open to all adults Fri 18 June.

Most people will have booked an appointment for a week or two's time, plus it takes a couple of weeks for the vaccine to come up to full strength. So call it a month for partial first dose immunity effects to kick in and it's 8 July for eager 25-29 year olds and 18 July for eager 18-23.

The peak in cases (by specimen date) was 15 July.

There's also immunity via infection, with 1.25 million official cases since the start of the third wave, a lot of which are in the 18-30 range.

I think it's easy to forget how early 18-30 year olds got their first doses, because our view is distorted by the rollout fizzling out on 11 July and the govt declaring target officially met on 19 July. A lot of sensible young people raced to get first doses in June and had pretty decent immunity levels by mid July.
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Re: COVID-19

Post by shpalman » Tue Jul 27, 2021 9:34 am

shpalman wrote:
Mon Jul 26, 2021 3:49 pm
f.cked if I know.
But I'm just some moron on the internet, let's ask an expert.
Professor Neil Ferguson of Imperial College London and member of the Scientific Advisory Group for Emergencies wrote:Me neither
https://www.theguardian.com/world/2021/ ... ays-expert

Oh.
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Re: COVID-19

Post by lpm » Tue Jul 27, 2021 11:02 am

People are desperate to force the "it was football" narrative, no matter the facts.

Here's the latest. The FT has usually been a source of well presented info but this is terrible. They started with the conclusion and rigged the chart to fit.

A quick glance and it looks like infections coincide with football matches. But the little footnote gives the trick away. The football dates are adjusted by 4 days, i.e. to show daily cases four days after the match.

This is of course wrong. If you crowd into a pub to watch a match on Sunday evening, breathing in the Covid fumes, there's no way you'll show up in the stats on Thursday - 3.5 days later. The time from infection is in the range 2 to 12 days, with 5 being typical (possibly the median for Delta is a bit quicker at 4 days). Then there's the time to do a LFT and arrange a PCR and get the positive and get into the stats pipeline and be reported. Normally cases today tells us about infections 7 to 10 days earlier. The lines on the chart need to be shifted 3 to 6 days to the right.

It's clear the men vs women rates diverged before the Euro 2020 started. Probably the explanation is worse vaccine rates for men in the <50 groups. Men vs women narrowed in Scotland before Scotland went out.

And of course there's the basic fact that people go to the pub on a non-football Saturday night as well as a big match on Sunday night. And it's not just men 20-34 who watch football in pubs. And slightly more men than women go to pubs overall.

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