New Covid Variants

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Thu Jun 03, 2021 9:55 pm

Thread giving the key highlights: increased transmissibility and mild reduction in vaccine effectiveness.

https://twitter.com/billhanage/status/1 ... 44608?s=21

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Re: New Covid Variants

Post by hakwright » Fri Jun 04, 2021 12:05 pm

Woodchopper wrote:
Thu Jun 03, 2021 9:55 pm
Thread giving the key highlights: increased transmissibility and mild reduction in vaccine effectiveness.

https://twitter.com/billhanage/status/1 ... 44608?s=21
I think I might have to stop reading this forum thread. The moderately large pile of fairly worrying stats about the delta variant seems to have grown over the last few days, into a bigger pile of much more worrying stats. There's still some uncertainty of course, with somewhat limited data (and time) to do the analyses, but it doesn't feel good.

We thought the delta variant had higher transmissibility over alpha of 40-50%, now looks like 60-70%.
We now know delta increases your chances of being hospitalised by more than a factor of 2.
We now know delta increases your chances of being admitted to emergency care by a little under a factor of 2.
Schools are now known to be the primary transmission route in the UK.
Delta is now the dominant variant pretty much everywhere in the UK.

The slightly good (or not very bad) news is that protection from 2 doses of vaccine is not greatly reduced against delta. Protection from 1 dose is lower by a greater margin.

I fear that the current hand-wringing in the media about how awkward it is that people can't go to holiday in Portugal any more (or Spain, Greece...) will soon change to focussing on the growth of new cases and rising hospitalisation rates.

Previous modelling (assuming 40-50% increased transmissibility, and no change to restrictions on June 21st) looked bad, with a peak of hospitalisations about the same as the UK's last wave. If the 60-70% figure is nearer the truth, and the increased risks of hospitalisations are true, then it could easily be much worse.

Perhaps the other bit of not-quite-so-bad news is that the number of deaths ought to be way lower than before, but long-term and serious (if not fatal) health consequences could be widespread.

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lpm
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Re: New Covid Variants

Post by lpm » Fri Jun 04, 2021 12:38 pm

All true.

However the 3rd wave is starting at very very low hospitalisation rates - we are way below even the most optimistic SAGE estimate for this stage of the unlockdown.

And UK cases of 5,000 aren't a disaster yet - if action happens now, we'd only see another doubling and would stabilise at 10,000. I mean, obviously this govt won't take action now, and we'll get at least two doublings to 20,000, but even that's still a way off disaster scenarios.

Of the original 1-9 cohorts, we are currently 2nd dosing groups 8 and 9. Basically the second doses are done for these groups by the end of next week, ignoring the usual stragglers. Give it another week for for responses to kick in and by 15 June we are two-dosed for 99% of the death risk.

And the partial protection of one dose is fine for under 50s. Their original death rate and hospitalisation rates were so tiny, then one dose gives a partial help, leaving really tiny rates. It's going to be multiplied up by massive case numbers in the 3rd wave of course. The race has always been close and we only just lost it - a few weeks longer is all we really needed to get all adults 1st dosed. Closing down arrivals from India would have given Johnson a massive victory. He's such an idiot.

The way to get Johnson to react is to get EU countries to close their borders to the UK. It's absolutely mad that Portugal and Spain want British visitors to crowd in. If they tell Brits to f.ck off, Johnson will feel the pain - he wrecked Christmas with his f.ck ups, now he's wrecking the sacred right enshrined in Magna Carta to a week's sunburning on the Costa del Sol.

I think all we need to do is freeze at Stage 3 and set back the 21 June unlockdown indefinitely, plus encourage an outdoor lifestyle all summer, plus maximise every possible measure in schools, plus full firebreak lockdowns in all the B towns (now adding in the extra towns its spreading to). We just need to trade a bit of unlockdown in return for four more weeks of vaccines.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Fri Jun 04, 2021 1:05 pm

hakwright wrote:
Fri Jun 04, 2021 12:05 pm
Woodchopper wrote:
Thu Jun 03, 2021 9:55 pm
Thread giving the key highlights: increased transmissibility and mild reduction in vaccine effectiveness.

https://twitter.com/billhanage/status/1 ... 44608?s=21
I think I might have to stop reading this forum thread. The moderately large pile of fairly worrying stats about the delta variant seems to have grown over the last few days, into a bigger pile of much more worrying stats. There's still some uncertainty of course, with somewhat limited data (and time) to do the analyses, but it doesn't feel good.

We thought the delta variant had higher transmissibility over alpha of 40-50%, now looks like 60-70%.
We now know delta increases your chances of being hospitalised by more than a factor of 2.
We now know delta increases your chances of being admitted to emergency care by a little under a factor of 2.
Schools are now known to be the primary transmission route in the UK.
Delta is now the dominant variant pretty much everywhere in the UK.

The slightly good (or not very bad) news is that protection from 2 doses of vaccine is not greatly reduced against delta. Protection from 1 dose is lower by a greater margin.

I fear that the current hand-wringing in the media about how awkward it is that people can't go to holiday in Portugal any more (or Spain, Greece...) will soon change to focussing on the growth of new cases and rising hospitalisation rates.

Previous modelling (assuming 40-50% increased transmissibility, and no change to restrictions on June 21st) looked bad, with a peak of hospitalisations about the same as the UK's last wave. If the 60-70% figure is nearer the truth, and the increased risks of hospitalisations are true, then it could easily be much worse.

Perhaps the other bit of not-quite-so-bad news is that the number of deaths ought to be way lower than before, but long-term and serious (if not fatal) health consequences could be widespread.
One ray of hope is that the UK research is based upon small numbers of cases and some noisy data. So its probably best to treat the above as tentative rather than clear findings. That said, the research from India and the UK tends to present a similar picture. So it looks like Delta is bad, but we aren't completely sure yet how bad.

The big political question is obviously how and whether the UK continues to open up. I hope that even if the government doesn't change course that people will still take it seriously and keep distancing etc

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Fri Jun 04, 2021 1:10 pm

lpm wrote:
Fri Jun 04, 2021 12:38 pm
All true.

However the 3rd wave is starting at very very low hospitalisation rates - we are way below even the most optimistic SAGE estimate for this stage of the unlockdown.

And UK cases of 5,000 aren't a disaster yet - if action happens now, we'd only see another doubling and would stabilise at 10,000. I mean, obviously this govt won't take action now, and we'll get at least two doublings to 20,000, but even that's still a way off disaster scenarios.

Of the original 1-9 cohorts, we are currently 2nd dosing groups 8 and 9. Basically the second doses are done for these groups by the end of next week, ignoring the usual stragglers. Give it another week for for responses to kick in and by 15 June we are two-dosed for 99% of the death risk.

And the partial protection of one dose is fine for under 50s. Their original death rate and hospitalisation rates were so tiny, then one dose gives a partial help, leaving really tiny rates. It's going to be multiplied up by massive case numbers in the 3rd wave of course. The race has always been close and we only just lost it - a few weeks longer is all we really needed to get all adults 1st dosed. Closing down arrivals from India would have given Johnson a massive victory. He's such an idiot.

The way to get Johnson to react is to get EU countries to close their borders to the UK. It's absolutely mad that Portugal and Spain want British visitors to crowd in. If they tell Brits to f.ck off, Johnson will feel the pain - he wrecked Christmas with his f.ck ups, now he's wrecking the sacred right enshrined in Magna Carta to a week's sunburning on the Costa del Sol.

I think all we need to do is freeze at Stage 3 and set back the 21 June unlockdown indefinitely, plus encourage an outdoor lifestyle all summer, plus maximise every possible measure in schools, plus full firebreak lockdowns in all the B towns (now adding in the extra towns its spreading to). We just need to trade a bit of unlockdown in return for four more weeks of vaccines.
I agree, if there is to be a Delta wave its probably a month or two before we see serious pressure on hospitals, and mortality should be far lower. That said, younger people getting Covid will still constitute a serious public health emergency given that many would experience long periods of severe illness even if very few will die.

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Sat Jun 05, 2021 8:50 am

Woodchopper wrote:
Fri Jun 04, 2021 1:05 pm
hakwright wrote:
Fri Jun 04, 2021 12:05 pm
Woodchopper wrote:
Thu Jun 03, 2021 9:55 pm
Thread giving the key highlights: increased transmissibility and mild reduction in vaccine effectiveness.

https://twitter.com/billhanage/status/1 ... 44608?s=21
I think I might have to stop reading this forum thread. The moderately large pile of fairly worrying stats about the delta variant seems to have grown over the last few days, into a bigger pile of much more worrying stats. There's still some uncertainty of course, with somewhat limited data (and time) to do the analyses, but it doesn't feel good.

We thought the delta variant had higher transmissibility over alpha of 40-50%, now looks like 60-70%.
We now know delta increases your chances of being hospitalised by more than a factor of 2.
We now know delta increases your chances of being admitted to emergency care by a little under a factor of 2.
Schools are now known to be the primary transmission route in the UK.
Delta is now the dominant variant pretty much everywhere in the UK.

The slightly good (or not very bad) news is that protection from 2 doses of vaccine is not greatly reduced against delta. Protection from 1 dose is lower by a greater margin.

I fear that the current hand-wringing in the media about how awkward it is that people can't go to holiday in Portugal any more (or Spain, Greece...) will soon change to focussing on the growth of new cases and rising hospitalisation rates.

Previous modelling (assuming 40-50% increased transmissibility, and no change to restrictions on June 21st) looked bad, with a peak of hospitalisations about the same as the UK's last wave. If the 60-70% figure is nearer the truth, and the increased risks of hospitalisations are true, then it could easily be much worse.

Perhaps the other bit of not-quite-so-bad news is that the number of deaths ought to be way lower than before, but long-term and serious (if not fatal) health consequences could be widespread.
One ray of hope is that the UK research is based upon small numbers of cases and some noisy data. So its probably best to treat the above as tentative rather than clear findings. That said, the research from India and the UK tends to present a similar picture. So it looks like Delta is bad, but we aren't completely sure yet how bad.

The big political question is obviously how and whether the UK continues to open up. I hope that even if the government doesn't change course that people will still take it seriously and keep distancing etc
James Ward also sees some positive news out of the latest PHE data

PHE’s estimate of Delta’s Secondary Attack Rate (SAR) has come down, from 67% higher than Alpha in last week’s report, to +50% in this week’s. That might not sound like a big deal, but it’s probably the figure we care about most.

The SAR tells us how likely someone is to infect one of their close contacts, so it feeds directly into our estimate of R. We have other analysis (e.g. from @alexselby1770 and @TWenseleers) suggesting that Delta is spreading 70-75% faster than Alpha, which appeared to fit…

… neatly with PHE’s +67% estimate from last week. But if the SAR is only 50% higher, it re-opens the question as to whether there are other environmental effects which could be causing the remaining ~15% of the apparent transmission gain; if so, that would be good news.

More in the thread.

https://twitter.com/jamesward73/status/ ... 50657?s=21

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Re: New Covid Variants

Post by Millennie Al » Sun Jun 06, 2021 12:55 am

lpm wrote:
Fri Jun 04, 2021 12:38 pm
visitors to crowd in. If they tell Brits to f.ck off, Johnson will feel the pain - he wrecked Christmas with his f.ck ups, now he's wrecking the sacred right enshrined in Magna Carta to a week's sunburning on the Costa del Sol.
Is it the solstices? He has to make a human sacrifice at each one?
Covid-19 - Don't catch it: don't spread it.

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lpm
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Re: New Covid Variants

Post by lpm » Mon Jun 07, 2021 3:05 pm

UK 126 hospital Delta admissions:

- 83 unvaccinated
- 28 first dosed
- 3 double dosed
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by Herainestold » Mon Jun 07, 2021 4:49 pm

lpm wrote:
Mon Jun 07, 2021 3:05 pm
UK 126 hospital Delta admissions:

- 83 unvaccinated
- 28 first dosed
- 3 double dosed
Protection against Delta requires two doses. For people currently unvaccinated that is a five week time line to reasonable protection. You can't go in to hotspots and vaccinate people and cross your fingers and wait two weeks. You have to be much more focussed. We need to lockdown now to stop the spread and aggressively vaccinate and then follow up with second doses.

If we had a Delta variant booster, that would help a lot.
Delta changes everything.

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Re: New Covid Variants

Post by Grumble » Mon Jun 07, 2021 5:04 pm

Herainestold wrote:
Mon Jun 07, 2021 4:49 pm
lpm wrote:
Mon Jun 07, 2021 3:05 pm
UK 126 hospital Delta admissions:

- 83 unvaccinated
- 28 first dosed
- 3 double dosed
Protection against Delta requires two doses. For people currently unvaccinated that is a five week time line to reasonable protection. You can't go in to hotspots and vaccinate people and cross your fingers and wait two weeks. You have to be much more focussed. We need to lockdown now to stop the spread and aggressively vaccinate and then follow up with second doses.

If we had a Delta variant booster, that would help a lot.
There is some protection with 1 dose.
You’ve got no chutzpah, your organisational skills are lacklustre and your timekeeping is abysmal.

Herainestold
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Re: New Covid Variants

Post by Herainestold » Mon Jun 07, 2021 5:11 pm

Grumble wrote:
Mon Jun 07, 2021 5:04 pm
Herainestold wrote:
Mon Jun 07, 2021 4:49 pm
lpm wrote:
Mon Jun 07, 2021 3:05 pm
UK 126 hospital Delta admissions:

- 83 unvaccinated
- 28 first dosed
- 3 double dosed
Protection against Delta requires two doses. For people currently unvaccinated that is a five week time line to reasonable protection. You can't go in to hotspots and vaccinate people and cross your fingers and wait two weeks. You have to be much more focussed. We need to lockdown now to stop the spread and aggressively vaccinate and then follow up with second doses.

If we had a Delta variant booster, that would help a lot.
There is some protection with 1 dose.
About 33%, I believe. At what point would it be better to stop first doses in hot spots and only do second doses?
Delta changes everything.

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Re: New Covid Variants

Post by Grumble » Mon Jun 07, 2021 5:21 pm

Herainestold wrote:
Mon Jun 07, 2021 5:11 pm
About 33%, I believe. At what point would it be better to stop first doses in hot spots and only do second doses?
Never. Surge both if you want to surge.
You’ve got no chutzpah, your organisational skills are lacklustre and your timekeeping is abysmal.

Herainestold
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Re: New Covid Variants

Post by Herainestold » Mon Jun 07, 2021 6:20 pm

Grumble wrote:
Mon Jun 07, 2021 5:21 pm
Herainestold wrote:
Mon Jun 07, 2021 5:11 pm
About 33%, I believe. At what point would it be better to stop first doses in hot spots and only do second doses?
Never. Surge both if you want to surge.
I would agree if we have the resources, but we don't. If the incremental protection offered by the second dose is 1.5x the first dose, then it makes more sense to only do second doses until everybody has been doubled up, then go back to first doses, and follow the manufactureres recommended schedule of 21 or 28 days until second jab.
Delta changes everything.

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Re: New Covid Variants

Post by Sciolus » Mon Jun 07, 2021 8:14 pm

But those currently vaccinated are those who would otherwise be at highest risk of being hospitalised, so both double-doses and single-doses are much more effective than LPM's numbers suggest on a naive reading.

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Re: New Covid Variants

Post by Grumble » Tue Jun 08, 2021 5:11 am

Also, changing vaccination strategy now would be hugely damaging to public confidence. Which in itself could be worse for the pandemic.
You’ve got no chutzpah, your organisational skills are lacklustre and your timekeeping is abysmal.

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Re: New Covid Variants

Post by lpm » Tue Jun 08, 2021 6:55 am

? There can't be a change to UK vaccination strategy because it's now the end game. By the end of this week pretty much all the 1-9 cohorts will be doubled dosed. I don't believe you'll find, for example, anyone on this forum from 1-9 still waiting after this week.

We're about to lap ourselves. The huge bulge of second doses on the charts is ending.

From next week it's about firsts for <30 and seconds for 45-50. With the mix of vaccines increasingly bringing forward seconds is the inevitable outcome of the maths.

The only actual choice left is whether to start 12-18 in early July. Everything else is locked in.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by lpm » Tue Jun 08, 2021 7:16 am

Yep, looking at the stats, about 2 million seconds left to do for Group 9, which was 50-55. We are at about 2.3m seconds per week so that's finished by Sunday.

Around 25% of <30s already first dosed. Mostly due to being clinically vulnerable or health workers, so were in 1-9, partly due to geographical variation e.g Wales so far ahead.

Discussion about UK vaccination strategy is like talking about the strategy for D-Day - it's now an unchangeable historical event.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by shpalman » Tue Jun 08, 2021 7:49 am

Do you have something like this for the UK?
Italy-doses-by-age-20210608.png
Italy-doses-by-age-20210608.png (87.34 KiB) Viewed 297 times
(from here)

(ok I see there are heatmaps by age for England at least)
molto tricky

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Re: New Covid Variants

Post by lpm » Tue Jun 08, 2021 9:32 am

Various twitterers are maintaining charts for that.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by lpm » Tue Jun 08, 2021 9:55 am

Here's an England only one from John Roberts. The soon to be independent nations of Wales, Scotland and Northern Ireland are currently ahead of England.
https://twitter.com/john_actuary

Image
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by lpm » Tue Jun 08, 2021 10:16 am

The other key point is the kink in the UK's first dose chart. This was on 30 March - exactly 10 weeks ago. That was the point when 1-9 were basically finished and first dosing was stepped down. The main second dosing programming started at this point - 11/12 weeks after the start of first dosing in Jan.

We always knew this would be the slow patch for first dosing, until we lapped ourselves, and with the bring forward from 11/12 weeks to 10/11 we're pretty much done. But the acceleration of first doses depends a lot on Pfizer/Moderna rather than AZ supplies.

https://ourworldindata.org/grapher/peop ... untry=~GBR
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Covid Variants

Post by shpalman » Tue Jun 08, 2021 11:49 am

molto tricky

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Tue Jun 08, 2021 11:53 am

Yesterday Sanger Institute data were updated, so here also some updated fits. Growth rate advantage of B.1.617.2/Delta vs B.1.1.7/Alfa of 10.8%/day, which with generation time of 5.5 days would translate to 81% higher infectiousness (due to increased transmissibility+immune esc).
https://twitter.com/TWenseleers/status/ ... 07044?s=20

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Tue Jun 08, 2021 11:57 am

Interesting thread warning about hindsight bias regarding the problem posed by Delta.
https://twitter.com/jcbarret/status/140 ... 01729?s=20

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Re: New Covid Variants

Post by jimbob » Tue Jun 08, 2021 8:14 pm

shpalman wrote:
Tue Jun 08, 2021 7:49 am
Do you have something like this for the UK?

Italy-doses-by-age-20210608.png

(from here)

(ok I see there are heatmaps by age for England at least)
Yes down to local-authority level


For example
https://coronavirus.data.gov.uk/details ... ame=Bolton
Screenshot 2021-06-08 211330.png
Screenshot 2021-06-08 211330.png (132 KiB) Viewed 192 times
After a very poor start, the data is now pretty good for the UK and especially England.
Have you considered stupidity as an explanation

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