New Variant Covid-19 VUI 202012/01

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shpalman
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Jan 02, 2021 8:28 am

If the UK needs to order - and enforce - a full schools-closed urgent-trips-outside-only lockdown now, and hope that it's not already too late.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 8:37 am

The high infectivity of SARS-CoV-2 B.1.1.7 is associated with increased interaction force between Spike-ACE2 caused by the viral N501Y mutation
https://www.biorxiv.org/content/10.1101 ... 9.424708v1

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Sat Jan 02, 2021 8:39 am

Yes, it's so obvious. Max out now. If figures fall fast (they won't) you can allow some schools to reopen.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 8:42 am

Woodchopper wrote:
Sat Jan 02, 2021 8:10 am
Updated data from COG-UK, as well as Pillar 2 testing data from Public Health England, now show that the frequency of the variant has grown substantially in all regions of England.
[...]

The spread of this variant is now apparent from both sequencing data from COG-UK and S gene target failure data from Pillar 2 testing (Fig U1). There is a pattern of spread in two distinct phases, involving south-east England followed by the north of England (Fig U2, U3).
https://cmmid.github.io/topics/covid19/ ... date_1.pdf
Some commentary by one of the authors:
https://twitter.com/_nickdavies/status/ ... 01952?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 8:46 am

lpm wrote:
Sat Jan 02, 2021 8:39 am
Yes, it's so obvious. Max out now. If figures fall fast (they won't) you can allow some schools to reopen.
I agree with you and shpalman. It doesn’t even look like the above fully took into account mass travel out of London to the regions over Christmas. (I’m assuming a lags between infection, testing, reporting analysis and publication).

As far as the UK goes it’s April again.

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Re: New Variant Covid-19 VUI 202012/01

Post by Martin_B » Sat Jan 02, 2021 10:54 am

shpalman wrote:
Sat Jan 02, 2021 8:28 am
If the UK needs to order - and enforce - a full schools-closed urgent-trips-outside-only lockdown now, and hope that it's not already too late.
Looking in from outside, from a country which has low numbers of cases and all of those originating from travellers returning (even if the quarantine isn't always perfect), yes, you need to have a proper lockdown of ~4-6 weeks, to get to zero (or close to) cases and then start track and trace of the few cases which crop up.

Of course, with the amount of travel between the UK and Europe it'll be very difficult to achieve this; but if the alternative is thousands of deaths, isn't it worth trying? The talk of 'the economy will be ruined' is rubbish, because constant moving between different tier levels is ruining the economy anyway. And once you get back to low/zero case levels the economy can open up, which'll be sooner than mucking about with different tiers through the winter/spring.
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Re: New Variant Covid-19 VUI 202012/01

Post by headshot » Sat Jan 02, 2021 11:03 am

Haven’t we been saying this since April?

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Sat Jan 02, 2021 11:05 am

4-6 weeks lockdown is nothing like enough to get close to zero, even for the original version. You perhaps don't appreciate how high our cases are.

For the English variant maybe 4 months is needed to get back to test & traceable levels - something like 10% reduction per week.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Jan 02, 2021 11:22 am

lpm wrote:
Sat Jan 02, 2021 11:05 am
4-6 weeks lockdown is nothing like enough to get close to zero, even for the original version. You perhaps don't appreciate how high our cases are.

For the English variant maybe 4 months is needed to get back to test & traceable levels - something like 10% reduction per week.
Maybe it would go down faster if the English lockdown were actually a proper lockdown.

Italy halved its average case rate in 7 weeks or so (which does indeed roughly correspond to 10% per week) since early November; Lombardy's rate is a quarter of what it was at that peak (it's about 120/100,000/week now).

However, it seems to have stopped going down. Statistics are messed up a bit by all the holidays. Some regions, such as Veneto, lost control and had a double peak.
Last edited by shpalman on Sat Jan 02, 2021 11:31 am, edited 1 time in total.
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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Sat Jan 02, 2021 11:31 am

The March to May 2020 lockdown worked ok in England. But that was pre Cummings. A repeat in Jan to March 2021 will be less powerful. It doesn't seem likely this govt will get the English variant to R<1.
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Re: New Variant Covid-19 VUI 202012/01

Post by bob sterman » Sat Jan 02, 2021 12:58 pm

shpalman wrote:
Sat Jan 02, 2021 11:22 am
Maybe it would go down faster if the English lockdown were actually a proper lockdown.
Indeed - currently here in Tier 4 this weekend, I can pop inside the local Costa to get a takeaway croissant and latte, kids saturday morning soccer is on (organised outdoor sport for under 18s is allowed), I can pop to the DIY store to get that shelf I've really been meaning to fit in the bathroom.

Tomorrow I can attend a "place of worship" for a service, and then visit the garden centre to buy a gnome for the lawn. Then I might pop in to the local archery club for some practice, play a round of golf and visit a zoo.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 1:53 pm

Covid wards 'full of children' for first time in pandemic, warn nurses
https://news.yahoo.com/covid-wards-full ... 10680.html
Medics are starting to see “whole wards of children” suffering from Covid for the first time during the pandemic, a senior nurse has warned.

Laura Duffell, a matron at King’s College Hospital, London, said the new strain of Covid was affecting children and younger adults with no underlying health conditions in worrying numbers.

She said: “It’s very different. That’s what makes it so much scarier for us as doctors, nurses and porters and everyone else who is working on the front line.

“We have children who are coming in. It was minimally affecting children in the first wave... we now have a whole ward of children here and I know that some of my colleagues are in the same position, where they have a whole ward of children with Covid.”

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Sat Jan 02, 2021 1:56 pm

Somebody on twitter says that's bollocks. Children with Covid in hospital remains very rare.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 2:37 pm

lpm wrote:
Sat Jan 02, 2021 1:56 pm
Somebody on twitter says that's bollocks. Children with Covid in hospital remains very rare.
There have definitely been more cases among children:

See the heatmap here: https://coronavirus.data.gov.uk/details ... ame=London

See here pages 7-8 https://www.imperial.ac.uk/mrc-global-i ... 2-variant/

Here page 5 https://assets.publishing.service.gov.u ... _FINAL.pdf

Even if a small proportion of children are admitted to hospital, the large number of cases will still add up to a lot.

Would be good to see some data on hospital admissions disaggregated by age.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 3:27 pm

Woodchopper wrote:
Sat Jan 02, 2021 1:53 pm
Covid wards 'full of children' for first time in pandemic, warn nurses
https://news.yahoo.com/covid-wards-full ... 10680.html
Medics are starting to see “whole wards of children” suffering from Covid for the first time during the pandemic, a senior nurse has warned.

Laura Duffell, a matron at King’s College Hospital, London, said the new strain of Covid was affecting children and younger adults with no underlying health conditions in worrying numbers.

She said: “It’s very different. That’s what makes it so much scarier for us as doctors, nurses and porters and everyone else who is working on the front line.

“We have children who are coming in. It was minimally affecting children in the first wave... we now have a whole ward of children here and I know that some of my colleagues are in the same position, where they have a whole ward of children with Covid.”
Looks like this BBC report is the original source: https://twitter.com/bbc5live/status/134 ... 63552?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 3:39 pm

Woodchopper wrote:
Sat Jan 02, 2021 2:37 pm
lpm wrote:
Sat Jan 02, 2021 1:56 pm
Somebody on twitter says that's bollocks. Children with Covid in hospital remains very rare.
There have definitely been more cases among children:

See the heatmap here: https://coronavirus.data.gov.uk/details ... ame=London

See here pages 7-8 https://www.imperial.ac.uk/mrc-global-i ... 2-variant/

Here page 5 https://assets.publishing.service.gov.u ... _FINAL.pdf

Even if a small proportion of children are admitted to hospital, the large number of cases will still add up to a lot.

Would be good to see some data on hospital admissions disaggregated by age.
On cases see also:

4. Age analysis of the number of people in England who had COVID-19

In the most recent week (12 to 18 December), the percentages testing positive have increased for all age groups except those aged 50 to 69 years where there are early signs of an increase, and those aged 70 years and above in whom there are early signs of a decrease. Secondary school-age children continue to have the highest percentage testing positive. Caution should be taken in over-interpreting small movements in the narrower age groups, which have wider credible intervals.
https://www.ons.gov.uk/peoplepopulation ... cember2020

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Re: New Variant Covid-19 VUI 202012/01

Post by bob sterman » Sat Jan 02, 2021 3:40 pm

Woodchopper wrote:
Sat Jan 02, 2021 2:37 pm
Would be good to see some data on hospital admissions disaggregated by age.
This is only up to week ending Dec 13th but hospital admission rates per 100,000 population split by age are in Figure 7 here...

https://www.ons.gov.uk/peoplepopulation ... and-deaths

They note "Hospital admissions increased among all groups aged 45 years and over in the week ending 13 December" so presumably up until that point there was no increase in admission rates among children.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 9:46 pm

I found some data here: https://coronavirus.data.gov.uk/details/download

Total hospital admissions 1 Sep - 29 Dec 2020
Age 0-5: 135
Age 6-17: 115

The trend has been going upward since about 12 Dec.
Hospital 0 - 5 Sep-Dec.jpg
Hospital 0 - 5 Sep-Dec.jpg (67.6 KiB) Viewed 158 times
Hospital 6 - 17 Sep-Dec.jpg
Hospital 6 - 17 Sep-Dec.jpg (84.13 KiB) Viewed 158 times


Compared to the 1st wave:

Total hospital admissions 1 Apr - 30 Jul 2020
Age 0-5: 122
Age 6-17: 189
Hospital 0 - 5 Apr - Jul 1st wave.jpg
Hospital 0 - 5 Apr - Jul 1st wave.jpg (90.72 KiB) Viewed 158 times
Hospital 6 - 17 Apr - Jul  1st wave.jpg
Hospital 6 - 17 Apr - Jul 1st wave.jpg (79.63 KiB) Viewed 158 times

It appears that since mid-December hospital admissions for children have been at a similar level to April 2020. This period coincides with the spread through London of the new variant. Increasing child case numbers appear to be reflected in increasing child hospital admissions.

That said, the numbers are relatively modest. Are there wards full of child Covid cases? I assume it'll depend upon how many are on a ward, how long children stay in the wards and whether children from a wide area are moved to single wards. I don't know any of that.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 10:10 pm

Statement by the Royal College of Paediatrics and Child Health: https://www.rcpch.ac.uk/news-events/new ... e-covid-19

Not a big problem across the UK

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Sun Jan 03, 2021 1:08 am

Woodchopper wrote:
Sat Jan 02, 2021 10:10 pm
Statement by the Royal College of Paediatrics and Child Health: https://www.rcpch.ac.uk/news-events/new ... e-covid-19

Not a big problem across the UK
In the first wave, out of every 100 people who got a positive there were probably only 1 or 2 children (did I read that Michael Gove got one for his daughter?), simply because you mostly had to be showing symptoms to get a test. (And for those 100 people there were probably 400 more who were positive but never got a test).

In the second wave I would expect actual prevalence to be higher among, if not small kids, then certainly teenagers and young adults. They take more risks generally, and an awful lot of over-60s are just not going out thank you very much.

So I suspect you could have a lot more kids on wards just from the distribution, without the virus needing to have become more infectious or more harmful. As Stephen Senn says, "every statistician should always ask ‘how did I get to see what I see?'".
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Jan 03, 2021 8:17 am

sTeamTraen wrote:
Sun Jan 03, 2021 1:08 am
Woodchopper wrote:
Sat Jan 02, 2021 10:10 pm
Statement by the Royal College of Paediatrics and Child Health: https://www.rcpch.ac.uk/news-events/new ... e-covid-19

Not a big problem across the UK
In the first wave, out of every 100 people who got a positive there were probably only 1 or 2 children (did I read that Michael Gove got one for his daughter?), simply because you mostly had to be showing symptoms to get a test. (And for those 100 people there were probably 400 more who were positive but never got a test).

In the second wave I would expect actual prevalence to be higher among, if not small kids, then certainly teenagers and young adults. They take more risks generally, and an awful lot of over-60s are just not going out thank you very much.

So I suspect you could have a lot more kids on wards just from the distribution, without the virus needing to have become more infectious or more harmful. As Stephen Senn says, "every statistician should always ask ‘how did I get to see what I see?'".
Why would you expect the prevalence to be higher among teenagers and young adults in the second wave as compared to the first one? And you would have noticed if there would have been lots of children in hospital during the first wave whether or not they'd managed to get covid tests.
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Re: New Variant Covid-19 VUI 202012/01

Post by bob sterman » Sun Jan 03, 2021 8:59 am

shpalman wrote:
Sun Jan 03, 2021 8:17 am
Why would you expect the prevalence to be higher among teenagers and young adults in the second wave as compared to the first one?
In the UK schools were closed and all face-to-face teaching at universities was stopped during first wave. Organised youth sport was also stopped.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Jan 03, 2021 11:49 am

New variant is spreading in Denmark

Week number, percent of sample:
47, 0.3
48, 0
49, 0.2
50, 0.5
51, 0.9
52, 2.3

In the latter period it’s doubling about every week.

Source (page 2): https://www.ssi.dk/-/media/cdn/files/op ... .pdf?la=da

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Jan 03, 2021 11:51 am

bob sterman wrote:
Sun Jan 03, 2021 8:59 am
shpalman wrote:
Sun Jan 03, 2021 8:17 am
Why would you expect the prevalence to be higher among teenagers and young adults in the second wave as compared to the first one?
In the UK schools were closed and all face-to-face teaching at universities was stopped during first wave. Organised youth sport was also stopped.
Yes, the larger number of cases among children could be due to different behaviour, or could be due to the variant being more transmissible.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Jan 03, 2021 12:08 pm

Is it fair to say that if a child gets it then the parents are quite likely to get it, and vice versa?
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