UKC

Friday Night Covid Plotting #43

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 wintertree 11 Sep 2021

This week’s thread is brought to you by heat/humidity induced sleep deprivation.  So, please excuse any lack of coherence or excessive typos…. Some butterfingered typing saw me nearly post it as "Friday Night Covid Plotting #1120".  The stuff of nightmares.

A cautionary note for this week:  I haven’t measured it, but the cases data has felt more provisional than normal over the last week or so.  So, please view the far right edge of all the plots about cases with a bit more skepticism than normal.

The vaccine plot  throws up another one of several red flags this week.

  • The first dose rate is collapsing right down over recent weeks.  An adult of any age is far more likely to get symptomatic Covid, to require hospitalisation and to die if they chose not to get vaccinated.  About 10% of adults are totally unvaccinated, and almost no more are getting  vaccinated.   We are where we are, and we have to deal with that and with the consequences.
  • The second dose rate is also dropping a lot however - and more than would be expected.    This is manifesting on my plot as the notional gap between vaccines increasing back form its low of 10-weeks.  It seems like quite a few people are’t returning for their second dose.   
  • We expect a drop-off like this to show in the top level data from ~10 weeks after August 4th, when JCVI recommended one dose only for those aged 16 and 17 [1].  It is over a month too soon for that to be causing the effect visible in this plot however.
  • An article I linked a couple of weeks ago suggested half a million people weren’t going back for their second AZ jab. It should be possible to pull out similar numbers for Pfizer (hopefully one of the people following the twitter vaccine analysers can link some informative content…).
  • It’s always tempting to assume a supply or demand problem; I do wonder about an issue with impedance mis-matching where people want the second dose but are struggling to make the time for it.
  • It would be nice to see this issue of prematurely flagging second doses getting more press time; it’s clear that for all adult ages a second dose makes a significant difference to various protections from the Delta variant in terms of individual risk, and getting these people their second doses feels like a relatively easy win to significantly reduce the remaining vulnerable fraction of the population.  

[1] https://www.gov.uk/government/news/jcvi-issues-updated-advice-on-covid-19-vaccination-of-young-people-aged-16-to-17

Link to previous thread: https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_42-738812

Post edited at 20:43

 wintertree 11 Sep 2021
In reply to wintertree:

England - Part I 

  • Cases: We’re still more or less in a holding pattern, cases have been drifting very gradually upwards for a month.  The leading edge is pointing convincingly down, we’ll see if that is sustained.  I go in to the demographics behind this near-level behaviour in the next post.
  • Deaths: These are rising faster than cases (in exponential terms) - visible from both plot 8e (steeper gradient on a long/log plot) and plot 9e (larger rate constant or faster doubling time).   This comes across as another potential red flag; it seems likely the changing demographics behind the near constant top level cases are partly behind this - they’ve been falling in young adults and rising in older people.  The next post looks at this.
  • Hospital occupancy: This continues to creep up - no doubt in part related to the changing demographics, and also related to the lag from admissions to departure.  We’re now at about 1/5th of the all-time peak for Covid occupancy; this may sound like a lot less but that peak was an absolutely bonkers time that pushed healthcare well beyond any sustainable limits and required widespread lockdown measures.  The control measures saved our bacon last year by eliminating influenza; there’s so much uncertainty over the coming flue season however, no control measures right now and lots of international travel.  I’m very much hoping that we start to see a sustained fall in cases very soon; if we don’t it seems prudent to start turning on as many minimally invasive control measures as possible around things like mask wearing and enforced ventilation on public transport etc.

 wintertree 11 Sep 2021
In reply to wintertree:

England - Part 2

The week-on-week method cases rate constant plot for England:

  • This is a bit weird to my eye
  • The number of cases was depressed on the bank holiday Monday as we’d expect from historic observations of bank holidays and weekends.   Then we had a discontinuous jump from falling to rising cases for a week, and the most recent two days are falling.
  • Perhaps there’s some more lag than normal and that fall will change; either way the preceding week is a bit irregular looking to my eye
  • It’s also one of the rare times the “passband values” (difference from a recent average) for temperature and rate constant are the same sign - shows as the red shading on the far right of the passband plot.  This means that it’s been warmer than average recently: usually at such a time cases are falling on the timescale of a week or so; recently they’ve been rising.  Perhaps this is the return of schools falling in the timescale of the passband; if so the effect should fade out pretty soon as a new normal establishes itself.  This makes me a bit more cautious than normal about interpreting the leading edge of the English plots however.

English Demographics:

  • The decay that was just setting in on plot D1.c as a feint blue band for adult ages last week has not lasted, we’re back to low rate growth but it’s in the provisional zone and the values are low.  The big fall in cases in ages 20-35 looks to be coming to an end. 
  • That big fall in a few ages had been opposing the gradual rise in other ages in just the right way to lead to a near constant number of top level cases; that can’t continue as the number of cases in the decreasing bands gets ever smaller, meaning it can no longer balance the ever increasing number of cases in the bands. 
  • The collapse of cases in young adults is really clear in plot P1.e which shows a couple of sections through the case numbers from plot D1.c; less in young adults, more in school aged children and more in older adults; with total cases remaining a similar level this offers a simple explanation for why deaths are rising - fewer young adults and more older adults are catching Covid. 
    • Again, this is worrying as the component that is rising is going to contribute a larger fraction of its membership to hospitalisations, and the one that is falling is running out of fall to give. 
    • I haven’t tried to confirm that this demographic shift is the only cause of the widening disparity between cases and deaths - the data to do a proper job for that is not on the dashboard.
  • So, my hunch from this plot would be that we’re about to go for growth, but the 7-day rate constant plot looks like we’re going for decay. 
    • The plots don’t necessarily square off as the demographics includes unconfirmed and confirmed LFDs but the PCR plot doesn’t.  So, a lot of uncertainty over cases for the week ahead in England. 
    • My gut say cases are going to fall over the coming week but I can’t really make a logical case for that from the data!
  • There’s no signs of a giant rise (circa 4-day doubling times) in young adults in England immediately following the reopening of schools, which IMO  is the last - and final - nail in the coffin of the idea from various quarters that the recent massive spike in Scotland was primarily down to schools returning.  I’m a bit concerned over the last few weeks at the genera tone of messaging around rising cases, the approach of winter and the role of vaccinating children and extending school closures over half terms; this all worries me because - as always - I like to see a good understanding of the evidence (in the form of the data) informing policy and there seems to be some jumping to conclusions going on here.  If the wrong areas are identified as the cause of the problems, “fixing” them won’t fix the problems.

English Regional Rate Constants for Cases:

  • Plot 18 looks much the same as last week.  The highly provisional leading edge for cases is showing a large tip to decay, but then again it did that two weeks ago and it didn’t really pan out.  Give it a few more days to see...

 ablackett 11 Sep 2021
In reply to wintertree:

You are going to kick yourself when you see what you have called this thread.

 wintertree 11 Sep 2021
In reply to wintertree:

Scotland - Part 1

  • Last week I said cases looked like they wanted to turn to decay; this week they look like they’re decaying. 
  • Hospital admissions and now deaths are still rising as the lag plays out. 
  • Admissions are getting close to an all time high for Scotland - much less than one doubling, and occupancy isn’t much more than one doubling away from the previous peak...  
  • The way the recent burst of cases was concentrated in young adults really reflects in plot 9 - the spike in the doubling times (or rate constants) for cases is much bigger than the emerging spike for hospitalisation, and that in turn looks like it could be bigger than the one for deaths.
    • Catching up on antibodies that the similar cohort got in England during the Euros?

 wintertree 11 Sep 2021
In reply to wintertree:

Scotland - Part 2

The week-on-week method cases rate constant plot for Scotland:

  • Looking at the week-on-week method rate constant plots for Scotland, the big rise in cases following the final dropping of restrictions in Scotland looks to be ending, with 6 days of very low rate growth (exponentially speaking) and a day of provisional decay.  The data seems a bit more provisional than normal, let's hope this day of decay holds up against it.

Scottish Demographics:

  • I’ve changed the cases/day (left side) heat map on D1.c to be normalised to case per 100k people using their 2019 mid year population estimates.  This makes interpretation of the plot much easier given the bizarrely irregular demographic bands in the data.
  • Much like for England but on a larger scale, D1.c  and the line plot make it clear that the top level decay is being driven by the collapse in cases in young adults.  That collapse can’t go on for much longer as cases tend to a low number in those ages. 
    • Notably however the rate constant for under 14s is decreasing as if it wants to turn to decay - yet more suggestions that schools are not a major driver of demographic-wide cases IMO.  
    • To my eye it looks like everything under 74 years of age is heading for decay - the rate constants are decreasing towards the decay side, and they always seem to have some momentum... A promising sign, let’s hope it holds.

 wintertree 11 Sep 2021
In reply to wintertree:

The four nations plots

  • Much like last week really
  • Wales has seen cases grow quite a lot, that looks to be ending.
  • Notable how Scotland's rate constant plummeted out of rapid growth first in June 2021, and then sustained growth the most in recent weeks. 

 wintertree 11 Sep 2021
In reply to ablackett:

> You are going to kick yourself when you see what you have called this thread.

@£$@£%!£, thanks.  

It turns out the thread titles are editable, who knew!  

Not the most embarrassing mistake that autocorrect has led me in to...

 wintertree 11 Sep 2021
In reply to wintertree:

I’ve been in two minds about making this post.

Let me be clear - I am no authority here.  These are not “my” threads.  The long standing etiquette on UKC seems to be that the originating poster has no special say or privilege on the thread they start.

I continue to share my plotting, basic analysis and interpretation on a weekly basis because

  1. I find it useful to go through the process of preparing it
  2. The feedback I receive in public and in private gives me motivation 
  3. The big one - these threads often precipitates a wide range of informed discussion from a range of knowledgable and capable posters that I and others find informative and interesting.  

There is an account who joined just over a month ago and who has been posting entirely one-sided content to these threads towards the covid denialism / anti-vax side of the spectrum.

They have now admitted to having been banned multiplied times over their Covid posts and have admitted to provoking the bans - in my opinion by deliberately posting factually false content that downplays the risks from Covid

I am 95% sure I know which their other accounts have been, and previous incarnations were more outright in their lies and misrepresentations of data.  I believe this makes a material difference to the interpretation of the current incarnations motivations.  They are not posting on these threads in good faith in my opinion

They have said many times that their past bans are down to some conspiracy to suppress inconvenient opinions.  I do not believe this to be the case.

In the last plotting thread they posted a number they calculated from a table in a government document and which they stripped of context and severely misrepresented as a “death rate from Covid”.  By any reasonable interpretation their number was too low by between 20x and 80x.  They refused all attempts to constructively unpick what was either an accidental misunderstanding or a deliberate misrepresentation.  This could be incompetence, it could be malicious intent.  I don’t know and to be honest I don’t care.  This is very much falling back in to the pattern of systematic misrepresentation used by what I think are some of their former incarnations.

This week, I ask that nobody engage with the poster currently known as  “oureed” on this thread.  If we all ignore their replies, perhaps they will get bored and go away.  Sort of like the opposite of Tinkerbell.  This requires a collective buy in from everyone, and is one way to keep these threads in better condition.   I expect they’ll present this an an Orwellian attempt to stifle debate, I rather see it as an effort to lower the noise levels.  I can't require this of anyone, and I will not do anything differently if things do not go as I have asked.

But I'd like to try something a little different.  It won't be an elephant in the room that their posts are going unanswered.

Post edited at 21:02
 elsewhere 11 Sep 2021
In reply to wintertree:

Incompetence* or  innumeracy (and maybe ignorance) would randomly both exaggerate and minimise the impacts Covid. 

You can't be one-sidedly incompetent, it's just not plausible.

You can't be innumerate in a consistent direction, it's just not plausible.

I conclude delusion, dishonesty and/or bad faith rather than implausible incompetence etc.

*competent people make mistakes too, but not consistently often (or they consistently spot most before they open their mouths) and rarely so one-sided.

In reply to wintertree:

On second doses:

  • Return rate has always been ~95%, weirdly. And worsening going down the ages. So if you haven't baked that in from the start your deductions could compound some weirdness.
  • There's tons of vaccine. EU export authorisations remove any doubt about that. edit to add: https://mobile.twitter.com/PaulMainwood/status/1433455570271473671
  • There's the issue of having to cancel second jabs and wait longer after catching covid. The groups going for jab #2 will be the same that have crazy high case rates right now. That won't be a huge effect but it might not be a negligible one.
Post edited at 21:44
 wintertree 11 Sep 2021
In reply to wintertree:

Nobody ever guessed the waterfall from a few weeks back.  This week’s puzzler is to guess the flavour of today’s home made ice cream.

In reply to elsewhere:

Quite, it’s a two-tailed test.  

In reply to Longsufferingropeholder:

> Return rate has always been ~95%, weirdly. And worsening going down the ages. So if you haven't baked that in from the start your deductions could compound some weirdness.

Intentionally not baked in to my plot.   I wonder if there’s a correlation between first dose side effects and not returning?

> There's the issue of having to cancel second jabs and wait longer after catching covid. The groups going for jab #2 will be the same that have crazy high case rates right now. That won't be a huge effect but it might not be a negligible one.

Sorry; someone (you?) mentioned this a while back and I forgot to acknowledge it. It’s a very good point.

Post edited at 21:34

 elsewhere 11 Sep 2021
In reply to wintertree:

This is manifesting on my plot as the notional gap between vaccines increasing back form its low of 10-weeks.

At some point the notional gap increases by one week every week.

Supposing total UK population is 100.

Supposing 76 have first jab.

Supposing 69 have second jab.

Supposing the 7 who have had first jab but not second jab have no intention of getting second jab and first/second jabs cease entirely.

If notional gap due to those 7 people is 10 weeks now, then next week, the week after and the week after that the notional gaps will be 11, 12, 13...

Even if it were 76 and 75 with just one person singly jabbed it would be 11,12,13... 

Multiply those percentages by 66.7M for the real UK and it's not really going to be a gap increasing by 1 week every week as vaccination won't end completely.

I'll let you guess where I got what are actually Scottish percentages.

Are we getting to that sort of situation?

Increasing deaths - cases are rising in 40+ as they/we are not socially/medically isolated from the earlier rise (and now falling except under 15s) in younger age groups. I've not checked exact age ranges but that's what the picture looked like recently.

Post edited at 21:48

> Intentionally not baked in to my plot.   I wonder if there’s a correlation between first dose side effects and not returning?

Not sure, but as elsewhere points out and I've been trying to gently nudge, if you don't account for it you end up with a tendency towards garbage.

> Sorry; someone (you?) mentioned this a while back and I forgot to acknowledge it. It’s a very good point.

I did mention that a week or two ago, yeah. It does need a bit of thought to get an order of magnitude before deciding whether to discount or care.

 elsewhere 11 Sep 2021
In reply to wintertree:

Anyway, sod Covid, what's the photo?

 wintertree 11 Sep 2021
In reply to Longsufferingropeholder:

> Not sure, but as elsewhere points out and I've been trying to gently nudge

I think we're talking at cross-purposes here somewhat.  I feel in the spirit of things we should continue to do so for at least another month...

I understand exactly this, and that's why I've always been at pains to call it a "notional delay".  We don't have access to the longitudinal data to know what the distribution of delays are for people who actually go for their second doses, so this is all we can calculate form the public data.

> if you don't account for it you end up with a tendency towards garbage.

The notional delay rising and rising is a clear indication that the fraction of people not returning is now signifiant, so it's not "garbage" - it has a meaning, just not relating to the actual delay.    

Discussing it has nudged my thinking on a bit though; the drop in second doses seen now makes a lot more sense if we look about two weeks ahead of the blue/green transition in my plot where the notional delay has first doses coming due.  Account for the holdouts and that leading edge is further to the right.

In reply to Elsewhere:

> Are we getting to that sort of situation?

I think so.  The number of non-returners is now significant compared to the weekly rate of vaccination so I think the notional delay has passed the point of usefulness.

Non-returners are a large enough fraction of the non-fully-vaccinated adult population that they seem to be quite important.

> Anyway, sod Covid, what's the photo?

It's looking in to my ice-cream maker as it stirs a setting ice-cream; a double cream and duck egg custard base with a fruit-derived flavouring added.  Guess the flavour.

Post edited at 21:56
 ablackett 11 Sep 2021
In reply to wintertree:

Bacon flavour.

edit, just seen it is a fruit derived flavour.

Fruit derived bacon?

Post edited at 22:04
 minimike 11 Sep 2021
In reply to wintertree:

Bilberry

 elsewhere 11 Sep 2021
In reply to wintertree:

Half a million is bugger all, it's down in the noise of whim, weather, forgetfulness and what's on TV when the 2nd jab is due. 

It's about 1 in 50 to 1 in 100 of AZ first jabs. The average reliability of the human population is not 98-99% and I'm definitely far from 98-99% reliable!

Is it really as few as half a million? Perhaps people are more reliable than I thought.

As always many thanks for you data presentation, analysis and insight.

Post edited at 22:10
In reply to wintertree:

Garbage was a bad choice of word. I wasn't meaning to dismiss it. You end up with not a notional delay, but asymptote towards a missing doses, when your notional delay is increasing at 1 second per second. If that's intentional, then that's still useful but I might suggest grabbing a biro and scratching through the axis label....

On delaying because of infection.... Doesn't actually take much thought does it? It's gonna be 10^3 - 10^4 people a day having to cancel and rebook, right? So some of it will be that for sure.

In reply to wintertree:

> Hospital occupancy: This continues to creep up - no doubt in part related to the changing demographics, and also related to the lag from admissions to departure.  We’re now at about 1/5th of the all-time peak for Covid occupancy; this may sound like a lot less but that peak was an absolutely bonkers time that pushed healthcare well beyond any sustainable limits and required widespread lockdown measures. 

In Cumbria things were very dicey recently on the health and social care front, probably as bad as they've ever been since Covid reared it's head, which points to a lot of local variation.

 wintertree 11 Sep 2021
In reply to Longsufferingropeholder:

I think it's time for that to go.  I'd not really thought through the asymptote before as things change.  It was useful to see the gap shortening, and it rising again interpretable, but as you and elsewhere say, it's probably just going up from now on.

> On delaying because of infection.... Doesn't actually take much thought does it? It's gonna be 10^3 - 10^4 people a day having to cancel and rebook, right? So some of it will be that for sure.

Although the demographics shift cases a lot over the last month towards those for whom second doses are coming due.

In reply to elsewhere:

> Half a million is bugger all, it's down in the noise of whim, weather, forgetfulness and what's on TV when the 2nd jab is due.

That's a good way of looking at it.  

> Is it really as few as half a million? Perhaps people are more reliable than I thought.

That was the number given for AZ, I haven't seen a number for Pfizer. 

Call it 1 million in total; it's still a small fraction of the population but in terms of the virus mechanic what matters is that as a fraction of the population without full vaccination - especially as Delta shifts emphasis much more to the second dose.  In terms of that denominator, it's not so insignificant.

In reply to minimike:

> Bilberry

No, although now I wish it was.

In reply to ablackett:

> Bacon flavour.

No, and I do not wish it was.  Bacon goes all right in muffins, but given my experience of bacon fudge I have no interest in trying bacon ice cream. 

> edit, just seen it is a fruit derived flavour.

> Fruit derived bacon?

Given the history of the land, it's entirely possible it's porcine derive fruit.  Pig bones everywhere.

In reply to Ridge:

> In Cumbria things were very dicey recently on the health and social care front, probably as bad as they've ever been since Covid reared it's head, which points to a lot of local variation.

Thanks for the comment.  I haven't really looked at regional occupancy.  The rate constant plots on admissions show change nicely but not absolute values.  People in healthcare must be exhausted; it's hard to imagine that they could sustain the level from January 2021 again, or anywhere that near it.  I imagine there's quite a lot of PTSD in many medical workers after the last wave; I know one poster on here is involved in a support role not unrelated to that.

There's a separate discussion going on in the politics thread touching on the number of people living and working "off the grid"; I started wondering how they go about getting vaccinated, and how much more susceptible they are to Covid.  I can see that being a factor in local/regional differences I'd not thought about before.

Post edited at 22:26
In reply to wintertree:

> This week, I ask that nobody engage with the poster currently known as 

Actually, i thought I'd missed the memo on this last week; a series of posts resulted in tumbleweed.

 elsewhere 11 Sep 2021
In reply to wintertree:

In my understanding a million single jabbed is nothing compared 16 million unjabbed (majority of whom are children). Looking around the world at different outcomes I don't think we understand Covid at the level of a nation to 1 part in 16.

A million matters if they are vulnerable but no reason to assume more vulnerable than average, less vulnerable than average seems more likely.

There are currently 5 million single jabbed who will mostly turn up for second jab when it is due about 10 weeks after the first jab.

There are 46 million double jabbed with bloody good vaccines that are not 100% effective.

In a population of 66.7, a million only makes a difference if the other 65.7 million are fully immune.

To be honest I don't understand the significance of a trivially small number like a million.

Maybe I shouldn't be so flippant about a million as some of them definitely will die avoidable deaths if they don't get a second jab that reduces but does not eliminate risk of death.

Post edited at 23:01
 wintertree 11 Sep 2021
In reply to Ridge:

> Plum

No; the plums had no fruit this year, a bit growth mad after some serious pruning.  I did get my first gage this year though; taste took me back in time 30 years.

In reply to captain paranoia:

> Actually, i thought I'd missed the memo on this last week; a series of posts resulted in tumbleweed.

No memo that I’m aware of.  You did get the one about the cover sheets on the TPS reports though?

> In my understanding a million single jabbed is nothing compared 16 million unjabbed (majority of whom are children). Looking around the world at different outcomes I don't think we understand Covid at the level of a nation to 1 part in 16.

Infection acquired immunity - often without symptoms - could be quite high in children though, so I’m not sure I agree on the numbers.  Further, close contacts are not uniform across the ages by any means.  We’ve spent the last month a gantt’s whisker from decay of cases and decay of hospital occupancy - two things we desperately need.  The number of single jabbed who missed a second dose seems enough to change that.  Unlike those unwilling to go for a first dose, this cohort has shown willing which suggests they might be easier to get over the line with some 1:1 phone calls and flexible appointments.  At this point, offering single dose AZ recipients who are hold outs a second dose of Pfizer might also move things on, and doesn’t open any floodgates to more such demands.

> Maybe I shouldn't be so flippant about a million as some of them definitely will die avoidable deaths if they don't get a second jab that reduces but not eliminate risk of death.

The way I see it; with a non-linear mechanic the small changes don’t add up, they multiply.   I’m more concerned with avoidable hospitalisations than avoidable deaths.  A couple of posters have suggested over the last couple of weeks that there’s something of a comms blackout imposed on NHS trusts over their current situations, and winter is coming.  

Post edited at 23:12
 elsewhere 11 Sep 2021
In reply to wintertree:

As usual you have reasoning that sounds like you are more right than I am. I struggle see signs we are teetering on the edge of improvement so I never quite believe you. Hopefully you are right.

Opening floodgates for vaccine demand would be a good thing and if Pfizer after AZ does that I'm all in favour.

 wintertree 11 Sep 2021
In reply to elsewhere:

> As usual you have reasoning that sounds like you are more right than I am.

Sounding right and being right are not the same thing.  Perhaps I’ve just spent to long hanging around people who make a career out of sounding right…

> Opening floodgates for vaccine demand would be a good thing and if Pfizer after AZ does that I'm all in favour.

Agreed.  At this point I don’t see how offering it could backfire in terms of getting more people through the door, but I often don’t think through unintended consequences.

In reply to wintertree:

> We’ve spent the last month a gantt’s whisker from decay

That's just bad planning...

In reply to wintertree:

Medlar?

In reply to wintertree:

Damson?

In reply to elsewhere:

> In a population of 66.7, a million only makes a difference if the other 65.7 million are fully immune.

> To be honest I don't understand the significance of a trivially small number like a million.

This is arguably not the best way to think about it; if there are 16 million not fully vaccinated people, getting another million will have a 1/16 effect on all the metrics, not 1/65.

Also worth noting that people who have had one jab are in many ways low hanging fruit; they're obviously not anti vaxxers or medically unvaccinatable.

That said, it's still not a huge number of people so I'm not really disagreeing with you, just offering other ways to see it.

In reply to wintertree:

> Although the demographics shift cases a lot over the last month towards those for whom second doses are coming due.

I had accounted for that in my one of two orders of magnitude estimate. Can't you tell?

 wintertree 12 Sep 2021
In reply to Dr.S at work:

> Medlar?

No.  Only found out about these a month back, I want to taste one now.

In reply to BusyLizzie:

> Damson?

Nop.  What a fruit is damson though.

In reply to captain paranoia:

> That's just bad planning...

Quite.  

I doubt we could have held cases this level through adapting policy if we’d tried.  I was feeling a bit suspicious about this, but they’re not level in any demographic, it’s more of a “some rising some falling” thing.

In reply to Longsufferingropeholder:

Yes, I think closer to 1/16th, and low hanging fruit.

> I had accounted for that in my one of two orders of magnitude estimate. Can't you tell?

You didn’t show your workings!  More importantly perhaps, it’s not an effect that can keep giving indefinitely.

In reply to thread:

BBC story on rising pressures in Scottish A&E.  

https://www.bbc.co.uk/news/uk-scotland-58530550 

In reply to wintertree:

> In reply to captain paranoia:

> > That's just bad planning...

I think this was a (very good) joke about the typo above, gantt instead of gnat. 

> In reply to Longsufferingropeholder:

> You didn’t show your workings!  More importantly perhaps, it’s not an effect that can keep giving indefinitely.

Few to low teens of k cases in those age bands, probably. Couple tens k booked for dose 2, probably. Wave hands and chunter a bit, few k per day probably need to cancel & rebook. 

 wintertree 12 Sep 2021
In reply to Longsufferingropeholder:

> I think this was a (very good) joke about the typo above, gantt instead of gnat. 

Ah.  I tend to read what I think I wrote when it comes to words that look similar….  Good one captain paranoia, it went totally over my head…

I got similar workings; add in a 3 week period to rebook and it gives OOM 100k delayed cases, or about 4 days addition to the “notional lag” at current first dose rates.  Not a big effect.

 Si dH 12 Sep 2021
In reply to wintertree:

Well vaccine passports won't be used to help those uptake numbers in young adults any more. I do suspect the whole thing may have been a ruse from the start.

I wonder what other gems will be in Boris' winter plan on Tuesday? Confess I'm not really sure what I think should be in it given current status (edit: meaning current data).

Post edited at 10:40
 wintertree 12 Sep 2021
In reply to Si dH:

> Well vaccine passports won't be used to help those uptake numbers in young adults any more. I do suspect the whole thing may have been a ruse from the start.

Well, that blindsided literally nobody in the room...  A ruse?  Such cynicism...

> I wonder what other gems will be in Boris' winter plan on Tuesday? Confess I'm not really sure what I think should be in it given current status (edit: meaning current data).

Yes, cause and effect into the future is not so clear now we're out of the obvious "exponential spread against a mostly susceptible population" phase ; we just have to see where cases and hospitalisations take us...   I'm pretty unconvinced by the predictive power of modelling at the moment.

So the plan I think needs some clearly defined thresholds at which more control would/will be taken over transmission before it is too late for healthcare, keeping in mind the lags involved.  With pre-defined thresholds and triggers healthcare, businesses, education and individuals can have some coherent plans. Oh, and have every single ventilator window on every single bus welded open. 

Having some pre-determined plans to involved the armed forces or other auxiliary staffing in health provision to maintain service levels and - critically - stop the NHS staff from falling under endless, unyielding pressure - seems sensible to me, but I know basically nothing about delivering healthcare and realise there could be all sorts of issues to making this work.  But, better to have a plan in advance I think given where we are, than to end up reaching for a panic button.

 elsewhere 12 Sep 2021
In reply to wintertree:

> So the plan I think needs some clearly defined thresholds at which more control would/will be taken over transmission before it is too late for healthcare, keeping in mind the lags involved.  With pre-defined thresholds and triggers healthcare, businesses, education and individuals can have some coherent plans.

That's my understanding of how it worked (works?) in German Lander. Anyone could see how published numbers change and plan ahead for when the published thresholds would be met and published restrictions would apply.

Fat chance here.

 Si dH 12 Sep 2021
In reply to elsewhere:

> That's my understanding of how it worked (works?) in German Lander. Anyone could see how published numbers change and plan ahead for when the published thresholds would be met and published restrictions would apply.

> Fat chance here.

You mean, like, being able to plan ahead for when vaccine passports would be required to enter nightclubs and stadia?

Oh wait...

In reply to Si dH:

> Well vaccine passports won't be used to help those uptake numbers in young adults any more. I do suspect the whole thing may have been a ruse from the start.

I was never really convinced by the vaccine passport for nightclubs thing, especially the insane idea of opening nightclubs for a few months before introducing them so basically the horse would have bolted.   You could probably get the stragglers done faster by offering them 50 quid and parking a vaccination bus beside a nightclub queue or having a mobile clinic at football ground or train station.  

There's probably also a correlation between not being jagged and already having antibodies because you've caught it before.  For two reasons a. people who have caught it may think they don't need jagged and b. people who think Covid risks are a myth will probably do risky things which result in catching it.

The low hanging fruit in terms of getting the % of the population increased fast is jagging secondary school kids at school.

Looking at the death numbers creep up it seems like they are slow motioning into exactly the same mistakes as in the last two waves.   They're already making linear extrapolations of growth, thinking 'maybe we will need a circuit breaker lockdown in two months' and letting it get that bad before they do.  WHy can't they just do a few sensible things like keeping nightclubs/cinemas/theatres closed, encouraging those who can work from home to work from home and mandating a specified standard of mask on public transport.

The UK needs to ask itself how come German which has 83 million population to our 66.5 million has had 90,000 Covid deaths to our 136,000.   It's not like we have fewer lockdown days from always waiting until the last minute to do anything.

Post edited at 16:56
 wintertree 12 Sep 2021
In reply to tom_in_edinburgh:

> The low hanging fruit in terms of getting the % of the population increased fast is jagging secondary school kids at school.

Easy it may be, but is it worthwhile?  The JCVI decision for 16 and 17 year olds is for only dose of Pfizer for now, as the second dose is identified as having on the order of a 9x higher risk of significant side effects.  This would seem to set a precedent for ages 12-15, and it’s clear one dose does little to reduce transmission of delta.

With proper herd immunity now likely of the cards through vaccination alone, the main motivation for increasing % vaccinated is now more than ever not in forcing R<1 but in reducing hospitalisation (and deaths) by protecting those at risk of hospitalisation, which is adults.  Vaccinating 12-15 year olds is not going to make much difference to hospital admissions from unvaccinated adults, and it’s not going to make much difference to R.

Its important to remember *why* we’re vaccinating now.  We’ll see what the CMOs say, but I hope they approach it from the science and not political optics.

>There's probably also a correlation between not being jagged and already having antibodies because you've caught it before.

Some but not enough I think, given the rates for admissions in vaccinated vs unvaccinated under 40 year olds ….

>   They're already making linear extrapolations of growth,

Are they?  Any sources to back that statement up?  Seems to me a range of possible futures are being considered…?

 wintertree 12 Sep 2021
In reply to thread:

The turn to falling cases in Scotland and England looks a lot less provisional with today's update - clear week-on-week falls for 3 days in a row for both nations.

I'm don't think that the odd discontinuity in the English data showing rise over the week after the bank holiday Monday is really indicating a rise in actual infections; rather that more case are being detected.  

  • The plots "Weekly number of people receiving a PCR test and positivity" and "Rapid lateral flow tests conducted" [1] show a big switch on of testing over the last ten days.
  • This would bias up the first week of rate constant measurements after the switch-on feeds through to confirmatory PCR testing.  I've annotated this set of points in the final plot below.
  • Once LFDs switch off, if there's still appreciable positivity in them, there will be a matching low bias in this plot.  For now though, I think we're back in to rate constants that better reflect the change of infections. 
  • Some disruption of the data not related to changes in cases fits with this period violating the passband temperature anti-correlation as I noted yesterday.  Also, after months of staring at these rate constant plots, it just looks wrong.

So, with an optimistic hat on, it feels like we may finally be running out of adults people without antibodies, leading to a decay of symptomatic Covid.  Eyes now turn to hospitalisation numbers in about a week's time to look for confirmation that infections also went in to decay, as well as cases. 

Edit:  Looking at the various breakdowns of cases available from the API, I'm not convinced it is as simple as just a switch-on of a lot more LFDs.  Nice to be trying to unpick why cases are falling for a change.  Normally rising in cases, PCR tests and positivity go together, but the most recent rise in cases comes with rising PCR tests but constant positivity.  Over 90% of people going for PCR tests do not have Covid.  I've often wondered how much of what is detected is detected because of symptoms from something else, forming a random sampling component to the P2 results.  It could be that we have other infections rising that share symptoms with the triggers for testing...  As with the "wrong" look by eye and the braking of the weather anti-correlation, this is another flag that something different happened over the last couple of weeks...

 [1] https://coronavirus.data.gov.uk/details/testing?areaType=nation&areaName=England

Post edited at 19:45

 groovejunkie 12 Sep 2021
In reply to wintertree:

"Nice to be trying to unpick why cases are falling for a change". 

It certainly is, let's hope having our optimistic hats on isn't short term! Thanks for the analysis (to others too), all your effort is massively appreciated.  

In reply to wintertree:

> The turn to falling cases in Scotland and England looks a lot less provisional with today's update - clear week-on-week falls for 3 days in a row for both nations.

Freshers week is just starting in Edinburgh and based on what I see on local websites and what I hear from my daughter my forecast is another spike is coming.   Levels are already high in Scotland and there's massive queues outside nightclubs and the pubs are rammed with freshers.  It's a shame, another month and almost all of them would have been at 2 jags plus three weeks.

 wintertree 12 Sep 2021
In reply to tom_in_edinburgh:

> Freshers week

Indeed. 

Reaching back in the archives, here's the D1.c from plotting #10.  

  • Pre-delta, there wasn't much obvious bleed-through from undergraduate cases to older ages.  There were some bonkers rate constants (doubling times) in the u/g ages with some clear, identifiable institutional spikes down at the MSOA level and in the press.

Bit of a wild card this time around - a lot more naturally induced immune responses in the u/g cohorts, a lot more vaccination, and a more transmissive variant.  If the growth is as contained to the demographic as last time around, it’s not going to drive much hospitalisation.  This time though face to face teaching is currently planned a lot more than last year…

Still, right now cases genuinely seem to be falling; and every previous university event has been limited duration.  Fingers crossed…

Post edited at 21:46

 Si dH 12 Sep 2021
In reply to wintertree:.

> Over 90% of people going for PCR tests do not have Covid.  I've often wondered how much of what is detected is detected because of symptoms from something else, forming a random sampling component to the P2 results.

You reminded me of something I saw that surprised me a few weeks ago. Here it is (or rather, an updated version). Overall reported PCR positivity is under 10% at the moment, and I have always naively assumed that meant 90% of people, or at least something close to that, with the reported classic symptoms didn't have covid. Not so. Check out the attached graph, which is from page 16 of the weekly covid and flu surveillance report:

https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season

Awful lot of people are obviously booking tests without symptoms, keeping the dashboard numbers down.

Apart from the huge numbers on the positivity line for people with symptoms, it's also interesting to compare the different waves, and then look at the same comparison for overall positivity from the dashboard.

Post edited at 22:18

In reply to Si dH:

Presumably contacts getting PCR’s rather then sitting at home for a few days?
 

would be great to pull that dataset apart.

 wintertree 12 Sep 2021
In reply to Si dH:

Nice spot, thanks for that.  I haven't read those reports in a while.

Really interesting; positivity on both scale with how widespread infection is, but it scales a lot higher on the symptomatic tests.

> Overall reported PCR positivity is under 10% at the moment, and I have always naively assumed that meant 90% of people, or at least something close to that, with the reported classic symptoms didn't have covid. Not so. 

Indeed - looks like I've been equally wrong in that assumption there.

With some rather unpleasant backing out of numbers from a screenshot of the graph in the PDF it should be possible to split the daily "PCR only" cases actual data for England by symptomatic status.  I'll put that down on my "if procrastination strikes" list.  The rate constant for symptomatic only testing would be very informative.

In reply to Dr.S at work:

> Presumably contacts getting PCR’s rather then sitting at home for a few days?

That could be the missing link that explains why the relatively small rise in positive LFDs is being accompanied by a larger rise in PCR tests...?

> would be great to pull that dataset apart.

Indeed; how maddening that the data has this level of granularity but that it's not apparently being analysed to its potential.

 Misha 13 Sep 2021
In reply to wintertree:

Thanks again. The fall in recent days is indeed curious. It might be connected with the nice weather. If anything, I’d expect the numbers to be going up due to the return of schools and office workers. As ever, we should avoid drawing conclusions from a few days of data but of course any fall is welcome. If the case numbers remain constant or reduce further over the coming week, that would suggest we’ve managed to ride out the return to schools and offices - at least until the weather closes in and we get more cases from indoor socialising.

The winter plan seems to consist of things which we should be doing anyway, such as face masks, WFH where possible and perhaps vaccine passports making an appearance after all. Will it be sufficient? Will it be introduced early enough? I’m not convinced, given past experience, though we do have vaccination on our side. I very much doubt there would need to be another lockdown but restrictions on large gatherings and a rule of 6 or similar indoors may well need to be reintroduced…

 girlymonkey 13 Sep 2021
In reply to Si dH:

We all do a weekly PCR at work. I presume all health and social care do. That is a lot of weekly, non-symptomatic, PCR tests. 

Having been away last week doing some guiding work (first in 2 years!! Exciting times!), I will be going into the care home to do one tomorrow as a precaution before I am back on shift. LFT aren't accurate enough for our setting

 Si dH 13 Sep 2021
In reply to girlymonkey:

> We all do a weekly PCR at work. I presume all health and social care do. That is a lot of weekly, non-symptomatic, PCR tests. 

Do yours count as pillar 1 or pillar 2? That graph I showed excludes pillar 1, which is NHS testing of staff etc.

Dr. S has hit on another likely cause that I had forgotten about too. I bet that's a lot of people taking PCR to avoid isolation at the moment while cases are so high.

I also suspect there are lots more people now at the cautious end of the spectrum booking tests who only have a sore throat or runny nose, so tick 'no' to the classic 3 symptoms, because of the publicity there has been from things like the Zoe study about Delta having a wider range of common symptoms.

So that's three reasons at least

Post edited at 08:15
 wintertree 13 Sep 2021
In reply to girlymonkey:

> Having been away last week doing some guiding work (first in 2 years!! Exciting times!)

Excellent! 

In reply to thread:

I was miffed this morning to see the UK has cancelled it’s contract with Valneva on disputed grounds relating to supply.  I still await their phase 3 results with interest and hope they can help people globally with their output.  Least the UK could have done was to keep the contract and donate the results.  Wonder if we’ll see a lawsuit or settlement over this?

https://www.bbc.co.uk/news/business-58499064

 Offwidth 13 Sep 2021
In reply to girlymonkey:

The NHS staff I know take routine precautionary LFTs unless they they suspect they might have covid, when a PCR is booked (have symptoms, know close contacts, contacted by track and trace etc).

 oureed 13 Sep 2021
In reply to wintertree:

> This week, I ask that nobody engage with the poster currently known as  “oureed” on this thread. 

I felt a small flicker of pride while reading through this post. Always happy to be the counter-voice.

I assure you all that I am a mass-Covid vaxx-questioner rather than 'anti-vaxx' and 100% not a Covid denier (otherwise I wouldn't even bother showing up). I act in good faith and if my posts seem one-sided that's because the other side gets 95% of the air-time on here.

My opinion on mass-Covid vaccinations have evolved over the past year. Perhaps counter-intuitively I was much more concerned last December when the manufacturers were claiming 95% efficacy without differentiating between transmission and protection. I realised this would generate severe selective pressure which would facilitate the spread of unknown variants.

However, it turns out that the vaccines' much lower transmission efficacy against the Delta variant allows it to circulate while effectively lowering rates of hospitalization/deaths. Fortunately Delta has proved to be no more virulent than the original virus. 

As such my concerns are now more about the proportionality of the vaccination campaign for young people and the great inequality between rich and poor countries when it comes to protecting vulnerable people. This issue has become much more relevant with the realisation that waning immunity requires the use of booster doses.

I have always said that vulnerable people should be protected by vaccination. After it became clear that mass-vaccination was the government's adopted strategy I have also said it is in everyone's personal interest to get jabbed.

But overall I agree with Wintertree on the point he made in this post. Read my arguments by all means but please don't feel the need to reply. It will save me a lot of time To be honest even disliking them will just encourage me! 

In reply to wintertree:

> I was miffed this morning to see the UK has cancelled it’s contract with Valneva on disputed grounds relating to supply.  I still await their phase 3 results with interest and hope they can help people globally with their output.  Least the UK could have done was to keep the contract and donate the results.  Wonder if we’ll see a lawsuit or settlement over this?

An EU company based in Scotland and not in one of the few Tory constituencies.  I'm surprised it lasted this long.

This is the kind of sh*t that happens to your industries when you are subject to a corrupt colonial government.

If the EU or US concludes the stuff is good then I hope Scotland buys some on our own account to use here.   

For all the people who raged at me suggesting that Tories doing an 'at cost' deal with an Indian billionaire for vaccine technology which gave him a $600 million a month business was potentially dodgy just a few days later Pritti Patel gets caught fixing meetings for an Indian billionaire who gave money to the Tories.

https://www.independent.co.uk/news/uk/politics/priti-patel-labour-heathrow-meeting-b1918537.html

Post edited at 09:44
 girlymonkey 13 Sep 2021
In reply to Offwidth:

Maybe different in Scotland and England? I am in the care sector, but I think NHS up here do the same. It's all done at work. 2 X LFT and one PCR each week. Residents also get PCR every so often as precaution. Not sure the frequency of that.

 wintertree 13 Sep 2021
In reply to tom_in_edinburgh:

> For all the people who raged at me suggesting that Tories doing an 'at cost' deal 

The possibility wasn't being argued against - it would take a special kind of denialism to argue against the possibility of such dealings from the current government.

I for one raised serious issues with the various reasons you were building your case on, which included what I consider to be some serious confusion over university IP licensing and your umbrage that we weren't profiting enough from licensing vaccine IP during a global health crisis. 

Perhaps evidence will come out that there has been something untoward on this deal, it would not surprise me.   

But, I fully support the decision by the University of Oxford to not profit from their IP on this vaccine during the pandemic phase, and I take serious issues with the level of support you brought to your case.   

I have a lot of commonality with your underlying views on this government, and it's clear I hope that I have been very unhappy with the way the first year went - as you said up thread our outcomes are very poor for that period compared to e.g. Germany.  There is no shortage of evidence for dodgy deals made in a hurry over the last 18 months.

But in my opinion you go well beyond the evidence and end up undermining your own case. 

 Offwidth 13 Sep 2021
In reply to wintertree:

It was argued about. Someone said to Tom about the Indian deal that it was cynical even for him. Given the lack of transparency we will likely never know, but my money is on Tom being right on that. Dodgy and nepotistic deals have happened so many times in the pandemic with this government that even if Tom was wrong his cynicism was justified. The news about Pritti talking completely outside protocol yet again is no surprise at all, and something that would be career ending  prior to Boris  being PM will almost certainly be ignored again. 

You could help by calling out bad behaviour here on any side of such arguments. The science position needs to take the moral high ground. These are emotive times and we all make mistakes but we should own them and apologise (as you do).

Post edited at 10:29
 wintertree 13 Sep 2021
In reply to Offwidth:

> You could help by calling out bad behaviour on any side of such arguments

I'm almost as poor at spotting when I or others are becoming flippant or dismissive as I am at spotting spelling errors and homonyms/homophones... I have to work quite hard at not being an ass given my obvious limitations.  Sometimes I wonder if it's worth the effort...

I've been wondering about putting some mediated video calls in to action.  I can think of several of the arguments that have gone on here recently which could be rapidly resolved I think to the benefit of all, and it would save a lot of time.  Plus, with it being video based it can't end in a proper melee...  

> The news about Pritti talking completely outside protocol yet again is no surprise at all and something that would be career ending  prior to Boris  being PM will be ignored again.  

It's the consequences within and for the civil service that worry me more than anything here; the damage being done there will outlast this cabinet and even a total change in government.  I'd expect to see a certain kind of pressure emerging from the civil service over this incident.

One recurring theme of Covid is that it seems to accelerate change along the directions it was already set on - some for the better, others for the worse.  

In terms of pandemic stage Covid accelerating change, this may even extend in to one of our built in  ageing mechanisms...   Early days in the literature for drawing firm conclusions, but interesting. 

https://pubmed.ncbi.nlm.nih.gov/33464637/

  • Genome-wide DNA methylation profiling of peripheral blood reveals an epigenetic signature associated with severe COVID-19

 Offwidth 13 Sep 2021
In reply to wintertree:

What you do on these threads is incredibly valuable. You don't need to spot bad behaviour, supporting the message is enough. Being kind is important when people are justifiably frightened or angry.

 wintertree 13 Sep 2021
In reply to Offwidth:

>  Someone said to Tom about the Indian deal that it was cynical even for him

This comment has been getting mulled over by my subconscious.  It just reported back and it disagrees.  I went back to the archive [1].  These words were saiid, but not about the Indian deal.  It's easy for us all to loose sight of the details when this much acrimony is crossing swords however.

The statement precipitating the "cynical even for you" comment Tom suggested was "Pretty obvious that the main reason they bought 4x as many vaccines as needed for the UK was to use the excess as trading cards. ".  

This was absolutely not about the Indian deal but about our orders.

It seemed clear to me at the time that we signed full-sized orders with multiple different suppliers because neither the safety or efficacy data existed at the time for any of the candidates, because money was needed to pay for manufacturing plant, and because there is a lot of risk attached to getting even a successful compound and it's at-scale manufacture through approvals and authorisation.  Backing every horse.

Consider today's news over cancelling the Valneva order - does that lean towards "backing every horse in advance" or "trading cards.  

[1] https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_41-738560?v=1#x9513493

 wintertree 13 Sep 2021
In reply to thread:

Some quick summaries from my lunchtime reading.

An Ars article talking through some CDC findings on the level of protection offered against Delta by vaccination - if these findings are accurate, it seems that vaccination still offers a 5x reduced chance of catching the virus, significantly reducing the number of people able to spread the virus.  So, whilst the efficacy of the vaccine itself against transmission from an infected person may be much reduced, the efficacy of the vaccine against transmission at a societal level remains significant.

Studies are emerging from peer review and at the "credible institution" pre-print stage showing a significant increase in virulence from Delta.  It's still early days - unpicking changes to virulence takes a lot of time and effort - but it seems to be pointing towards "worse".

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01358-1/fulltext

  • Risk of COVID-19 hospital admission was approximately doubled in those with the Delta VOC when compared to the Alpha VOC, with risk of admission particularly increased in those with five or more relevant comorbidities.
  • (Note from me - Kent/Alpha VOC was eventually found to be a lot more virulent than the original virus, so by extension Delta could be looking even more virulent than the numbers given above which compare it to Kent/Alpha - but it's conflated because so much was learnt over clinical care and through repurposing trials between the first wave and Kent/Alpha, and testing was so low in the first wave)

https://www.medrxiv.org/content/10.1101/2021.07.05.21260050v3.full

  • Results: Compared to non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (43-62%) for hospitalization; 89% (67-116%) for ICU admission; and 51% (30-74%) for death. Increases with Delta variant were more pronounced: 108% (80-138%) for hospitalization; 234% (164-331%) for ICU admission; and 132% (47-230%) for death.
Post edited at 12:38
In reply to tom_in_edinburgh:

There is plenty of global demand for vaccines so I am sure the plant in Scotland will have no porblem in selling it elsewhere as long as its a good vaccine.

You could equally argue that for this reason it was sensible to cancel the contract as it improves global capacity instead of hoarding it here in the UK .

 Offwidth 13 Sep 2021
In reply to wintertree:

Firstly, I doubt many would regard it as cynical even for Tom, given Matt Hancock  and others have talked about benefits of oversupply and we have traded vacinces and in giving them away we get soft power benefits. The Indian deal was part of producing that supply. I'd admit I'm wrong and apologise if we find out one day that everything involved was fair and above board but the chances seem small given political graft in India and the behaviour of our government on trade. Lets not forget a Boris trade visit seems to be linked to India not going on the red list despite delta.

More importantly these are not standard UKC threads. They are discussions on covid science and data. The arguments with Tom are generally asymmetric. I'd expect even kids in a playground fight not to pummel an opponent they know they can easily beat. Scientists should have much higher ethical principles than the general public in public discussion on a science thread.

Post edited at 13:16
 Offwidth 13 Sep 2021
In reply to wintertree:

Back to science I spotted something interesting in a side-argument on the Keir thread and thought it worth copying here. One of the narratives of Sweden from covid lockdown deniers is they did quite well with very limited restrictions and were unlucky with care homes. We know the actual restrictions pretty well now and that their per capita death rate wasn't so far behind the UK (despite the terrible mistakes made by Boris)  but something new I spotted was the seemingly proportionally higher cases in kids and lower cases in old people compared to the UK. From that thread : 

> It looks like Sweden have a higher case rate in the young and a lower case rate in the old than the UK from the links below. That makes the death rates look even more concerning for Sweden, as the average age of covid death in the UK is around 80

Post edited at 13:28
 wintertree 13 Sep 2021
In reply to Longsufferingropeholder:

I'm not sure I've ever actually said it, but I've been really very grateful to the ONS this last year.  They produce very clear, legible and well qualified reports that are often critically insightful, and this is no exception.

Their findings are very reassuring, especially over breakthrough deaths.  

I would be very interested in a similar analysis on "breakthrough hospitalisations" - both number and length of stay.  That feels like a good piece of information towards understanding the picture over hospital occupancy this winter.

 elsewhere 13 Sep 2021

Valneva - any ideas/guesses what the story is?

I think deliveries were due only in 2022.

 Offwidth 13 Sep 2021
In reply to wintertree:

I'd second that view on the ONS.

Indie SAGE slides here from Friday. They plotted normalised hospitalisations and mortality for the vaccinated and unvaccinated on the same age group charts charts. I'd love to see cross correlation with antibody studies to see how many of the unvaccinated have had covid, as I suspect from the high level of the population with antibodies and the significant higher probability of hospitalisations and mortality for the unvaccinated might include a majority of those unvaccinated having previously been infected.

https://www.independentsage.org/wp-content/uploads/2021/09/WeeklySlides_10September2021.pdf

 wintertree 13 Sep 2021
In reply to elsewhere:

> Valneva - any ideas/guesses what the story is?

No, that one totally blindsided me.  As you know I'd been holding out hope it would be offered as a booster.   Well, hope is dashed.   Really odd as they just started submitting rolling data to the MHRA from their phase 3 trial for rolling review [1] and their comments today don't suggest anything has shaken their faith in the vaccine, so I don't think it can be related to the data.

In reply to Misha:

>  The fall in recent days is indeed curious. 

It's a great Rorschach test this; to me it was the preceding plateau of growth that was curious.    Definitely something curious about this recent period.  It's the plateau which breaks the "organic" look of the plot and which breaks the weather relationship; perhaps the switch-on of LFDs and also more symptom free PCRs.  

Update to the week-on-week rate constant plots - a 4th day of decay, and the provisionality in the previous 3 days has been a lot less than it was a week ago. From the demographics (not shown here) it looks like the fall is in all adult ages, rising in school ages.  If this is a real fall in infections (no stand out reason to doubt it, and the data has always been reliable in the past), hopefully that means a larger fall in hospitalisation than we'd expect from the top level cases data alone.   It'll be great to start draining the tension out of healthcare.

In reply to wintertree::

> The JCVI decision for 16 and 17 year olds is for only dose of Pfizer for now, as the second dose is identified as having on the order of a 9x higher risk of significant side effects.  This would seem to set a precedent for ages 12-15, and it’s clear one dose does little to reduce transmission of delta.

Indeed, the CMOs have only recommended a single dose for ages 12-15 - the BBC article [2] is worth a careful read. So, we are still following a different path to e.g. the USA and Germany. 

Prof Whitty's statement is notable.  My take is that this absolutely is not about reducing R but about striking the right balance on protecting children across a board range including educational and health effects.

  • Prof Chris Whitty, the lead CMO for the UK, said it was a "difficult decision" and should not be seen as a "silver bullet".  But he said it could be an "important and useful tool" in reducing school disruption in the coming months and when combined with the marginal health benefit identified by the vaccination committee, meant offering a Covid vaccine to all children was appropriate.

 [1] https://valneva.com/press-release/valneva-commences-rolling-submission-to-mhra-for-its-inactivated-adjuvanted-covid-19-vaccine/

[2] https://www.bbc.co.uk/news/health-58547659

I do fear this issue is going to be weaponised by certain quarters.


 Misha 13 Sep 2021
In reply to wintertree:

There is a whole bunch of factors at play. Return of schools / office workers and associated increase in PCR / LFD catching more asymptomatic cases. Weather. Perhaps reduced socialising as we go into September. No doubt various other things. So it’s not surprising that the numbers are moving around in somewhat unpredictable ways. I’ll take any reduction on offer, as it were… but wouldn’t assume that any reduction would be sustained. If there’s growth in kids in the tests coming through now, that could translate into growth in parents and subsequently grandparents in a week. Hard to predict as the more or less steady state we had for most of August has been disrupted. I imagine some kind of uniform trend, be it plateau, growth or decay will re-emerge by mid October. Until then it will be a bit all over the place (Uni return being the other significant disruption to existing patterns).

In reply to wintertree:

For the benefit of anyone not following the other car crash of a thread, following up on the /100k thing:

https://theconversation.com/covid-19-why-infection-rates-among-double-vaccinated-older-adults-look-worse-than-they-are-167836

 AJM 14 Sep 2021
In reply to wintertree:

> I'm not sure I've ever actually said it, but I've been really very grateful to the ONS this last year.  They produce very clear, legible and well qualified reports that are often critically insightful, and this is no exception.

+1

In reply to neilh:

> There is plenty of global demand for vaccines so I am sure the plant in Scotland will have no porblem in selling it elsewhere as long as its a good vaccine.

Maybe.  But Valneva share price crashed 40% and the French management are probably looking at their business plan for the Scottish operation based on this 100 million dose order and thinking  they should never have trusted a Tory.  

> You could equally argue that for this reason it was sensible to cancel the contract as it improves global capacity instead of hoarding it here in the UK .

Maybe I could, but I am actually going to argue that FT reports of Sunak having a spending crackdown and shortly thereafter a large UK government contract with a factory in an SNP constituency in Scotland getting cancelled are not unrelated.

https://www.ft.com/content/b7c47e4e-92e1-4d34-8a0f-91b40c360b00

In reply to tom_in_edinburgh:

Too many maybe's....maybe its just no good as we know that a few vaccines have just not performed as well as predicted. Its part of the very  risky territory of operating in the biotech sector. I can think of better uses for that money if its not working as I am well sure you can.

 Offwidth 14 Sep 2021
In reply to neilh:

Jon Read posted this article from an FT editor

https://overmatter.substack.com/p/the-november-story

on the origins of covid origins thread

https://www.ukclimbing.com/forums/off_belay/origins_of_covid-739118

I thought the link worth preserving for these threads.

 wintertree 14 Sep 2021
In reply to Misha:

> I’ll take any reduction on offer, as it were… 

More plummeting of both cases/day and the rate of exponential decay today.  Still little sign of the high provisionality from last week.

 I think we might finally be at the point we're running out of people getting their first "antibody free" infection.  It's felt imminently looming for some time, and we're running out of conflating factors...  It wouldn't necessarily mean infections are falling as fast as symptomatic infections, but it should mean that hospitalisations start to fall at least as fast soon enough.

> Hard to predict as the more or less steady state we had for most of August has been disrupted. I imagine some kind of uniform trend, be it plateau, growth or decay will re-emerge by mid October. Until then it will be a bit all over the place (Uni return being the other significant disruption to existing patterns).

It was never really steady state in the demographics, just at the top level; now it looks like it's falling in all adult ages and rising in children - which means the decay rates in those susceptible to hospitalisation and death is faster than the top level data suggests.

Re: Unis; indeed - the obvious next source of conflation; I'm worried cases from what feels like the inevitable freshers week explosions may not be as demographically confined as past times given the lack of restrictions imposed on the hospitality industry and the rush to restore face-to-face teaching at many institutions.  My local one managed a 4-day doubling time last September/October with Alpha...  Talk today of taking vaccination in to the universities, good.

But I'm feeling pretty optimistic about a general and sustained decay of systematic cases now with some road bumps on the way from predictable and unpredictable events.  Take with a pinch of salt; only time will tell.  There's always the wild card of an importation event of a worse escape mutation.

In reply to Offwidth:

> Jon Read posted this article from an FT editor

I saw Jon's post; that article has just displaced some rather dull and un-engaging technical documentation from my evening's reading list.  

Post edited at 17:02

 wintertree 14 Sep 2021
In reply to Longsufferingropeholder:

it was also clear to us that the vaccine in question that the company was developing would not get approval by the MHRA here in the UK,

Ouch, so it is perhaps related to the start of the rolling submission to the MHRA?  Seems pretty savage to release comments like this without evidence, and before the phase 3 data submission is complete.  Also at odds with what Valneva have said.  

Given Valneva's comment yesturday on intending to continue the submission to MHRA for approval, it's hard to understand the disconnect.

If there is some insurmountable problem, I'd have expected that to be cited as the reason for dropping the contract, not a contractual issue over supply.  

It all smells exceedingly fishy, we'll see where things end up.  

Delays seem to be rumbling on over approval of Novovax' production process as well; it all underscores how fortuitous it was we backed so many different candidate vaccines. 

https://www.reuters.com/business/healthcare-pharmaceuticals/eu-expects-key-data-novavax-vaccine-around-october-source-2021-08-20/

In reply to wintertree:

Yeah, looking for more detail but predictably finding nothing. Can only presume the MHRA saw a deal-breaker in the process/product somewhere. Does all seem odd. Hopeful more background will surface soon. In the meantime I'll look forward to a confirmation bias driven rantsplanation of how it's all a Westminster conspiracy.

In reply to wintertree:

All I can find are hints and mumblings that efficacy isn't great. Trials should be very close to reporting, and MHRA would have access to the data, so I'm gonna bet 50p it's that. Or irn bru contamination.

Thought crossed my mind that using a whole virus they could be worried about the risk of causing recombinant nasties to emerge, but if it doesn't enter cells that can't happen, can it? Nor would that be a UK specific worry.

 wintertree 14 Sep 2021
In reply to Longsufferingropeholder:

> Trials should be very close to reporting, and MHRA would have access to the data, 

The rolling submission of trials data to MHRA started about 3 weeks ago

https://valneva.com/press-release/valneva-commences-rolling-submission-to-mhra-for-its-inactivated-adjuvanted-covid-19-vaccine/

> All I can find are hints and mumblings that efficacy isn't great

It's often weaker for inactivated virus vaccines, but their new adjuvant looked promising to raise it significantly over the alum-only adjuvanted ones (e.g Chinese ones). 

But efficacy is a broad church; what interested me with Valneva was not its efficacy as a first vaccination, but its board T-cell response against multiple different viral proteins which feels like a path to getting some much more future-proof immunity re: variants.  Guess I'll be getting that the old fashioned way then...

> Thought crossed my mind that using a whole virus they could be worried about the risk of causing recombinant nasties to emerge

I was under the impression that heat inactivation would prevent that?  

>  Or irn bru contamination.

A problem with the process side is one thing that would tick both the "contractual" and "MHRA" boxes and so align with the apparently contradictory comments given from our government over the last 36 hours.  But, such an issue would also seem addressable.

All very fishy.  Time to keep an open mind and see what else comes out.

In reply to thread:

A differently binned demographic rate constant plot for England splitting it into under and over 15.  This is by the old method of de-weekending and then exponential fitting which isn't so sharp on features as the week-on-week method, but the recent plateau interrupting decay is still visible.  I'm going with this relating to a change in the infection > case detection rate from the switch on of various non-symptomatic testings with the return of schools; taking that in to account it's really promising that the school-aged demographic still looks to be heading for decay; perhaps the additional infections caught by this extra testing will speed that decay up.  This really is staring at digital tea-leaves now and it needs another week or so to (hopefully) firm up.

Post edited at 18:57

 elsewhere 14 Sep 2021
In reply to Longsufferingropeholder:

Disappointing, but a surprising number of last year's bets on different vaccines & vaccine technologies have come good. Also far more and far quicker than might reasonably be expected!

Post edited at 19:13
In reply to wintertree:

Would have (still might) been interesting to see how that helped or didn't. Intuitively you would think building immunity against more than one target would be better. But intuitive doesn't seem to work for immunology.
There's that original sin thing. And also you'd expect to see a marked difference between vaccine and natural immunity appear as variants come through, and I don't know that we are yet (/haven't found literature). Must be a study somewhere in the works on reinfections of alpha patients with delta etc. and it'd be interesting to see if it changes the difference (which is in itself still not fully nailed down, just ask Rom. ((please don't))) between convalescent and vaccine induced protection.

I don't think it's obvious that it would definitely be better. I want to think it would, and I do think it would for the same reasons as you, but my understanding isn't good enough to say those are definitely valid, given the many seemingly intuitively obvious things I've learned I was wrong about. Cells are weird.

 wintertree 14 Sep 2021
In reply to Longsufferingropeholder:

Totally agree on the issues around “obvious” and “intuitive” when it comes to outsiders like thee and me trying to understand immunology.

Still…

> I don't think it's obvious that it would definitely be better

If the virus gets some recombinant mojo on in one of the many animal reservoirs and comes out to bite you with a new human-capable spike protein, which vaccine would you rather have?

> Cells are weird.

Not half as weird as what happens when you start sticking them together.  
 

Within a cell it’s the DC rotary motors that get me (bacterial flagellum).  Spinning at insane RPM and photobleaching recovery studies show that individual parts are in thermodynamic equilibrium with the gunk around it, being replaced in real time as they spin at insane RPM.  Madness.  

 mondite 14 Sep 2021
In reply to tom_in_edinburgh:

I really wish the tories were as competent, even in a self serving way, as you seem to believe they are.

In reply to wintertree:

> If the virus gets some recombinant mojo on in one of the many animal reservoirs and comes out to bite you with a new human-capable spike protein, which vaccine would you rather have?

I'd love to say "yeah, gimme them nucleocapsid antibodies, obviously", but I just don't know. I mean, in some subset of some arc of that scenario it's not impossible that there's a small but finite chance you might even be better off unvaccinated for certain initial conditions. It's just insanely unfathomable.
Also I don't know how likely we are to see a complete escape in the spike without an unrecognisable everything else too. Reading about the original sin thing, and following the reference trail, really stepped up my understanding of how pathetic my understanding is. It seems like a complete lottery until someone's done months of placebo controlled cat -herding.

> Within a cell it’s the DC rotary motors that get me (bacterial flagellum).  Spinning at insane RPM and photobleaching recovery studies show that individual parts are in thermodynamic equilibrium with the gunk around it, being replaced in real time as they spin at insane RPM.  Madness.  


I mean... just... mitochondria. That's a story packed with mind-blowing WTFs all the way.

 wintertree 14 Sep 2021
In reply to Longsufferingropeholder:

> Also I don't know how likely we are to see a complete escape in the spike without an unrecognisable everything else too.

Well, that's where really getting to the bottom of the story about how this particular virus came to be might be very illuminating.  I haven't found a good lay-reference going over such recombinant effects in this kind of virus.

> original sin 

The good news is that perhaps original sin can perhaps be forgiven one day in the future.  Depletion therapy for immune cells is becoming more widespread; get it selective enough and you could "erase" the memory of infection by an earlier variant and start all over again...  Suspect this sort of therapy might end up featuring in treating the post-viral fatigue components of long covid and other diseases....? 

https://www.nature.com/articles/s41573-020-00092-2

> I mean... just... mitochondria. That's a story packed with mind-blowing WTFs all the way.

Yup. 

The Plasmodium is even more bonkers in some ways - there's a whole organism that's been lost/integrated leaving only an extra set of membranes etc.  One that blew my mind was a theory I'd not heard before that cb294 mentioned last year - the idea that the nucleus may have been co-opted from a virus.  https://en.wikipedia.org/wiki/Viral_eukaryogenesis - that totally supplanted my previous mind=blown moment that now-endogenous retrovirus materials may have provided the critical parts needed to enable mammalian pregnancy - the giant multi-nucleated cells that form part of the placental exchange barrier and potentially some local immune suppression.  All this leaves me very curious about where it would all have ended up if self human level intelligence and opposable thumbs hadn't popped out of evolution and started to change tack significantly.

If anyone is reading and hasn't seen "Harvard's Inner Life of the Cell" it's mind-blowing.  Watch it and you'll end up wondering why dark matter and dark energy get so much PopSci time on the TV instead ofcellular biology...  youtube.com/watch?v=wJyUtbn0O5Y&

In reply to neilh:

> Too many maybe's....maybe its just no good as we know that a few vaccines have just not performed as well as predicted. Its part of the very  risky territory of operating in the biotech sector. I can think of better uses for that money if its not working as I am well sure you can.

This crowd of Tories have been caught out so many times in corrupt dealings that for me, just like Putin, or the boss of a drug cartel, they no longer get the benefit of the doubt.  If it looks dodgy I'm going to assume it is dodgy until proven otherwise.

 Misha 15 Sep 2021
In reply to wintertree:

Yes, I wonder if we’re now seeing the impact of ‘herd immunity’ (not proper herd immunity but something high enough to cause significant decay for a while). As you say, time will tell, though I’m not going to get too excited unless we’re still in decay around a week from now.

I also wonder what impact the return to the office will have - that’s a fairly gradual process in a lot of places.

Good point about Uni spread being less demographically contained this time round. I was hoping it would be largely self contained but as you say, with face to face teaching and no hospitality restrictions that’s probably wishful thinking. 

 Si dH 15 Sep 2021
In reply to thread:

Couple of new things up on the Sage website:

Interesting new analysis of waning vaccine efficacy using an approach I haven't seen before. Includes analysis with respect to symptomatic disease and severe disease separately. Looks, tentatively, like those who are in high risk groups and had AZ should get their booster sooner rather than later.

https://www.gov.uk/government/publications/phe-duration-of-protection-of-covid-19-vaccines-against-clinical-disease-9-september-2021

SPI-M-O still sticking to their guns on the potential for a big 4th wave.

https://www.gov.uk/government/publications/spi-m-o-consensus-statement-on-covid-19-8-september-2021

New SAGE meeting minutes also up but nothing particularly exciting.

Post edited at 07:26
 wintertree 15 Sep 2021
In reply to Si dH:

Some really interesting plots in that report - vaccine effectiveness against symptomatic disease peaks some months after the second dose with AZ, an effect visible for both variants.

> Looks, tentatively, like those who are in high risk groups and had AZ should get their booster sooner rather than later.

Agreed; the report notes the many confounding factors around vaccine manufacturer so let’s hope nobody uses this as a jumping off point to “prove” once vaccine is better than the other; that’s one clear interpretation but it’s not proof.  The CI on the critical data points are also very, very large spanning the range from “minor effect” to “oh shit”.  Best to act according to the worst. The top end of the CI is falling from shorter lags on all plots though so no question it’s real.

> SPI-M-O still sticking to their guns on the potential for a big 4th wave.

Let’s hope they’re wrong.

Edit: been thinking.  Devil’s advocate: The addition of more unknowns around a post-vaccination cohort and increasingly a post-(post-vaccination infection) cohort add so much uncertainty to the modelling I wonder if the time has come to stop it.  Is it now adding more noise and confusion than useful input?  It’s basically a Stingray document (“anything can happen in the next half hour”)

I don’t think we’re seeing signs there’s going to be sustained rising cases in schools, and sustained school based transmission is one half of their base for this; the other half being a return to offices.  Much more of a wild card?  There’s a measurable for this in terms of road traffic levels, will have to try and find the link…

Reading the grab bag of reasons lumped in to their point 10, I wish there was a sub-group dedicated to understanding the data in terms of looking for causality, in real time particularly by performing a bunch of measures against the data.  This could better inform both modelling and policy. As well as writing the text book on what questions to ask of the data in the next pandemic…

Post edited at 08:27
In reply to tom_in_edinburgh:

I would not expect anything else from you...the " its  dodgy Tory and SNP is perfect  bias".......I will just wait for more info and see what spills out.

 Jon Read 15 Sep 2021
In reply to wintertree:

> Reading the grab bag of reasons lumped in to their point 10, I wish there was a sub-group dedicated to understanding the data in terms of looking for causality, in real time particularly by performing a bunch of measures against the data.  This could better inform both modelling and policy. As well as writing the text book on what questions to ask of the data in the next pandemic…

This is basically developing an accurate and predicative model of the dynamics of human behavioural response to epidemics, the government, messaging, social networks, peer pressure, health, threats, media, etc etc. I dare say it's not impossible, but developing a new branch of social science (emphasis on the science) in the heat of an epidemic isn't going to be straightforward. 

 wintertree 15 Sep 2021
In reply to Jon Read:

I think you're interpreting a different kind of analysis to what I was thinking off - and I agree with your comments as applied to what you're interpreting.  I'm thinking of much simpler stuff that seeks to understand some of the causality but by no means all.  Low hanging fruit, basically.

I agree that many of the factors affecting causality come under social science but some of the stuff in the data was there at the time with regards this grab bag and other moments if only the right questions were asked of the data…

  • Football - that had a really strong change in the gender signal of cases during the rising phase; i didn’t look until I was scratching my head saying “why the sudden fall in cases?” - if that had been studied in real time it would have clued the modellers up that something was highly anomalous about the rising phase in July they were baselining from.
  • Weather - short term links between temperature and case exponential rate can be seen pretty well I think in terms of phenomenology.  Not so much epidemiologically understood.
  • The variant spread from Kent - this was strongly detectable from the geographic cases data.  Again, I only asked the question after a variant was put on the public table, but this is another question that can be asked in real time from cases giving a lower latency to detection than from sequencing (if present).   (The question to be asked doesn’t need a candidate epicentre)

Who knows what other gold mines there are in this data that aren’t really being systematically analysed, in terms of understanding the present better.  They get picked in to after an event, but could a lot of this stuff be turned in to real time warnings that something is changing and needs to be understood?

Basically analysis of the data to better understand the present, and particularly to look for anomalies that may not be understandable at the time, but that indicate things are changing tack and to be more cautious about baselining modelling etc.

I think there’s something of an asymmetry between the involvement of people beyond PHE in modelling vs looking for insight in the data, and I think there’s a lot of low hanging fruit in the data that falls well short of what you suggest (which I agree is not something that could be cobbled together during a pandemic!), but that has a lot of value.

Post edited at 10:11
 Offwidth 15 Sep 2021
In reply to wintertree:

The first six minutes of More or Less pick up on the NIMS vs ONS denominator issue on the Public Health England Table (including that although PHE have added a warning to the report they have done anything to the highly misleading data in their table) . James Ward guests this discussion.

https://www.bbc.co.uk/programmes/m000zkzq

 wintertree 15 Sep 2021
In reply to thread:

Updated rate constant plots including the English regional one.  The decay of top level cases is holding up for a 6th day running...

Plot 18 is really interesting - it looks like hospitalisations and deaths have already turned to  decay a few days ago in most regions - far too soon compared to cases for the typical lag...  

What's going on?

  •  I'm almost convinced true infections have been in week-on-week decay since August 24th, and that the positive plateau in rate constants around the turn of the month in to September is caused by the switch-on of additional testing picking up a larger fraction of infections as cases, and so does not represent a rise in infections.  
    • This "false plateau" is encircled in red on the annotated plot.
    • Supporting: The plateau region breaks the usual passband weather link
    • Supporting: Tests/day changes a lot in this period
    • Supporting: The timing of the turn to fall in admissions and deaths in most regions
  • Using the highly scientific method of running a flexible edge through the 'x' marks on the rate constants for cases, excluding the anomalous plateau and the bank holiday anomaly, a nice curve showing an accelerating decay (exponentially speaking) emerges.
    • 'x' marks added in red sharpie to show where I think the constant for infections might fall
  • The timing of the turn to decay for hospitalisations and deaths is a lot more normal for a turn to decaying cases in late August than for a week ago.

It'll be really interesting to see how plot 9 looks by Saturday's update.  

Wouldn't it be great if it turns out that infection has been decreasing for 24 days and there's a corresponding amount of slack lining up for the hospitals.

In reply to Offwidth:

> The first six minutes of More or Less pick up on the NIMS vs ONS denominator issue on the Public Health England Table (including that although PHE have added a warning to the report they have done anything to the highly misleading data in their table) . James Ward guests this discussion.

Thanks for the link.  Great to see James Ward elevating to fame over his work.  Embarrassing that it's falling to hobby scientists on Twitter (*) to drive understanding of this issue...

(*) - not meant as a put down by any means!

In reply to minimike:

> Bilberry

You were the closest - blackberry ice cream.  Minor incompetence on my end led to ice crystals forming in it, but still very tasty.  Compliment to an apple meringue pie.

Post edited at 16:42

In reply to wintertree:

Surely a demographic effect, like you say. Established decay in the hospitalisation age cases? [scrolsl back to look at demographic plots...]

> Embarrassing that it's falling to hobby scientists on Twitter (*) to drive understanding of this issue...

"I see the Telegraph has upgraded me from an "amateur" (July) to an "analyst" (September). Or possibly they're just working their way through the dictionary." - Paul Mainwood

Post edited at 16:48
 wintertree 15 Sep 2021
In reply to Longsufferingropeholder:

> Surely a demographic effect, like you say. Established decay in the hospitalisation age cases? [scrolsl back to look at demographic plots...]

This is probably the best plot [1].  From that and from the English D1.c I don't think past demographics could have led to falling deaths and hospitalisations now, unless the plateau in the 15+ band in the linked post is down to increased detection of infections as cases, rather than plateauing case numbers.  If cases in under 15s continue rising against falling cases in older people that would lead to hospital admissions to start falling against a background of rising top level cases in another week or so, but it's probably not a factor in the falls we're already seeing.

> "I see the Telegraph has upgraded me from an "amateur" (July) to an "analyst" (September). Or possibly they're just working their way through the dictionary." - Paul Mainwood

Nice.  I often think the term amateur is abused; the distinction is over motivation (hobby/interest vs professional/paid) and not the level of ability.  Which is why I haven't referred to That Table as "amateur hour at PHE".  It would be unfair to amateurs.

Edit: Lots of good stuff on Mainwood's twitter over the Valneva situation.  I really feel for the people on their clinical trials - inexplicable mixed messaging for people who've volunteered themselves.  

[1] https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_43-739033?v=1#x9517699

Post edited at 17:07
In reply to wintertree:

I think that's compatible.... the switch on of testing, decay in middle-aged to older people, shorter hospital stays (because there's no reason not to expect weather to affects severity/length of stay too. Discuss.), it's borderline long enough ago to start to show through, but could be grasping a bit.

 oureed 15 Sep 2021
In reply to Longsufferingropeholder:

>  it's not impossible that there's a small but finite chance you might even be better off unvaccinated for certain initial conditions. It's just insanely unfathomable.

It's only insanely unfathomable on a UKC Covid thread. Elsewhere it's just another somewhat plausible hypothesis. People from places starting with B have been considering this a possibility for some time.

 Misha 15 Sep 2021
In reply to wintertree:

Your explanation for the temporary rise in rate constants seems very plausible. The Scottish curve is different but there the equivalent switch on coincided with (caused) the peak and perhaps wasn’t as pronounced due to more office workers (non parents) staying at home after the schools had gone back compared to England (as the schools went back in mid August, so still in the traditional holiday season (edit - however I may be completely wrong as I’ve no idea whether the traditional holiday season in Scotland actually ends in mid August, plus people without children in England go on holiday in September, plus holidays are all over the place this year anyway, plus lots of people are still WFH, so may be just ignore this bit!). 

Post edited at 22:48
In reply to neilh:

> I would not expect anything else from you...the " its  dodgy Tory and SNP is perfect  bias".......I will just wait for more info and see what spills out.

Jesus wept.  Even I wouldn't have believed this one.  Javid will be lucky if Valneva do not sue.

youtube.com/watch?v=ZAI_TiQZCdU&

 wintertree 16:37 Thu
In reply to thread:

Cases for England and Scotland have now been in decay for 7 days by a week-on-week method.

As I said yesterday, I think infections in England have probably been in decay for over 3 weeks, with a masking effect from the switch-on of a bunch more testing associated with the return of schools, meaning that more infections are now being detected as cases.  No robust proof on that, just a bunch of observations and a hunch.  With the masking effect gone I'd expect the temperature anti-correlation to re-assert itself over these plots, meaning we're expecting to see rising rate constants over the coming 4 days; England looks low enough to hold in decay despite this, Scotland - not so much.  More hints of decay in the hospitalisation and deaths data for England, again suggesting the decay in infections has been more sustained than just the last 7 days of cases data...

In reply to tom_in_edinburgh:

> Jesus wept.  Even I wouldn't have believed this one.  Javid will be lucky if Valneva do not sue.

As clearly stated as the case in that video was, I don't think it adds anything to where we were yesterday.  I also think it is making a wrong assumption that phase 3 results are the only thing that MHRA have to approve to result in the vaccine going in to arms.  There are other possibilities.  

I repeat what I said - this smells very fishy, and I think in particular the minister's comments are disrespectful for those in the trial cohort.  That's not the only issue I have with the comments in terms of professionalism and potentially prejudicing all vaccine providers from entering into future contracts.

But... Now isn't the time to jump to conclusions based on what's currently been said in public by both sides.

Post edited at 16:40

 elsewhere 17:36 Thu
In reply to wintertree:

https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_43-739033?v=1#x9518611

The latest Scotland update directly above doesn't look right and within the figure/image it says Wales.

Post edited at 17:37
 wintertree 17:48 Thu
In reply to elsewhere:

> The latest Scotland update directly above doesn't look right and within the figure/image it says Wales.

Thanks for pointing that out! I should have engaged my brain a lot more there...   

Dragged and dropped the wrong image.  Decay in Scotland is looking reassuringly deep (cf Wales, above) so even if there is an upwards pivot with colder days ahead hopefully it stays in decay.


 Si dH 19:50 Thu
In reply to wintertree:

Thanks for the update, data looks very promising.

I just don't get the Javid thing. Am I remembering correctly that he told the press it was down to Valneva breaking some part of the supply agreement, but then said in Parliament that the MHRA wouldn't have approved it (the bit disputed in the video)? Normally politicians will say all sorts of stuff to the Press, but how many people watch BBC parliament?  I just can't understand why, if he wanted to make something up to make him look better in some way, he would do it in parliament having not done so to the press. If the other way around, sure, that would be classic fake news tactics.

So my hunch is there is still more to it.

In reply to Si dH:

> I just don't get the Javid thing. Am I remembering correctly that he told the press it was down to Valneva breaking some part of the supply agreement, but then said in Parliament that the MHRA wouldn't have approved it (the bit disputed in the video)? Normally politicians will say all sorts of stuff to the Press, but how many people watch BBC parliament?  I just can't understand why, if he wanted to make something up to make him look better in some way, he would do it in parliament having not done so to the press. 

Three possible explanations:

a. he's a pathological liar and when confronted reinforces his position by making stuff up without thinking about it

b. he's an egotistical tw*t who misremembered something he'd heard in a meeting and when he was challenged went off piste and talked sh*te 

c. it was a considered and intentional lie, as smokescreen for cancelling the order to save money and he did it in parliament because parliamentary privilege makes it harder to sue.

Post edited at 20:48
 wintertree 21:10 Thu
In reply to Si dH:

> Thanks for the update, data looks very promising.

It had better keep going that way too, if I'm going to pack this in with #52.

>  Am I remembering correctly that he told the press it was down to Valneva breaking some part of the supply agreement, but then said in Parliament that the MHRA wouldn't have approved it (the bit disputed in the video)?

That's my take.

> So my hunch is there is still more to it.

I just can't get my head around it.  Perhaps the case for Javid having effectively made this up is not as strong as  it first seems, although I do note TiE's observation over parliamentary privilege...

The assumption Hannah Bardell MP appears to have jumped to (letter to the government on her twitter [1] as well as TiE's video link) is that this is pre-empting findings from the blind phase 3 clinical trials.

  • I think it is possible that Javid was referring to an MHRA authorisation unrelated to the clinical trials, although if this was the case such a road block should not be fundamental at all.

The MP notes the trial has not been unblinded with the inference that it's too soon to tell if there's a problem

  • However, there is an open component to the trial - quote from [2] "In addition, approximately 1000 subjects aged 18-29 years will participate in this study in a non-randomized, open-label fashion to receive VLA2001." With the immune response to the AZ vaccine being well measured, comparisons can probably be made before the unblinding without resorting to cowboy levels of inference from the data.

But....

  • If this data from the open component was behind what Javid said, it's hard to see how that data could be firm enough to drop the order but not firm enough to foreshorten the trial on ethical grounds, and it's hard to understand Valneva's statements and their entering in to EU negotiations in the context of such a finding. 
  • The value in Valneva IMO is not in it's "virgin immunogenicity" that this trial is aiming to measure, as we're almost all vaccinated now, and we've got an established method with two vaccines already for anyone else who wants it.  It wouldn't be unexpected if the inactivated virus vaccine is less immunogenic than AZ and Pfizer vaccines when given as the first two doses, but...
    • It may prove to be more potent as a 3rd "booster" dose.  It's involved in a separate trial for that [3]
    • It has a somewhat hard to pin down (in advance) potential to be more "variant proof".

A general observation is that we're moving ahead with boosters now, and we have data from home and abroad on the already authorised vaccines from AZ, Pfizer and Moderna now and so there seems to be no role for Valneva in our plan for now.  Much the same could be said for Novovax, which also has a UK plant under construction on Teeside as well as the bottling operation in Barnard Castle.   Perhaps they have better contract lawyers...

I really hope that Javid's comments don't derail the cov-compare or cov-boost trials, as the Valneva vaccine seems like it has an important role to play especially if some of the more bogeyman possibilities for mutation/recombination emerge.  More generally, if we want the UK to continue to grow as a knowledge economy, stuff like this over clinical trials could be disastrous.

Sorry; slightly incoherent set of thoughts - I don't think the issue is as binary as it's being presented; I also struggle to find much trust or time for Javid right now given the rank unprofessionalism of dropping that bomb as he did, and as TiE notes it's the MHRA comment that falls under the protection of parliamentary privilege.

I hope some clarity emerges soon, this whole situation stinks, and it seems to me no way for us to conduct ourselves.

[1] https://twitter.com/HannahB4LiviMP/status/1438533258879410176

[2] https://www.clinicaltrials.gov/ct2/show/NCT04864561

[3] https://www.covboost.org.uk/about

Post edited at 21:33
In reply to Si dH:

> So my hunch is there is still more to it.

There definitely is because it doesn't add up. The only thing that's not been said already here is that the phase 2 results were meh*, so sticking with my 50p bet it turns out to be efficacy. But nobody should know that yet if (that's a big if) none of the data got unblinded yet. Not sure how binary that process is. Suspect it's not all or nothing, but I don't know. Someone somewhere probably knows something preliminary about how well it's working. Good point about parliamentary privilege, Tom.

* Relatively. In absolute terms, great, but we're spoilt now.

In reply to tom_in_edinburgh:

> he did it in parliament because parliamentary privilege makes it harder to sue

That used to be balanced out by considerable censure for lying to the House. But those days seem to be long gone, and lying to the House goes unremarked and unpunished.

 Misha 22:03 Thu
In reply to wintertree:

Thanks. Interesting question to what extent cases are rising in U16s and then to what extent they translates into cases in their parents. I was fully expecting cases to be rising again so happy to have been proved wrong but don’t think we’re out of the woods yet. 

In reply to captain paranoia:

Not clear to me whether it's a lie or something true that he really really shouldn't have made public. Kinda think it's the latter.

In reply to wintertree:

> > Thanks for the update, data looks very promising.

> It had better keep going that way too, if I'm going to pack this in with #52.

Hmm, we shall have to see about that; your threads have become a way of life. Perhaps you could switch to Friday night what-is-this-waterfall plotting, or similar, rather than packing in altogether.

 wintertree 07:59 Fri
In reply to Misha:

> Interesting question to what extent cases are rising in U16s and then to what extent they translates into cases in their parents

That’s jumping to a conclusion about which side of the age barrier is driving which side…. (He says, not revealing his cards until the next thread…. To be fair they’re mostly about before schools returned).  

> but don’t think we’re out of the woods yet. 

I think we could be, but in the analogy it’s too foggy to tell.  Best keep running just in case…

In reply to longsufferingropeholder:

> none of the data got unblinded yet.

See the link in my post; 1/4th of the compound arm of the trial was not blind except to the recipients.  The control arm (AZ) is blind but has already been characterised elsewhere.  

In reply to wintertree:

> See the link in my post; 

Oh, yeah. Be that then. 50p -> a quid.

 Offwidth 13:20 Fri
 Offwidth 14:44 Fri

In reply

Latest Indie SAGE had a quite short data round-up this week with the most notable information being: a really nasty schools outbreak in Leicester (who went back 10 days early compared to most of England) ; 1/5th of critical care beds already occupied by covid patients. Slides normally link from the website by Monday.

youtube.com/watch?v=uAjNQsF0gys&

Later on in the Youtube presentation (about 15 minutes in) there is a highly critical view on the public communication of CMOs on vaccination of 12 to 15 year olds for completely understating the overall known medical benefits for teens, especially wrt long covid and subsequent permanent organ damage (when mainly just stressing the difference of their decision from the JCVI, about lack of disruption to schooling). Plus of course critical on the ongoing issues around lack of action from government on ventilation, masks and track and trace for schools. 

 Offwidth 16:14 Fri

In reply

New travel testing proposals will no longer allow fast detection of new variants of concern:

https://www.theguardian.com/world/2021/sep/17/uk-scientist-warns-relaxation-covid-travel-rules-genome-surveillance

 wintertree 16:29 Fri
In reply to Offwidth:

> when mainly just stressing the difference of their decision from the JCVI, about lack of disruption to schooling

I think I must be missing something somewhere over all this?.  The single dose that's been authorised for ages 12-15 isn't likely to make much difference to transmission, and with the current guidance for schools and PHE I don't see how a single dose vaccine is actually going to change anything, other than reducing the small number of children to become unwell.   I agree that JCVI recognised marginal health benefits and it's odd not to message on that.  

>  1/5th of critical care beds already occupied by covid patients.

Hopefully we can watch that number drop over the next 3 weeks....  Today is day no 8 in the data of week-on-week decay for cases in England and Scotland, and I reckon admissions and deaths in England have both clearly turned the corner into decay now with occupancy probably about to do so it; I really do think we've had actual new daily adult infections in decay for 3 weeks now, enough to take a serious chunk of pressure of the hospitals as that plays out.

> New travel testing proposals will no longer allow fast detection of new variants of concern:

There's not been so much talk about the sequencing lately; I'd be interested to know how samples are getting prioritised for it - e.g. breakthrough, inbound, reinfection etc.  It'll be comforting when PCR cases are low enough that they can all go for sequencing - although not as comforting as if inbound travel was still PCR based...  We've got the capacity, why not use it?

> Latest ONS data release on infections.

It's worth noting that trends in this lag dashboard cases and real infections by a couple of weeks as it shows "live" infections which blurs shape in the new infections/day curve forwards in time by the duration of infection.  

Post edited at 16:43
 Offwidth 16:44 Fri
In reply to wintertree:

I agree with your current trends but this new Leicester school age outbreak has dented my optimism short term. I can easily see a bit of up and down in case levels for a month or so yet and potentially serious problems if school peaks spread out to older relatives, increasingly relaxing their precautionary behaviour as our government pumps out bs good news.

In reply to tom_in_edinburgh:

Well that is normal commercial practise these day anyway, it would be almost disappointing if they did not.

Lets see if Valneva gets approved in other countries before we jump down everyone's throats.That is probably the more realistic  guide.

 kirsten 18:39 Fri
In reply to Offwidth:

> In reply

> New travel testing proposals will no longer allow fast detection of new variants of concern:

I wonder how many they were really picking up though, given the negative test requirement before departure. As for that, there was at least some comfort that everyone on the plane/boat had tested negative. 

Post edited at 18:40
In reply to kirsten:

The positive tests will still have occurred though. Those people will no longer be travelling. But the results of their tests will still be available for sequencing.

 wintertree 19:17 Fri
In reply to Offwidth:

> I can easily see a bit of up and down in case levels for a month or so yet and potentially serious problems if school peaks spread out to older relatives

Always with the negative waves, Moriarty.  Schools haven't apparently driven cases in adults in bulk in Scotland, so we just might see sustained decay.  

> increasingly relaxing their precautionary behaviour as our government pumps out bs good news.

I was very disappointed to hear more prattling on about hand washing in the soundbites coming out of government over the latest dropping of restrictions, and not one utterance of "ventilation".  In terms of children driving cases in adults or vice-versa, schools are at least supposed to be ventilating and there are systems in place for this.  Private houses - not so much, and as we go in to winter, children are going to spend > 3x as long in poorly ventilated houses with their relatives as in schools.  

The busses though.  The situation with the ventilator windows on the busses I see is a joke.  Weld them open.

Latest ONS antibody survey its out

https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19latestinsights/antibodies

  • 93.6% with antibodies estimated for adults in England.
  • Data on antibodies exclusively from infection not from current vaccines - about one third of teachers have antibodies from infection
  • The section "Antibodies by age" is very, very interesting.
    • Ages 16-24 shows naturally acquired antibodies surging ahead of vaccination.  A shame there isn't data for <16.
    • Ages 65-79 show antibodies decreasing slightly in the months after vaccination - but remember there's a lot more to immune persistence than antibodies - e.g. T-cells, and memory B and T cells.
  • I haven't dived in to the details of their methodology, but as a random sampling survey, the inference over very small percentages without antibodies shouldn't be biassed by the issue of unknown population sizes....?

In reply to various over Allan McNally's comments on inbound testing in the article Offwidth linked:

As I understand it, they're replacing PCR in these cases with LFT; PCR goes to a central lab for processing and the output of the PCR process will be what goes for sequencing.  LFTs are not centrally collected/analysed and don't amplify the DNA as needed for sequencing.

 Si dH 19:43 Fri
In reply to Offwidth:

Leicester and Leicestershire both have high cases generally in a number of places for some reason. It's not mostly school outbreaks and they have been at those high levels for a while. It would be utterly absurd to postulate a causal link to the local hospitalisation levels from a school outbreak in the last week or two - if Indie SAGE implied that (the message I got from your post - apologies if I misunderstood) then it can only be for political reasons because it's way off the mark.

Post edited at 19:44
 Offwidth 09:43 Sat
In reply to Si dH:

I keep an eye on the overall local numbers and this is something new as I didn't know the age profile before (plus their data is all in pdfs which take more work that the Notts interactive graphs). Leicester have had a very tough pandemic and deserve a bit of  luck.

Overall SAGE seem to me to be the more pessimistic in their case predictions right now.

Indie SAGE in the headline numbers only raised concern about rapid case increases in school ages and that Leicester were the earliest to go back; the slides are up early this week so have a look:

https://www.independentsage.org/wp-content/uploads/2021/09/WeeklySlides_17September2021.pdf

Post edited at 09:53
 Offwidth 10:07 Sat
In reply to wintertree:

Dented optimism short term and worried about a few more ups and downs in case numbers due to school (or Uni) infections isn't the same as pessimism. I'm more worried about age demographic spread in England for good reasons: of much poorer public health messaging, lower restrictions and being about a month later into shifting behaviour at a time when reportedly about a fifth of English hopitals are at OPEL 4, so with no capacity.... I'm not expecting a massive shift but there are a lot of vulnerable people even in a small percentage and not much wiggle room to deal with increases. Scotland is pretty close to the limit of what they can cope with in hospitals.

Post edited at 10:18

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