UKH

Post 1 - Four Nations Plots

Thread #48.  I’ve often felt a year should have 48 weeks in it, but short of changing the rotation rate of the Earth it’s never going to make much sense. 

I’m going to quickly rattle through the plots this week, then end on some interpretation that’s even more speculative and wooly than normal.

The four nations plots show England having the strongest growth of case and Scotland the strongest decay.  There’s some coherence returning between these two nations although that’s much clearer in the week-on-week rate constant plots (in a later post) than the cases.  Probably some important lessons in where things are similar and where things are different.

Link to previous thread: https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_47-...

Post 2 - England I

Plot 9e shows two significant period of growth recently in cases, in the form of two positive valued peaks in the cases rate constant.

• The first one is centred around September 18 is when growth in school aged cases really broke through and also apparently started downstream adult cases (presumably household infections).  This is what I think is driving current hospitalisations; these have a much lower growth rate constant (longer doubling time) which we;’d expect given the unprecedented demographic shift of cases then towards school aged children.
• The second one is ongoing and is not such good news; the next post will look at the demographics which are shifting to older ages, and the interpretation at the end returns to what it might all mean.
  • Although there was a gap between the two periods of rising cases, the variability between individuals will probably blur this out in the hospitalisations data so that we see continued growth 

With rising hospital admissions in plot 7.1e comes rising occupancy in plot 7.2e; for now the deaths in plot 8e are still decreasing - just; we’ll see where that ends up as the new rise in cases plays out.  Still, fast changes in therapeutics with one MAB treatment recently having gone live in the UK, a separate MAB cocktail going for approvals in the US and the Merck anti-viral going for approvals in the US.

Post 3 - England II

The week-on-week rate constant plot shows that we’re back in to significant growth with now almost two weeks’ of data showing week-on-week growth in cases.  It’s a slow doubling time, but applied to such a high baseline number of cases it still means a lot of real world growth.  We’ve had 3 recent periods of significant growth in cases, which I’ve labelled; they are all quite different to each other I think.

• (a) I think this was mostly the switch-on of testing associated with schools
• (b) This is where rising cases from school related transmission broke through the masking effect of falling cases from everything else (including those induced in children from adults in their household, following adult cases turning to decay earlier on), and then the capacity for growth ran out in the school demographic
• (c)  This is the highest pucker-factor period of growth recently; plot D1.c shows that in exponential terms, this growth is concentrated in older adults where to date there’s been a lot more hospitalisation potential.  If it plays out for much longer it’ll shift the demographic of cases back towards that more vulnerable end of the range.  There’s no real lag between different ages unlike the summer holidays (adults leading children) and the schools peak (children leading adults); it’s also coincident with a similar growth spurt in Scotland and some really crap weather.  I return to this in the interpretation post.

There’s lots going on in plot D1.c; I talked about it more at the end of the last thread here - https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_47-...

Plot 18 shows the return to growth is pretty synchronous across England; a couple of stand out high values in the provisional leading edge, if they don't fade as more data comes in that becomes noteworthy.

Post 4 - Scotland I

Everything continues to fall in Scotland, but the decay of cases had a blip with very slight growth for a few days coincident with the centre of growth peak (c) in the English data.  Again, this feels to me like a weather effect.  Looks like Scotland is also slowly heading for general growth however.

It’s interesting that’s Scotland is remaining in decay for cases and England isn’t.   It’s tempting to jump to the obvious conclusion about the effects of mandatory mask wearing in public places, isn’t it…

Occupancy continues to fall very slowly vs admissions compared to England.  

Post 5 - Scotland II

I’ve put the Scottish and English week-on-week method rate constant plots in so you can flick-book between them (on a computer anyhow, using the arrow keys) to see how the raised rate constants happen at the same time as peak (c) for England.  Scotland has better decay so it took them in to growth for less time, but nonetheless the rate constants are drifting towards growth.

 It seems to me that now symmetry breakers like the football and the different school start dates are in the past, their rate constants are converging in terms of behaviour.

As with England, the D1.c plot shows the growth to be concentrated in older people (brightest orange in older ages on the far right of the rate constant plot).

Post 6 - Verbose Waffle 

It’s been getting harder and harder to produce an interpretation that is consistent and that isn’t making an endless serious of wild suppositions in the dark - the complexity of the situation has exploded as vaccination and past infections raise immune and time chips away at it, and the data easily available doesn’t capture this.

So, out on a real limb here. 

It seems to me like the last two months have been a good time - Covid hasn’t really wanted to spread with R>1 except where we’ve had specific things that give it an extra helping shove, like the football, schools returning along with downstream household infection and so on, or nightclubs reopening in Scotland (football covered that in England, I think). Much of the infection in this period has been in young adults and children, and the reflects in the stand-out low ratio of detected cases to deaths in the UK vs comparator nations (our recent case fatality rate).  This suggests to me that what has been driving cases has largely been the filling in of the gaps in vaccination.

Against this is a very slow but measurable fade in immunity particularly in older people; immunity is not a binary thing, and the normal order of things is that protection against catching something fades comparatively sooner than immunity against a serious health clobbering  if it’s caught - and we know Delta has lowered the barrier to individuals catching the virus, particularly in older folks, but that the variant has not compromised protection from severe illness.

Now we seem to have run out of ways to “encourage” (*) Covid to spread in the young

• The football spike collapsed back down with the end of the football
• The schools growth collapsed back down despite terms continuing in data both in England and Scotland
• There is no sign of university associated outbreaks in the top level data
  • Third time lucky for HE? Ironically the first time outbreaks within universities wouldn't' represent such a high risk to the communities around them.
• Regions of high growth in young adults almost look to be leaving “shadows” in the rate constants going forwards.

So, the appetite for growth in presumably unvaccinated younger adults is gone.  Before winter.  That’s probably a good thing.

(* - I use the term "encourage" loosely as different people have very different views, and there’s an elephant or two in the room here blocking view of the real government policy, whatever that may be)

Then, really crap weather came.  The sort that sees me putting my shorts away before December, people closing their windows and doing all socialising inside.  The kind that has me out in my 25 year old wax jacket with a shovel desperately repairing the drainage in the lower field at 11 pm.

Seasonality.  Perhaps this is why we’re now seeing cases grow significantly in adults over 55 for the first time since the football. I've a true believer in the link between weather and the rate constants for cases - I can make a solid, statistically bounded case for the link over the timescales of a few weeks; that's not to the mechanisms behind this  don't also have effects over longer time scales, just that the conflating factors pile up and analysis becomes less trivial - but it's increasingly emerging from careful studies done by actual epidemiologists for other diseases. 

Given vaccine uptake rates in these older ages, case rates over the summer and the ONS antibody surveys, and the previous lack of appetite for growth…  Is this the start of seasonally compressed spread of post-immunity infection?  If so, it marks another step in our journey towards the end game.  The rise in cases in older adults clearly presents a risk to healthcare, but if (big if - and I’m hoping someone is going to test it against some of the SAGE documents as they filter through) we are seeing a move to post vaccination breakthrough infections allowing R>1 with seasonal effects, we expect the hospitalisation rate to be quite a bit lower than in earlier periods where R>1 was sustained in the unvaccinated.   

This is a lot of supposition from me however, and if I was in charge I wouldn’t want to bet the house on it.  I’d want analyses of cases by age and vaccination status, and I’d want longitudinal case > hospitalisation conversion rates also by age and vaccination status.  It’s long been maddening that there’s all sorts of data that seems critical to understanding the situation, that can be extracted from the healthcare records, and that doesn’t seem to flow - to the point that the “connected” academic groups submitting modelling to SAGE also seem to be trying to work around lack of access to suitably anonymised longitudinal data.

Speaking of seasonality, the US GFS models are starting to forecast several periods of snow for the Cairngorm plateau in the next couple of weeks, and the very end of October is shaping up for the first snow in the North Pennies.   There have been signs for a few weeks that the polar vortex could be weakening…

Post 7:

It's been ages since I posted any case fatality rate plots.  

I made a new one using data from "Ourworldindata" for us and a few of our neighbours.  This is a near-instantaneous CFR, measured using 7-day rolling averages on the input cases and deaths time series, then with a 7-day rolling average on the output for good measure.

The shading represents the range spanned by CFRs measured for 7-, 14-, 21- and 28-day lags between cases and deaths.  The idea behind this is that the "real" or longitudinally derived CFR almost certainly falls within the shaded regions.

To understand this a bit, deaths data is likely to be highly reliable in terms of detection of Covid in all nations shown.  The relationship between cases and true infections varies widely I think however, and there are demographic differences in the distribution of cases.  Both these two factors lead to dramatically different CFRs between the nations.  The takeaway from this is that by extension the case rates of different nations are by no means comparable at all.

This plot is what I refer to in post 6 when I state "the stand-out low ratio of detected cases to deaths in the UK vs comparator nations"

Coarse interoperation might be that when somewhere's CFR is more than 1% they're almost certainly not detecting all infections as cases, and where it's much less than 1%, the spread of cases is mostly in the younger and the vaccinated.

I have no idea what was going on in Germany in late June, it looks like they more or less stopped testing for Covid and at one point had the same death rate as the UK but a 50 times lower case rate.  If anyone can enlighten me, I'd be most grateful.

Thanks again for all this work.

The same thing happened to Germany at the beginning of 2021 as I've linked on last week's  thread (to keep the discussion tidier).

Why 'running hot' is serious right now:

https://www.theguardian.com/uk-news/2021/oct/16/ae-crisis-leaves-patients-w...

Things will likely only get worse as we move into winter. I really feel for the staff having to deal with this level of pressure.

But Brexit is giving the NHS an extra £350m per week! We are living in the land of milk and honey! This must all be lies!

I would be interested to know how much of the pressure is directly Covid patients and how much is other conditions which haven't been dealt with due to Covid pressures or lack of access to GPs etc. 

Indeed, and dysfunction from the pressure itself has drastic resource consumption in some cases that makes provision worse again.  The levels of burn out in staff that must be building up behind the scenes is terrifying to think about.

Covid may not be the immediate root of all the problems, but it is one whose pressure can be controlled in the short term.  The ~30% reduction in admissions and occupancy (now rising again) over the last two months doesn’t seem to have reduced the number of news reports on overload coming out.

It seems counter intuitive that the situation with covid is so much better than last year and yet we’re hitting the same problems; I know the same is happening in other sectors and it worries me a lot that what they have in common appears to be running on the good will of the front line people, and that good will is being replaced with exhaustion and increasing resentment.   Worse in healthcare though because delaying almost anything leads to a net total increase in work to be done.

A tense month ahead, I’m hoping for government to go very soon for the low hanging control measures such as masks in public, and some clearer messaging on the risks for older and more vulnerable people.  

Indeed. 

I also hope we will soon start to see the effects of the boosters kicking in. 

I also wonder how much this stinking cold which is going around will hit those most vulnerable too. My husband and I have both just had it (PCR tested negative for both of us) as have many of our friends. Given that we still have masks in Scotland and my husband and I still don't really socialise indoors, I'm not even really sure where we got it! It wiped us out enough that I could imagine it causing more serious infections in elderly etc.

With no evidence, I wonder whether colds are perhaps just a bit more frequent and a bit worse than usual for some people this year because very few people had them last winter? There is always lots going around in the autumn.

Re: hospital pressure. Only a single case, but I spent a week in and out of Liverpool Women's Hospital the other week as our new arrival came along and had an infection, so had to stay in for a while. No covid patients in this hospital and no issue with inability to discharge people to social care (which I saw reported the other day is currently a problem almost as big as covid for some hospitals, due to lack of social care staff.)  I believe most of the staff are specialised (midwives, pediatricians etc) so presumably not being redeployed. Presumably there are some staff impacted by isolation requirements but rates are not sky high round here so I would have thought this would be an annoyance rather than a huge problem.  The only other pandemic impact should have been the measures to prevent transmission, which were really quite mild. Masks, sanitizer, limits on visitors and keeping single maternity rooms free in case someone tested positive and needed isolating - I think that was about it. So, if all the NHS's problems were due to covid, the place should have been running smoothly. Yet, they were seemingly run ragged. Almost every midwife we saw complained of staff shortages and some days there were so few around that my wife only saw the student midwife in her ward all day. So it seems to me that covid is perhaps no longer the root cause of NHS pressure in many places and what we need is the underlying state to be sorted out.

Indeed. One of the ‘successes’ of this government is managing to spin the story that the NHS problems stem from a pandemic rather than decades of underinvestment, restructuring and toxic competition in a closed market, leading to degraded pay, working conditions and morale. Add brexit and our current ‘cold welcome’ immigration policy..

I'm not sure that's entirely the case in terms of current news or the government wouldn't be pushing NHS comms to avoid bad news getting out or getting at GPs on face to face appointments, as a distraction. I think they are terrified of the politics of NHS pressures spiling over this winter.

Its pretty obvious covid is only part of the problem, but the combination of infection control measures, staff isolating as contacts or off with covid, and fairly high covid hospitalisations, at a time of severe pressure isn't helping. Many of the staff have been through hell and pressures won't calm down now for months even if covid slowly declines.

Here are some graphs from the last four weekly vaccine surveillance reports showing the number of positive cases in unvaccinated and fully vaccinated people. These use NIMS population data, which as previously discussed probably significantly over-estimates the total UK population and therefore the number of unvaccinated people in the UK, which makes the case rates for unvaccinated people and underestimate. However, any observable trends with time should be reliable, I think.

There is an observable trend towards an increased proportion of (adult) cases being in vaccinated people. This was also the case a few months ago in the data that is reported for Delta in the technical variant reports, but then it was easy to postulate that the trend was just down to increasing proportion of the population being fully vaccinated; I don't think that's the case now for anyone over 30. One obvious potential root cause would be waning immunity. Are there others? Worth a think. Edit: one is that more and more unvaccinated people have now got some immunity from infection.

I will also have a quick look at the equivalent graphs for hospitalisations and deaths.

Edit - I would say there is a similar trend inboth hospitalisations and deaths for over 80s (is, an increasing proportion of them are double vaccinated), but any trend in other age groups is too small to see by eye.

on the potential impact of masks in Scotland driving differences between case rates with England - how good do you think public observation is in Scotland now? I’m not long back from my first trip up since the pandemic began and I was not really bowled away by the difference in mask wearing on public transport between England and Scotland, and certainly apart from staff masks not very evident in pubs (but n=1 on that front)

(excellent trip, sleeper to crianlarich then on to falls of Cruachan, two sunkist days walking north and east from there, then two wet and rainy days, a night in a bothy, and some fun nav in the clag. Lost my new water bottle)

I think masks are also required indoors in Wales, where rates remain the highest in the UK. The relative improvement in Scotland compared to England is more recent than when the difference in masks regs came about. The Scottish rates are still not that much lower (lower 300s rather than upper 300s - it's not night and day. Rates in London remain significantly lower than the Scottish average - low 200s.) So, I am sceptical whether the mask rules are actually making much difference.

In reply

Mixed messages on vaccination safety for pregnant women still causing problems:

https://www.theguardian.com/society/2021/oct/17/pregnant-women-at-risk-from...

I like your new case fatality rate graph. Any interest in doing the same for regions/home nations of the UK? I ask because I have long been puzzled by cases v deaths data during the last winter: England, Wales and Northern Ireland all had similarly high case rates in comparison to Scotland. England and Wales had correspondingly higher death rates than Scotland - nothing to explain there (except the cause of lower case rates in Scotland). However, despite having much higher cases, Northern Ireland had death rates that were very similar to those of Scotland. (Travelling tabby illustrates this pretty well).

The most obvious explanation would be higher levels of testing in NI than elsewhere in the UK during that winter, but my half-arsed exploration of the testing data did not seem to support this hypothesis (although potentially complex and unstable relationships between infection rate and testing rate makes this non-simple). This leaves the possibilities of different demographic case-distribution in NI that winter (but why?....another graph for a rainy day perhaps?) or better health outcomes/lower mortality within a given demographic in NI (again, why?). Some impact from differing initial vaccination strategy is not impossible, but not convincing as the effect is visible as early as Oct 2020. Any other possible and vaguely plausible explanations I've missed?

A CFR graph won't provide any answers in terms of selecting between competing hypotheses, but it might help focus the questions by revealing other anomolous periods. Any readers from Northern Ireland with any insight?

Thanks; I was really chuffed with the way the plot worked out for comparison of different places; it's not so great for looking within the UK as the differences aren't so large.

it was very quick to switch the plot to the four nations dataset; it'll take longer to do it regionally so that's a rainy day job (I'm more interested in doing it for a single nation by demographic - that I think would be very interesting but is also a rainy day job - then again the rainy day list is quite large given my general sense of impending chaos over basically everything this winter...)

In terms of your observations, my take:

• October 2020 - yes, NI has a stand-out good CFR vs a stand-out bad one for Scotland [*] - at this point the behaviour of cases and deaths is such that the lag almost drops out of CFR measurements, indicated by the colour streams being very tight.
• Coming in to November/December, the conflation from changing behaviours and uncertainty over the measurement lag grows a lot, but Scotland still stands out as high vs Wales as low, with England and NI somewhere in the middle.

> A CFR graph won't provide any answers in terms of selecting between competing hypotheses, but it might help focus the questions by revealing other anomolous periods.

I totally agree with this take, hence my annotation [*] marked above and commented on below.  In terms of other anomalous periods - April/May 2021 for Wales stands out.

[*] - To anyone reading this and preparing to launch in to a political defence of the motherland, this is a discussion about periods where the data is not apparently suitable for comparison between the nations, and is a sign that a deeper dive is needed in to the data to understand what's going on, it is not a criticism of the policy or competence of the Scottish government when it comes to controlling the virus vs the policy or competence of those in Westminster.  

Demographic effects are the obvious go-to source of differences between nations; if there is a source of Scottish demographic deaths data someone can point me to I can do the analysis for Scotland and England based on a couple of narrow age bands, which would bring some clarity.  Likewise, if there's demographic data for Wales or NI anyone can point me too...  If these differences persist in limited age ranges, it becomes more interesting.

A lot more clarity would be here if the instantaneous CFR was computed and published from longitudinal health records by age and vaccination status.  I'm mystified as to why this isn't done and published, or if it is as to how my google-fu has missed it.

Thanks for extracting those plots.  

Lots of complexity in interpreting them and some bit pratfalls, but as you infer (I think) much of that should drop out of relative change over time between the vaccinated and unvaccinated cohorts in the older age bands where vaccination status is not changing much.  

Lots to think about - I wonder how much behavioural loop closing their is from being vaccinated vs unvaccinated especially in older ages?  Also, I wonder how much past infection status has affected the decision to decline vaccination in the oldest ages?  So much stuff I can think of in basically any direction and no obvious way to test any of it.  

Edit: In terms of cases, it's not the first time I've wondered about correlation between engagement with testing and engagement with vaccination, but no obvious reason why that would start changing over time.  Cases always have moved in mysterious ways however.

The testing rate dropped by about 40% in Germany at the start of the summer holidays and picked up again to normal levels when they finished end of August, not suprising really.

I'm interested in the number of cases and the number of deaths per 100,000, I'm not sure there's much to learn from instantaneous CFR, too hard to understand what is going on.

The interesting thing for me this week is that Scotland has got its sh*t back together in terms of absolute numbers of cases,

https://twitter.com/IndigoFast/status/1449082386889723907

It is perhaps unsurprising to have a long, sustained drop in cases after having just had a long, high wave of infection that took deaths per 100,000 in Scotland to twice the level of England.  Just like I've observed the "shadow" of recent outbreaks in the English demographic rate constant data, I suspect something similar is happening with the Scottish data.   

As is often the case, the real differences aren't in instantaneous per-capita measures as the plot you linked shows, but in the water under the bridge; and there the differences are not so large in recent months.  Both Scottish and English cases are turning more to growth; that's visible in the week-on-week rate constant plots and in the cases one you linked as a change in the gradient and curvature of the Scottish line; the demographics of the growth are also similar - in older adults who were least affected by the differently timed bursts of growth in younger adults the two nations have seen over the last few months.    

In reply to jimtitt:

Thanks.  We certainly had testing artefacts here I think from school related changes to testing so not surprising as you say.  The big spike is earlier on to just be that though I think, I'm wondering if its also an artefact of a long tail of deaths from the proceeding wave; I don't know what the cut-off for reporting is (like the 28 days criteria in the UK).

Hey, thanks very much for that wintertree - reveals aspects of the situation that were not previously clear to me - and very attractive plots too.

Can't help on the demographic data source for Scotland I'm afraid.

I may be missing something but it seems to me that CFR is going to be heavily impacted by testing rates, which are going to be different over time in the same country, as well as between different countries at any one point in time (perhaps not within the UK). IFR is a better measure but is still going to be an estimate. Changes in the IFR would reflect the lethality of the virus and improvements in healthcare. Also when deaths are low, CFR / IFR could get pretty noisy. So I’m not clear what the CFR graphs are trying to actually show.

In order to understand how good / bad the response in a particular country has been, I’d have thought it’s far better to look at deaths per 1m population, either cumulatively or over a certain period (noting that some countries have significantly undercounted deaths for various reasons). Better still, deaths per 1m / 100k for each 10 year age group.

Yes; perhaps I wasn’t clear enough.

Obviously, yes.  As I said: The relationship between cases and true infections varies widely I think however, and there are demographic differences in the distribution of cases.  

Obviously, yes.  As I said: Both these two factors lead to dramatically different CFRs between the nations.

They’re making the point I gave as the takeaway: The takeaway from this is that by extension the case rates of different nations are by no means comparable at all.

I picked a set of broadly comparable counties; with the reasonable assumptions that healthcare is similar and most deaths are well recorded, comparing CFRs shows us when we need to be careful about comparing cases between the nations as there are differences in either of both of the infection detection rates and/or the demographics.  I gave this comparison to back up my claim in an earlier post about the UK having a stand out low CFR and to hammer home they case rates aren’t fairly comparable internationally.

I addressed this point up front by explaining again that this was here as a warning over cases and not to compare how good / bad responsss have been.  […] this is a discussion about periods where the data is not apparently suitable for comparison between the nations, and is a sign that a deeper dive is needed in to the data to understand what's going on, it is not a criticism of the policy or competence of [one response vs another]

If I had been trying to compare public health outputs beteeen nations I would agree.  I was not, and I hope repeating some of my comments helps get that across.

Cases are an important measure for understanding where we are and where things are going, because whilst their relationship to infections changes constantly, they change is (usually) quite slow, so changed in cases are a good barometer of changes in infection, and they lead all other measures by weeks.  Hospitalisation data in the UK has very coarse demographics, and deaths (thankfully) tells us almost nothing about infection younger adults or children.

So, we look a lot at cases, and case rate comparisons are obviously made between different times for one place, and between different places.  The CFR is a way of understanding when comparisons of case rates is going to be misleading.  As Wicamoi said: “A CFR graph won't provide any answers in terms of selecting between competing hypotheses, but it might help focus the questions by revealing other anomolous periods”

Some reasonable assumptions can also help interpret differences between nations with comparable healthcare and vaccination status to us.  A CFR > 1% pretty much guarantees they’re stand out low testing going on, and a CFR << 1% suggests there’s a young demographic.  

So, I hope that covers everything.  I think I agree with everything you said (as usual) but I also in this instance thought I’d said if all clearly, already.

The plots hammer home the issues over cases, every issue you raise with the potential for mis interpretation of these plots stems from cases, and yet those issues are rarely at the fore of people’s minds when discussing cases I think. This is a way of getting mental gears turning on those lines and of getting some insight in to the differences.

They weren't this weekend. Or if they were nobody knew.

At the risk of throwing a cigarette butt into a recently extinguished oil well, we're finally starting to see some studies coming through and it looks like a pretty small, still worthwhile, but pretty small, effect.

 https://elischolar.library.yale.edu/cgi/viewcontent.cgi?article=2085&co...

The mask rules are effectively identical in Wales and Scotland. Mandatory in most indoor public places. There might be some difference in the details but not without spending lots of time reading. The rest of the rules are (almost?) the same too. Wales are bringing in their own covid pass next week, after Scotland just did so.

It doesn't surprise me that adherence is low; it had dropped off a lot here (England) while the rules were still in place.

Makes sense. I've always thought there must be a relatively small benefit outside of healthcare and other high risk settings (bouldering walls, haha...) where it must be significant.

Interesting thread here by LSE data scientist, John Burn-Murdoch, about the disparity between the situation in the UK and Europe, and why booster jabs are important.

https://mobile.twitter.com/jburnmurdoch/status/1449801652207239176?s=11

Really good thread that, thanks. It doesn't try to explain the CFR differences but covers all the other bases I think.

The elderly people in poverty data struck me - especially the difference with France.

JBM is great and this is up to his usual high standards.  He's an antidote to most of the media reporting on Covid - and on the human side as well as the data side.

(Edit: Oh boy.  I set out to give a few quick comments and ended up thinking more than I'd intended to.  The end result it that I'm not sure I'm buying all of JBM's conclusions right now, I'm not against them but I think it's a really poor time to try and infer much comparative stuff, because a freight train called winter is coming to all the nations on his plot.  I think both his take and mine are reasonable, but there is disagreement.  Just shows IMO how much we don't know)

A few thoughts:

• As Si dH says, he doesn't get in to the CFR; but the data does hint in that direction - the hospitalisations:deaths ratio for the UK is much lower than for the other countries and is not reasonably subject to the same ambiguity as the CHRs
  • A reasonable interpretation seems to be that on average, an individual going to hospital with Covid in the UK is much less sick than in Europe
    • Another sign that whilst we're running cases hotter than comparator nations, the individual consequences of doing so are, on average, much less bad
    • How much of this is down to vaccine uptake/refusal and how much is down to demographics is not so inferable, but it seem to run counter to a scenario where vaccine fade against severe illness is dominant issue in UK deaths (which is separate to fade against catching the virus potentially affecting UK cases)
• He's rounding up a bit (on average) to get 3x deaths for the UK, and it's not homogeneous across those nations.  A weighted average is closer to 2.6x I think.
• Interesting to read his take on Scotland; aligns with the observation I've made before that whilst cases are falling rapidly in exponential terms, hospital occupancy isn't - the opposite of the recent situation in the UK.  Which is probably why the ScotNat  Twitter Warrior someone linked up thread was only posting cases/100k graphs.  I've avoided coming back with detailed rebuttals, because it's one thing to look for understanding to try and bound apprehension over Big Scary Numbers not born out by the outcomes, but playing top trumps over different statistics feels crass and pointless.
• Boosters; what's going on with the rollout there?  

To give a slightly different take on the present moment:

• A general point about carrying out comparisons on the leading edge of the data right now - the general sense seems to be we're going to see winter waves everywhere; timing is radically different between different nations and JBM gets in to this with his plots on wanning; the last wave in different nations ended at different times, and weather and behavioural shifts land at different times in different counties.  All of this makes now a really sensitive time to these effects; so not a good time for comparisons of some things.
• Another point - instantaneous cases/100k and deaths/100k are a result of the journey we have already been on; in terms of the impact of control measures (masks and indoor mixing as he discusses) and other changes such as immunity/vaccination, it is the rate of change in these variables that tells us about "the now", and the future is a product of where were are now and the rates of change.

• So, where are things going?  The exponential rate constant for cases is heading for or has reached growth in every nation (taking the UK as a whole) used on JBMs plots over the last few days. I've made some plots of this from the OWiD data; they're not my prettiest plots by a long way.

  • In the immediate term this is worse news for the UK because it's being applied to infections causing a 2.6x higher death rate because of past policy differences and because healthcare here is highly stressed for many reasons

  • It's comforting to know those policy changes are likely potent and are there waiting to be made and as with JBM I hope to see some of them made promptly around masking and at least clear, blunt guidance on the actual risks of indoor socialising for the more vulnerable.  

  • The rate constant is rising faster for some other countries than the UK.  It feels to me like seasonality is kicking in across the board, and in terms of the potential for the virus to spread, the UK is no worse off or arguably better off than some comparators (despite being worse off in terms of case/infection/hospitalisation/ death numbers).  Likewise, the rate constants look to be rising to the same or higher levels elsewhere despite them being behind the UK in booster wanning and despite their higher levels of masking and lower levels of indoor mixing that JBM gets in to.  

  • (By "seasonality" I could also mean "bad escape variant" but I assume sequencing is good enough to rule this out....) 

This last week of data is looking like a turning point in cases; it takes a long time for that to play out in to full consequences, and so for the next months I think there's a lot of uncertainty out there.  

In reply to Si dH:

This virus ruthlessly exploits every form of structural inequality and poverty.  Some of the early response measures to the pandemic could have opened up some radical approaches to this within the UK, but like many changes for the better that it put on the table, little changed for the better.

I think you might have got this backwards. According to the Twitter thread, we have 7* cases, 6* hospitalisations and 3* deaths compared to other parts of Europe. So, the hospitalisations/deaths ratio is higher in the UK (approx double.)  However I would suggest that comparing hospitalisations is probably unreliable, like comparing cases, because different countries have different admission policies and health system structures. If available, comparing data on number of patients on mechanical ventilation might be better... but even policy for that has varied a lot through the pandemic and probably between countries. 

I did think the use of 5-month and 6-month cut offs had the potential to force a negative picture on the UK, since the policy here is that you cannot get a booster until *at least* 6 months after your first dose. I have no idea how well the booster programme is starting, but I was pleased to see the dashboard being modified the other day to allow the% of population with a third dose to be reported - with this information being easily available I'm sure the Govt will want it to go quickly.

You say a small difference I say a pretty big difference: over 9% reduction in infections and that's in rural Bangladesh.

As you regularly point out the best thing in terms of indoor public spaces,  to avoid covid spread, is for people not to go there. When you say it's small what are the big public health measures you think we can follow? I've seen nothing that indicates it's not up there with improved ventilation as the best thing we can do in indoor public spaces.

Edit: Yes, when I said “lower” i should have said higher.  I was thinking of a “hospitalisations fatality rate” in the style of CFR, which is lower, but that is not what I wrote.  Sorry.  I’ll leave the rest of my reply in although it’s probably redundant now…

It’s a bit of a mind bender this, let me try again - I don’t think I’m back to front here.

The way I see it is that as you say our hospitalisations:deaths ratio is much higher, which means less than half the fraction of people going in to hospital in the UK are dying there compared to comparator nations, which suggests to me that - on average - the cases of Covid requiring hospital treatment are less serious.   We have higher hospitalisations because Covid is more prevalent here, but perhaps a lower fraction of the people going in to hospital are dying because the spectrum of cases in the UK has a lower barycente on the “severity of covid” scale.  This fits well with our demographic distributions of cases and random sampling infections having had a young bathcentre of late.  It bodes ill for the changes coming to our distribution of cases.

I agree, but no measure is truly comparable but I think hospitalisations will be subject to less variation than cases, and the precedence of the various conversion ratios seem pretty consistent regardless of the comparator nation out of that group of close neighbours.

Yes; my alarm bells were sounding at the 5-month plot but I took his point; I’m glad he had both at least...  Given the way all the counties are apparently having a turn to growth over a dispersed timescale much shorter than the variation in hitting his 5-months thresholds, I worry that he’s borrowing future trouble to interpret the now.

Makes you wonder what would happen if government felt beholden to a few more KPIs instead of pushing them out on to everyone else.  

point of teleological order - its not concious, and to give it agency (even by use of language) colours thinking about what is happening.

I agree in that the fault lies entirely upon humanity and our acceptance of unequal living.

I disagree in that I believe that the process of evolution has some form of agency and that all forms of life (side stepping the debate about the life of viruses) are part of that.  My thinking is colouring my language. Edit: and you may well disagree strongly with my thinking!

Evolution has much randomness in it, but over sufficient timescales it has many senses (everything is indirectly measured by it, why is a polar bear white?) and significant computational potential.  Normally those timescales are geological but that is not so for a virus running hot globally.

Bit of a tangent here…

Good twitter thread if a bit understated:

So in summary, the UK has too lax controls on indoor public mixing compared to Europe, a delayed vaccination policy for kids, lower control measures indoors, a much higher proportion of elderly people in poverty than most of western Europe, and the lowest statutory sick pay in the OECD.  All areas where the UK government is doing less well than Europe. Even where the UK has done well (fast start to vaccination) it is now working against us as we are hitting waning sooner (and with a higher proportion of AZ). 

9% in absolute number after 8 weeks. Given what we (should) all now understand about exponential growth, that's small. Worth having, but definitely small.

Better to think about it as an addition to the rate constant or a multiplication on to R.  If it changes the sign of the rate constant (moves R from one side of unity to the other), it makes a massive difference to the exponential growth.  

If the name of the game is setting R<1 it’s a biggie.  It’s also a big difference for individuals using multiple control measures to reduce their personal risk.

There’s no one right or wrong interpretation.

Thanks for ignoring my question. 9% in that time scale where mask use was at one third of the level even in the control group, in rural Bangladesh, isn't so representative of the likely situation in the UK. Murdoch in that Twitter thread uses it as evidence of why we should still have a mask compulsion policy in England (knowing it's not the biggest thing we could do). I've never claimed mask use is a panacea, just that after vaccination it's alongside ventilation as the best we can do to cut risk in indoor public space and it's very cheap and has no significant economic downside. SAGE appendices described it as significant. Small is exactly what anti-mask people want to hear as self justification.

I think we are well beyond giving the benefit of the doubt to a duck quacking, duck looking, duck acting thing (again and again and again) pretending to be a swan (in the face of real evidence, again and again and again). This for me is fundamentally a public health critique of government management across all aspect of pandemic response and standing up for truth in that, it's not a party political thing.

It's patently obvious the lower death rates per hospitalisation in the UK we have right now is demographic: it was from encouraging (by political inaction and poor messaging) the pandemic to rip through our young. The key factors for me about where we are isn't a straight comparison with the EU its about the combined impact of our hospitals being under more pressure than those in Europe our deaths per capita higher, our long covid rates  higher and our school disruption higher, more vulnerable poor elderly, and more people less likely to self isolate as sick pay is the lowest in the OECD .....which all combined means at a time when we clearly need to be the most careful in western Europe, it's very worrying to see the opposite.

The latest phases of vaccinations isn't going so well either but so far the government errors and U turns seem to have been overlooked in all the big news (various IT issues in vaccine orders  ...the ongoing central booking system problems.... and the flip-flop on just turning up to a centre if past the 182 days since the second jab but had no notification/nothing early/convenient). It won't be long before people look harder for why the numbers are so poor.

Add a super stressed NHS, with massive urgent backlogs, to running hot on covid, a poor record of government response and a seasoning of flu and we are potentially (massively high consequence, significant possibility) in big big trouble this winter.

This is what Roy Lilley says today (an NHS management expert and previous tory govenment health management advisor)

"Don't hold yer breath...

_____________

The NHS is not under pressure.

The NHS is under water… drowning in demand and not enough people to cope. 

The sooner we admit it, the more likely we can get it back in its feet.

No19 is in denial; 

Pretending £250m of existing funding, spread around 8,000 GP practices, (less than £600 a week) is going to fix queues, telephone systems and hiring Locums.

Pretending, more staff in 5 years has any meaning, now. 

Pretending 40 hospitals will be built, is dreamland.

Pretending yer-granny is going to get a new hip in her lifetime…

… it’s delusional. 

More than that, No19’s on the run. Scheduled to attend the RCGP conference in Liverpool last week, he pulled out… that's gutless.

In management speak, this is denial. No19 has the 5, classic symptoms;

1.Denial of what we all know

The NHS is swamped, we know waiting list are unmanageable, we know it’s too late for money and we know there’s nothing he can do, in the short term. 

2.Denial of what's needed

Honesty, that acknowledges the predicament. We do not need Army Majors, the Daily Mail or dissembling press officers making things worse.

3.Denial that he's in control of events

Throwing £millions here and £billions there, is not ‘control’ and won’t fix people waiting 7 hours for an ambulance or hospitals declaring Opel 4. We know, there is nothing he can do.

4.Denial about trust and respect the NHS has for politicians.

Everyone recognises it’s, effectively, Number 10 running the NHS.

5.Denial that people working in the NHS, for years, with a huge experience, know better than he does.

All the money in the world, all his bullying and shouty-headlines, won’t work. 

He can fill his diary with visits and speak plastic words of praise but …. from a man who will join forces with a national newspaper to kick GPs and do a runner from their conference… 

… as a Secretary of State for health, he’s finished.

There are three steps to try and deal with an in-denial-boss:

show them the facts and the data. There’s a welter of it, No19 knows and choses to ignore it;

ask leading questions; ‘…you do know people are likely to die waiting for a new hip and for that matter, an ambulance’. He’ll repeat DH press office rubbish about money, recruitment and 40 hospitals;

tell them where all this is leading to. The consequences. ‘You do understand the NHS is imploding and the consequence is, people will lose their lives?’ Expect more press palaver.

I know what you’re thinking… none of this is going to work. 

You are right. He has no insight and is dangerous.

When the boss gets out of their depth, they can...

... accept the situation, bring in help, acquire new skills and ask people working in the organisation what to do. 

... or; do-a-Javid, point the finger, bully the organisation and set pointless targets.

Nothing looks like it's going to work. What's gone wrong? 

This type of management crisis was first identified in 1969, by a Canadian teacher, Laurence Peter. He identified foolish behaviour in politics, journalism, the military and law.

He defined the ‘Peter Principle’; people tend to rise to the level of their incompetence.

The NHS is a +£100bn-a-year ‘business’, in crisis. 

Aside from the banks, the only companies bigger, in the FTSE 100 are Shell and BP. If the NHS were a country it’d be around the 30th largest in the world.

Put simply; No19 is out of his depth. Nothing in his career, as a middle-rank-banker and trader, has prepared him for this task. 

He holds office thanks to his predecessors infidelity and BoJo’s patronage. 

If he were wise he’d say; 

‘… the NHS continues to be buffeted by events and is struggling.

We won’t have the level of service we are used to. We must all play our part in helping the NHS to come through this winter and recover.

I will do three things 

First, I’m putting-in all the funding I can get.

Second, now I will create a period of stability. 

Third, this is a national emergency and workforce is the key. 

With experts, I will generate an innovative plan to accelerate recruitment and training, invite retired colleagues back and prevent people leaving. 

I will deliver the outcome in 14 days and together, we will get the NHS on the road to recovery.’

I think we all know, this will need an honest acceptance of reality and guts.

Don’t hold yer-breath... "

Depending on circumstances and what you guess as an arbitrary 'cycle time', a 1-2% reduction in transmission could get you to a 9% difference in absolute numbers in 8 weeks if I've mathsed right (have I??). iirc papers we saw linked on ventilation suggested a bit of fresh air kicked crap out of that.

Irt offwidth:

Anti maskers are definitely unjustified and need correcting. But so do the "it's ok to do xyz, I'm wearing a mask" crew. Masks are a good intervention because they're tiny effort for a few percent gain that can tip the balance between growth and decay if it's on a knife edge. They're not a magic forcefield.

You did claim that they were the second best mitigation. They probably aren't that.

We only started this epic because you took issue when I suggested making more effort to stay away from more of the places that warrant a mask was probably a better idea, so we're in danger of getting to the violently agreeing phase again.

SAGE appendices claimed masks are the (roughly equal alongside ventilation improvement) second best mitigation indoors in public I just linked that via bruxist.

I never took issue with staying away from indoor public space being the best option:I agree completely with that. I took issue with the practicality of that for the poorest (and your implication is was still a choice for them).

Feel free to keep misrepresenting though.

https://www.bbc.co.uk/news/health-58952473
 

Possibly the news you were waiting for?

Still no news on the mystery behind the cancellation: from the article you linked...

Prof Penny Ward, a pharmaceutical expert at King's College London, said: "As we know the UK government is in dispute with Valneva having cancelled the UKs order of up to 100million doses, placed by the Vaccines Taskforce in 2020, in September.

The results today suggest that this decision might yet be regretted, but because of it Valneva might be able to provide an immediate supply of this vaccine for other countries struggling with the freezer shipping requirements of other, more expensive, vaccines. Good news for Covax and countries still awaiting supplies."

Certainly the news I had been anticipating.  It's their Cov-Compare trial I am most looking forwards to seeing the results on.  It's use as a 3rd dose booster is where to my limited understanding it would have the most potential for difference to other vaccines.   

I'm very happy to see a new vaccine come to fruition, and one with simple transport and storage requirements, and one that can hopefully make a difference to other parts of the world.

Javid has some explaining to do, for sure.

One thing I've not seen discussed - bit early really given the moral imperative to get global first and second doses up - are authorised Covid vaccines going to end up being offered on a paid-for at point of use basis to those who don't fall in the "free" category, as with the annual flu vaccine?  

An update checking in on the growth in cases.

This period of growth is sustaining for longer than a typical wobble associated with changing weather; hints that it's probably not going to go in to growth any time soon, and that the weather modulation is being super-imposed on a positive baseline of rising growth.  There's a similar pattern in the last two weeks for Scotland, but on a lower baseline so that wobbles are taking it in and out of growth.

The growth is very different to any other period in recent months, being the only recent period of growth to manifest in all ages simultaneously.  Feels to me like this is a big weather effect that surpasses typical week-to-week changes and heralds changes towards autumn/winter, but that's pretty loose speculation.

Concerns over vaccine fade seem completely incompatible with the synchronised onset of rise in all ages.  Whilst I think this spread is not related to fade of immunity, follow on consequences can likely be reduced by the booster program, hence my lack of joy at this news story landing today in addition to Offwidth's observations - https://www.bbc.co.uk/news/health-58954707

This looks like the kind of thing that's going to become a real problem if it's not stopped soon;  cases have a doubling time of about a month, but given the significant demographic shift the recent changes are likely to produce, hospitalisations could double faster once they start landing (we're currently I think transitioning from hospitalisation from the school associated burst of growth to this burst) and I'm not sure even a single doubling of hospitalisations is sustainable.  In early September, there had been talk of a firebreak lockdown around half term; I don't think schools are a major factor of this rise but now feels like a very good time to be taking more measures to pause the growth in cases..

(One explanation for what we see would be a new, more spreadable variant, but I've not seen anything to support this in terms of news reports etc; if it was the case it would have to be very uniformly distributed by importation to have avoided leaving a big signal in the regional data.  Not impossible with our new, more permissive approach to travel...)

Edit: The API finally got back with the regional data.  Growth looks pretty uniform across the regions, with the exception of the South West where the mother of all spikes appears to be landing, probably related to this... https://www.ukhillwalking.com/forums/off_belay/43000_incorrect_pcr_tests-74019...

AY.4.2 might be that variant: thought to have a 16% transmission advantage over pure Delta, now accounting for ~10% of sequenced cases, and apparently emerged in Scotland: https://twitter.com/CorneliusRoemer/status/1448708772415918083

BBC on point

BBC News - Covid: Is the pace of the vaccine booster rollout too slow?
https://www.bbc.co.uk/news/health-58954707

Congratulations, I hope they're both home and doing well now.

Thanks Wintertree for the work, the situation gets ever more complex but the efforts are appreciated. This week the covid has finally touched my immediate family, both my parents have it now. Fingers crossed thanks to their vaccines they seem to be doing ok but it's a worry.

Jk

Thanks, they are. Best of luck to your parents in getting through it without bad symptoms! It must be tough for you; my first son got it last year, for him it was just a cold but I spent a week or two pretty terrified he had given it to my mum a few hours before he started coughing (he hadn't.) At least with vaccines now, they stand a very good chance of it being mild.

One of the other problems is that the covid booster program isn't joined up with flu vaccination. Direct booking a covid vaccination doesn't have an option of also having flu, even in a centre doing both for GP/Pharmacy booked people.

Quack quack quack.

https://www.theguardian.com/world/2021/oct/18/uk-lab-immensa-false-negative...

Thanks. I must admit I only skimmed the discussion. I was just a bit confused that you were spending so much time on something that seems fairly obvious anyway (to you).

It’s a very good point that if you start from the reasonable assumption that IFR must be about the same for countries with similar healthcare capacities and at similar stages in their vaccination drives, the fact that CFRs are significantly different suggests that testing rates are also significantly different. Different demographics and vaccine roll out timelines mess up the picture somewhat but for most wealthier countries the vaccinated proportion has been about the same in the last couple of months. As for demographics, again they aren’t that different between different developed countries.

I would be careful with those poverty graphs. No more reliable than comparing CFRs… Poverty isn’t a fixed term and can be measured in many different ways. Comparing to mean income (for adults, presumably) is one way and not necessarily the best one. 

If it’s 9% in Bangladeshi villages, it might be a fair bit higher in a UK city?

Oh joy…

The elephant in the room is that the UK started vaccinating  earlier so the average number of months since second vaccination is larger than in EU countries and it used far more AZ vaccine which is not as effective as Pfizer,  92% effective instead of 96% means 8% chance of breakthrough infection compared with 4% i.e. twice as much.

https://twitter.com/jburnmurdoch/status/1449801678304260099

Because it started first and used a poorer vaccine the UK should be doing boosters with a decent vaccine much faster and it should be more cautious on masks and indoor contact and it isn't.  In fact the UK government cancelled a 100 million dose order for the Valneva vaccine which has now been shown to be effective.

England now has the worst Covid infection rates in the world

https://twitter.com/globalhlthtwit/status/1450216815246946310

Define “worst”.  How are the per-capita death rates over the last month between England and Scotland?  Wonder why you didn’t mention that?

Case rates are almost meaningless for comparison as the CFR and death rates show.

High infection rates with low mortality is historically how some pandemics have ended.  We’re clearly not there yet in the UK, but if we continue to have some of the stand out best testing in the world then we’re going to continue to have some of the highest case rates in the world if we do get to that kind of end point.  So depending on where in the transition we are, high case potentially rates goes from “disaster” to “meh” to “problem over”.  Not simple, not binary.

As already pointed out, positive tests are a pretty useless comparison due to differences in testing regimes. Maybe look at a comparison with Latvia - just announced a lockdown, and Romania, an absolute disaster on the scale of Lombardy in the first wave, despite all the progress made since then.

https://ourworldindata.org/explorers/coronavirus-data-explorer?zoomToSelect...

https://www.eureporter.co/world/romania/2021/10/18/romania-has-the-highest-...

The other side of the argument is that the UK, by having the highest infection rates in the world with relatively low deaths, is actually doing the best in the world.

We’re filling out the unvaccinated gaps in the population the fastest and we’re topping up the vaccinated populations immunity the fastest. Covid will be over in the UK sooner than anywhere else in the world.

If we continue to treat Covid as a “lethal pandemic” it will remain a lethal pandemic. We need to maximise population level immunity. There is simply no way around that.

I agree but that doesn’t mean we have to rush; the countries that held off waiting to give vaccines a chance of done objectively better by healthcare and economic measures.  As things progress, some benefits of holding off decrease, some increase and the risks of holding off increase, but I’ll be damned if I know where the tipping point is, and I doubt anyone else does either.  I can rattle off reasons in both direction but lack the wit or wisdom to know which supersedes which.

There are however many different ways to the destination that we are ignoring I think to our peril

• Protecting the more vulnerable through clear and consistent messaging and legal protections over basic control measures in public spaces would probably make a big difference as people wait for their winter boosters.
• Vaccines antigenic against multiple viral proteins, giving a broader base for the immune system to resist the mutation hotspots on the spike protein.

The problem with highly one sided arguments is that they take any remaining focus away from achievable differences.  

I completely agree with everything you say.

However I don’t think everyone is on the same page that “Covid will end when we have sufficient population immunity”. 

How we get to that end point is a melting pot of public health, political, societal and other considerations and I doubt there’s any right answers as to what the correct course to take is.

Running as hot as possible has some advantages (and you know that’s my preference), slowing things down has some advantages - it’s all a trade off that needs to be considered.

If committed to, it does however need

1. Clear messaging for those most at risk - the people who were most likely to die in this pandemic if it landed a century ago, and who now have to lean on control measures, boosters and emerging therapeutics to not get clobbered.  
2. A healthcare system that doesn't have a logjam throughout hospitals precipitated by discharging patients and an exceptionally high demand on the ambulance service at the same time,
3. A highly responsive approach to cooling things down the moment short term projections of the current situation (not models largely anchored in fantasy) show clear danger.  

Where we are on those bullets points is not where we should be if we were following this strategy.  The government won't openly and clearly acknowledge much in the way of strategy, and I think that's why (1) is such a muddle along with the PMs take if you believe the source [a].  (2) is rather beyond what I've been doing with these threads but there's a lot of posters with comments worth listening too, and it's not good.  In terms of (3), we've hurtled past the warning signals, the stop signals, and the barriers labelled "The Bridge Is Out" several times now, so I'm hoping to have my expectations exceeded should it be necessary.

[a] https://www.reuters.com/world/uk/uk-pms-former-adviser-confirms-johnson-sai...

Indeed. It's notable that New Zealand are now biting that bullet; I think they have done a stand out excellent example of protecting both the immediate health and the general way of life and wider health of their residents and citizens, but even they are now moving on to next steps.

It's continues to be a shit situation all around, and I think there's so much more we could be doing in the UK to make it less shit without denying the inevitable.  I also recognise the arguments about stalling for time for more therapeutics but they are one half of a two-sided argument.

A general observation here based on taking my dad for his booster jab at the weekend.

Cases going up? Check.

Background: So last time I went for my second jab there was a queue and booking system that ment you turned up just before your jab was due, got booked in, sat socially distanced in a big hall and crossed the room to the injection booth.

Sunday: Turn up at scout hall with dad and it is packed! Rammed! No social distancing, people pushing past and around us. Most of the small hall was taken up with rows of seating with no gaps between seats and full of old and young (healthworkers?) people. It looked like a village meeting when a by-pass is planned. The woman who asked dad about his medical history took off her mask to talk to him. We shuffled round her to get his jabs and afterwards she asked us to wait 15 mins in the hall (hence all the seating) in case of any adverse reactions. I politely said we would wait in the car outside.

I mean yes presumably everyone has been second jabbed but I personally know of two people with underlying conditions who died despite this.

I know COVID is all over, as people keep saying to me but I would have thought those dishing out the vaccines would have been a little more circumspect

Isn't evolution great....

I see it's made the Today Program on radio 4 this morning; "not disastrous" is the headline summary from the scientist they interviewed; as with my point about masks up-thread, a relativity small addition or subtraction to the rate constant can have a critical effect if it takes them over the line between decay and growth.  Still, if (big if right now) thats' the cause of the persistent rise, it will only take a small change to policy and control measures to send things back to decay.

One could read lots in to the messaging going on today, particularly over thresholds for a potential lockdown and the scale of pre-Covid flu seasons.  That runs the danger of equating the duration of life lost to a Covid death to the duration of life lost to a flu death, or at least of ignoring the possibility that one is still much greater than the other.   It would be good to see what the Government Actuary's Department has to say on that matter.

In reply to Duncan Bourne:

You see, it wouldn't even occur to me that booster vaccination clinics would be running in the way you just described....  

Interesting, as our mass vaccination centre is running as before - 2m distancing, one way system, masks all round (Wales).

That's reasuring to know.

I was gobsmacked by what I saw at the weekend. I just assumed it would be the same as for my previous jabs.

The weird thing is that the emergence of this variant has not been highlighted in the PHE/UKHSA briefings (it's almost an aside in the most recent one and not mentioned previously). Furthermore it has almost not been picked up by the UK press at all (one FT article behind a paywall I think), but if you Google AY4.2 there are several US articles linking it directly to the UK's high case rates.

Even the fact that almost all UK cases are now AY.4 and not the 'original' Delta B.1.617.2 (which is still predominant in the US, I'm not sure about Europe) has been hardly mentioned as far as I can tell. But a rise in AY.4 is currently seemingly big news in India. None of these changes to Delta have been assigned as VUIs as PHE/UKHSA. I'd like to know why!

I assume this is some kind of satire?

Voila: 

https://www.theguardian.com/world/2021/oct/19/fears-grow-in-england-over-ri...

What makes you think that?

It’s clear that we have to reach an point where population immunity is sufficiently high so that Covid behaves like any other “mild” seasonal virus.

The only question that there’s ever been is how we get that immunity. Now that vaccine uptake is largely saturated, how else do you increase population level immunity (aside from potentially using booster vaccines with multiple protein spikes from the virus or dead virus)?

Covid isn’t some kind of special killer virus. It’s just like any other novel disease that humanity has faced in the past.

However your reaction says a great deal about the problems government messaging has created and explains (at least to me) why the government is so reluctant to explain to the electorate the inevitable.

I suspect the situation you witnessed was far from universal and sounds so bad it probably deserves a formal complaint. I would have walked out. Some of those people being jabbed could have been highly vulnerable. Standard covid safety precautions should all be in place in all vaccination centres. https://www.england.nhs.uk/coronavirus/publication/quality-assurance-framew...

Of those I know who were jabbed in the last few weeks some were done in smaller venues (PCN and pharmacies) but a few went to bigger centres which they said were like ghost venues compared to last time. None reported safety issues. The overall vaccination figures also show on average things are very slow (the plan was more than double current numbers for the priority groups and even more than that for school kids).

The UK isn't "topping up" the vaccinated's immunity fastest. Whether Covid is "over" in the UK first is pure speculation and extremely unlikely, even discounting the cost in lives and to the economy.

Re topping up immunity, there’s two buckets of people catching Covid.

1) Those who haven’t been vaccinated and have no immunity.

And

2) Those who’ve been vaccinated, have some level of immunity, but are still susceptible to catching Covid.

What proportion of current infections is driven by each bucket is anyone’s guess, but I’d happily wager a large sum of money that the second bucket makes up a significant chunk of the total and it will be growing all the time.

Re Covid being over. Covid will never be over. It’s here to stay. However the public health consequences will fade into the background when, and only when, we have sufficient population immunity.

I would say the current economic impact of Covid is minimal (as we have limited restrictions is you’re not infected). In terms of lives lost, yes more people will die of Covid in the UK. There is no practical way (it might be impossible) of getting to a high level population without some deaths. 

You wrote "we’re topping up the vaccinated populations immunity the fastest. Covid will be over in the UK sooner than anywhere else in the world."

Now you are saying something else.

If you follow my logic through you get to my original conclusion. I’m just trying to explain it to you.

Put it another way (and I’ll give you an extreme example to make a point) - I’d rather be in the UK’s position right now than New Zealand as we have much higher immunity levels. We have minimal deaths to go until we get a high level of population immunity, they have a lot.

I prefer my logic to be presented concisely and accurately.

We’ll explain your point of view then. Why are Covid cases a bad thing if they don’t result in serious illness and how else do we get out of this mess?

I would hope it is far from universal.

Having witnessed it I would say the main problems were.

1) Having people wait 15 mins in the hall (yes I know the weather wasn't ideal but neither was the crowding)

2) not spacing the seating

3) Not spacing the bookings (I assume it was only people who had booked atending)

4) some sort of queue system on entering

5) a bit more adherance to mask policy

If you don't treat it as a lethal pandemic and it is, in fact, a lethal pandemic then you are screwed.  Even if infection doesn't result in death within a month it might result in long term health consequences.

There is absolutely no rush.  We know how to reduce case rates, most other sensible countries are running far lower case rates and economically the countries with low rates are doing at least as well as the UK.  So why not run prudent policies such as encouraging work from home, masks in shops and transport, no large crowds, and boosters, which result in far lower case rates and give it enough time to be certain before taking steps which could result in death, or even more likely, long term disease and poor health.

It isn't going to feel so smart if, for the sake of not being patient for 6 months or a year, we end up with a large cohort of people who can't work full time or regularly require NHS treatment for the rest of their life.

NZ has already delivered first vaccine doses to 70.5% (compared to UK's 73.7). NZ has only second-dosed 55.2% (cf UK's 67.6) but is progressing rapidly. In less than a month they'll likely be ahead of us on both measures. It's true that there will be very much less infection-derived immunity in NZ, but NZ is moving into summer and will face their first wave with established treatments in place and a well-funded, well-rested health service. Meanwhile the UK is moving into winter, with an exhausted, over-stretched, under-funded (and, unbelievably, under attack) health service. 

I would be surprised if the current economic impact were minimal. As although not the same as in lockdown many people, including myself, have not returned to former spending habits. I do not go to pubs, I do not go to large indoor gatherings, I do not go high street shopping, etc. I am sure some people do but there would still be a drop. Not to mention continued staffing problems across the board.

Looking at the government charts https://tradingeconomics.com/united-kingdom/gdp-growth

It shows a growth for July preceeeded by a fall in June. This suggests to me a wildly fluctuating economy. Some quarters will see an increase while others a decrease. I imagine the building trade and online services are doing quite well, while business in the hospitality sections see a more fluctuating situation. I know of many businesses that have gone to the wall over this.

Nonsense.  They'll give everybody two jags with something good and be in a better place than the UK, in terms of immunity levels, without having killed as many people to get there.

Also, remember they're in the Southern Hemisphere: their winter is June, July and August.

I did post a satirical version of VS's commentary but it was deemed "inappropriate" :/ Not sure how VS managed to get away with it!

My point of view is simple, you presented two statements as fact one of which is untrue and the other pure speculation. The rest is of no interest to me as it's clearly not worth reading.

Yes, I would far rather be in NZ.  You beat me to they reply.

I don’t think the timing of their decision to - very cautiously - open up is random, as you say it’s the start of their summer.

As well as the differences you list, there’s some more big ones that translate almost seamlessly between the nations.

People are unavoidably going to die in NZ from allowing the spread, but I would far rather take my chances now than 3-, 9- or 18-months ago, and if I was a more vulnerable person I would far rather have weathered the storm in NZ and face my chances now that have faced them over the last 18 months in the UK.  Why?  The progress in clinical care, the repurposing of pre-existing drugs and the approval of covid related therapeutics has improved survival and other health measure significantly over those timescales, despite the gains the virus has repeatedly made in lethality through variation (the lethality of delta if it had landed in early 2020 doesn’t bare thinking about.)

It’s possible the lack of infection granted immunity is going to make this wave hard for NZ, but that will cost them less much than the blood money we took from our people - particularly the marginalised  - to pay for ours.

It’s never been about which nation is going to “win” but which is going to successfully minimise their losses.  

>  (and, unbelievably, under attack)

The American “libertarians” (an oddly wrong term for puppet stooges) have been attacking the NHS for a decade.  Some of the pressures on the NHS now stem from how badly we handled the early stages of the pandemic.  The intent of the stooges in encouraging a catastrophic early response in the UK through lies, misinformation and the weaponisation of a few bent or delusional scientists starts to become clear.  Should be treated as the threat to national security it clearly is.  If it all goes wrong over here this winter it won’t be long before they’re pushing hard at home examples of the failure or socialist healthcare.  

Fairly straightforward.  Catching Covid is a bad thing so the highest rates are the worst.

Case rates are extremely meaningful and well defined compared to measures like CFR. 

Yes, it is simple and binary.  

Test the theory before trying it out on 67 million people.  Until you are sure, be careful and keep case rates low.

WTF do the english need to turn a disgraceful statistic like having more Covid cases than the rest of Europe combined  into a boast about 'we have stand out best testing'.  You probably don't.  You just had a PCR lab that f*cked up just about every test it did.   Advanced Asian countries and the EU countries have been consistently better at just about everything throughout this pandemic (except corruption) and since Biden was elected the US is far better too.

More news stories landing today in the UK process.

So, once again, the question emerges about why it is out-competing other strains:

• It was in the right place at the right time (a powerful facto when it comes to exponential growth)
• It is intrinsically more transmissive
• Increased immune escape against some or all forms of immunity in the popualtion

I get the impression answering this needs a very careful and detailed analysis of a lot of data; and it will be harder for this variant given the smaller effect.

Some advice from the Pythons -  youtube.com/watch?v=jHPOzQzk9Qo&

I've just about had it with these threads you know, and you're a signifiant contributor to that.

I was not boasting.  There is almost nothing to boast about when it comes to the disgraceful way this pandemic has been handled by the whole of the United Kingdom.   I would not boast about the areas I think we are doing comparatively better, not least because I pity the distasteful people who try and turn every single discussion on Covid in to a case of Top Trumps over who is winning when, for the western world, it's more a case of who has made the least catastrophically bad decisions.

This is bullshit Tom.  

Cases mean totally different things in different countries - another poster gave a vey clear example above that you have, characteristically, ignored.  

Here is their post that you ignored [1]. Perhaps you might address their post? 

Let's consider the meaning of cases, fatalities and CFR.  You write off CFR as a basis for International caparison - so do I.  I brought it up specifically to  make a point about international comparisons that you appear to be going out of your way to deny.

• You write off CFR as a basis for comparison.  I agree.
• You embrace cases as a "well defined" and "extremely" meaningful bassist's for International comparison.  I disagree
• CFR is a ratio between cases and fatalities.  
  • So, are you suggesting that fatalities are poorly defined and meaningless, or do you think there is a problem with the division operator?
  • I could draw a diagram with a triangle if you like?  Caption: "Why you can't have your cake and eat it"

However, the likelihood remains, the UK is detecting a much larger fraction of infections as cases than many comparator nations, as inferred by various reasonable means, there are many ways of seeing this.  

Your endless focus on cases only and not deaths to further your demented nationalist perspective denies this and is not a rational or evidence based look at the situation.  

You're cherry picking a flawed caparison because it gives you a bigger drum to beat for your anti-English racism.  This reminds me of your absolutely disgusting misuse of the Yellow Card Scheme data in the exact same way the anti-vaxx bridge do.  I've never seen an established poster so roundly criticised by so many people in such a consistent basis, and IMO you're at it again.   Posters who identified in various cases as not Scottish, as not being British and as being appalled at the UK government over various issues.  

Last week you were suggesting an independent Scotland should hold England to ransom over the supply of electrical power - in effect threatening to kill the most vulnerable - as a way of advancing trade.  [2]

I think you need to have a long, careful look at the level of hate within you and how it is turning your capability for rational, nuanced thought in to an ugly parody of a rabid nationalist.

[1] https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_48-...
[2] https://www.ukhillwalking.com/forums/off_belay/tidal_power-739540?v=1#x9526334

(For everyone else except you, Si dH!): The technical briefing that mentions AY.4.2 is here: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/...

Like you say. Really strange that it hasn't been acknowledged until now, especially if it was already accounting for ~10% of all cases over a week ago. Looks like the last time any variant was designated a VUI was back at the beginning of July. I'd have thought anything that looked capable of supplanting the dominant strain at such a rapid rate would have merited more attention. I'd like to know why too!

Simple facts:

a. England has the highest Covid case rate in the world right now and more cases than the EU nations put together.

b. Most diseases don't kill you in 28 days.  You can't characterise the damage from Covid infections simply in the number of people who die within 28 days.  A more interesting number would be the number of people who catch it who are fully recovered and as healthy as they were before they caught it within 3 or 6 months. 

c. Until there's an argument which includes long term health consequences as well as short term deaths the assumption should be that catching Covid is dangerous and the goal is to minimise the number of people who catch it.  The Tories seem to have decided that the number of cases doesn't matter.

d. Astra Zeneca is a great option compared to not being vaccinated but on every measure it is less good than the Pfizer and Moderna vaccines used in the US and EU.   The comparison I did on the side effect data was simple and brute force but the effect was very large and the analysis didn't need to be subtle.  The UK government put a warning on it for the 10x as bad symptom I was talking about and you still bang on about it.

If you are wondering why I am so relentlessly negative about England it is pretty straightforward:

There is a tide in the affairs of men.
Which, taken at the flood, leads on to fortune;
Omitted, all the voyage of their life
Is bound in shallows and in miseries.
On such a full sea are we now afloat,
And we must take the current when it serves,
Or lose our ventures.

Brexit and the mismanagement of Covid are the tide which, if taken at the flood, can get Scotland its independence.

Simple facts you say.  Nothing in this is simple, and an attempt to reduce it to simple facts just convinces me further that you have no interest in using your - evidently strong - analytical skills to try and understand the situation.

Here is an observation, I think it simple but I won’t presume to call it a fact.

You have repeatedly refused to engage with anyone pointing out how cases are a near meaningless basis for international comparisons.  I’ve spelt it out as simply as I can now in words and in pictures. You respond with nonsense and you can’t defend it.  You know you’re over reaching the evidence to support your emotional position, so you just don’t reply and move on to other areas.  

Here’s an example of someone who isn’t me raising the same issue.  You ignored them like you ignore every single evidence based challenge that doesn’t fit your anti English racism.

https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_48-...

In looking to effectively weaponise the debate over covid in pursuit of independence as you state here, I think you are every part as wrong as others who have sought to drive a wider agenda than public health from this disaster.  I think it has seen you reduced several times to the level of (self?) deceit used by the anti vaccination / pro death campaign, and it is a stain upon every conversation it touched.

That's not a fact. It's wrong. (cases per 100,000  past 7 days):

• Latvia 1165
• Lithuania 893
• Romania 758
• Bath and NE Somerset (highest upper tier LA in England) 759
• England 436

As many have shown over the last 48 why bother letting minor details like reality get in the way of things.

We might not be able to pull it off every year but what about one year with 48 weeks? We could go for another 1752 calendar change law if you can find one suitable to switch too.

Or just go for a 48 week year and whilst we are at it fix pi as well.

In fact both Wales and NI both also have higher case rates than England. I can't believe he isn't aware of that since he is always looking at differences between the nations.

He's just using straight up fake news. His debate tactics are almost identical to oureed et al, just with a different agenda.

Yes. Pushmi-pullyu. Best ignored.

Agreed, so why all these replies with more than that's plain embarrassingly wrong (England having highest case rates) and plain irrelevant (case rates are the least of England very significant problems right now).

It’s kind of lethal though with nearly 1,000 deaths a week…

Covid won’t ‘end’ without ongoing boosters for the whole population. It’s not clear what the rates of breakthrough cases / hospitalisations / deaths are but they aren’t nil. So simply alluding to population level immunity is a bit simplistic. 

Replying to yourself now? Pretty sure it’s the same person behind both profiles, VS is just a milder variant. 

They do result in serious illness and death. Witness the current stats. It’s not all due to the unvaccinated.

Healthcare is already under significant strain. Not to mention 1,000 deaths a week.

More cases mean more opportunities for variants. Witness the latest Delta Plus, wherever it came from.

I’ll take NZ any day. Literally hardly any deaths and life largely normal so far. They might get a higher death rate than the UK if their cases get out of hand but their population will probably behave more cautiously than here so I’d be surprised.

We should get out of this gradually and cautiously, particularly over the winter months. My big thing is boosters for everyone.

An outbreak in a large city will push up the national score for one of the smaller countries but a regional outbreak in England will be smoothed out by the other regions which are not experiencing outbreaks.  England is always going to be smoother and have less extreme trends.   If you want to compare England against a country with 20 or 30x lower population you need to do it over a longer time period.

I didn't say 'cases per 100,000, past 7 days', that's your criterion.  The data I used has a different criterion - most recent day, rather than smoothed over 7 days.  I'm basing my comment on this:

https://twitter.com/globalhlthtwit/status/1450216815246946310/photo/1

The basic point stands for both criteria: the UK's number is disgraceful.  Whether it is the absolute worst in the world or not it is right down there at the sh*tty end of the stick.

In reply to tom_in_edinburgh (05:15)

Guess you weren’t looking for a fair comparison then, going off your own advice 11 minutes before.  


 

You're picking and choosing your data to fit your racism. Dangerous game that.

One thing that stands out is that you don't seem to understand that number of detected cases does not equal number of infections.

Not really wanting to restart the conversation that we had last week, but it's this or watch kid's TV.

I agree about over 50s but do you think boosters in our age groups (30-40s) are really justified? Breakthrough hospitalisation rates are low in under 50s. For people in their 40s it's about 5 in every 100,000 people in a four week period at current rates (same data source as my graphs above.) That's about the same as for unvaccinated people in their 20s, or about 25% of the rate shown for unvaccinated people in their 40s. Alternative way to think about it: if a double vaccinated person in their 40s gets covid, they have approximately a 1 in 300 chance of needing hospital treatment. For those without underlying health conditions, this is undoubtedly a conservative estimate.

I'm sympathetic to arguments about healthcare overload if rates got very high (such that there was a risk of overload even post >50 boosters). However in terms of individual risk, I really think this is a risk that people like us should be willing to take in order to allow NHS staff to do more important work and to allow those vaccines to be used by countries with greater need. Obviously my argument applies to younger groups too.

Will be interesting to see data on case and hospitalisation rates post boosters of course. My thinking would change if it seemed giving everyone a booster would substantially boost population immunity against infection and bring case rates right down.

I'm not picking and choosing anything, I'm just reacting to what I see. The post I got the numbers from came up on my Twitter feed.  The guy who posted it is a reputable scientist,  his Twitter bio says he's an ex-director of WHO, Professor at UCL and on Independent SAGE.

One thing that stands out is people are grasping at straws to avoid facing the fact of just how bad the UK numbers are.

Look at it over a longer period and you can see there have been times where the UK case rates were as low as other countries if this was just because the UK has better testing they'd be consistently higher.    The UK numbers start going wild in the summer after the Tories took the lid off when other countries kept it on. 

https://ourworldindata.org/explorers/coronavirus-data-explorer?zoomToSelect...

If I’m following the numbers properly (haven’t done a detailed check for these) this is *not* a stand-out high risk compared to the risk of seasonal flu hospitalisation in a wider, overlapping age bracket - see table 1 here - https://bmcpublichealth.biomedcentral.com/track/pdf/10.1186/s12889-016-3128... (15/100,000 over the whole flu season for flu A+B in ages 18-49).

If covid cases/day go up significantly then the risk rises above that for flu.  If covid cases/day remain high for more than the next three months, that risk rises significantly above flu.  

In terms of reducing the risk of going to hospital this winter, you and Misha can perhaps achieve more by going for a paid flu jab.  I think I’m going to for the first time this winter.

Nobody is grasping at straws.  There have been open discussions comparing deaths and hospitalisations, and they’re in no way positive about the situation in the UK.  You just miss them because your anti-English racism demands you play Covid Top Trumps with the least relevant measure when it comes to international comparisons.

You’re not grasping at straws, you’re glued to them.

Edit: to make it clear Tom, early on in this pandemic I jumped on any egregious misuse of data to argue against control measures.  I didn’t do this because I was for more control measures then (although I was) but because gross misrepresentation or misuse of the data to bend it to a politically motivated position has no place in forming people’s opinions.  I’d still like more control measures now (mild ones) but I’d be a hypocrite if I supported your abuse of the data because it aligns with what I want.

Give it a rest, you tedious old parody of a racist.

Why boosters for everyone? Didn’t Einstein say “Insanity is going the same thing over and over again and expecting different results”.

I appreciate the immune system is a complex beast, and in some subsets of the population giving a booster with the same vaccine technology will likely have a beneficial impact, but for most people who are at lower risk would it not be beneficial for them to have a broader immune memory i.e. have an immune system that can deal with multiple viral surface proteins/ glycoproteins?

Any population immunity strategy that’s based around immunity via a single protein spike will make us incredibly vulnerable to future variants. 

Re New Zealand - I don’t feel as rosey about their chances over the next 12 months as most people on here. They’ll be back in lockdown before they get to the end in my opinion.

Deaths and hospitalisations are the 'top trump' argument in this because they completely ignore illness not serious enough to require hospital treatment or not fatal in 28 days.   

If you want to make an argument that catching Covid isn't that bad any more it needs to be based on the percentage of people who catch it who make a complete recovery and are as healthy as they were before, not the number not dying inside 28 days or not requiring hospital treatment.

Until there is data to support that argument I will stick with cases as the figure of interest.

Keep drinking the Tory Kool aid.   

What do you mean by this Tom? Nearly everyone makes a full recovery. If you’re referring to long-Covid/ CFS/ ME might I politely suggest it’s a disease of the mind, not the body.

Edit: my long Covid point probably deserves another thread in itself and I’m sure I’m going to get tonnes of down votes for saying it, but I’ve got to admit it feels like the most likely cause.

If we’re placing poorly informed bets on the cause, my money is on a pathological immune response with auto-antibodies being generated during the period of intense immune dysregulation, potentially also with disruption to the microbiome from messed up gut endothelial behaviour during the dysregulation.

I think we’re going to see the studies into long covid put to bed the - already highly suspect - idea that post viral fatigue is “of the mind”.

Nobody is making that argument.  You're imagining it.

And everyone else here it seems will stick to the comment that cases are not comparable between different nations.  Here is another poster making that argument.  You have never engaged with them [1], not even to accuse them of drinking Tory Kool aid.

[1] https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_48-...

If that's the whole flu season then presumably it's over a few months? So in a given 4-week period I assume the flu number would be more like 3-5 /100,000 or something of that ilk? If you look at the covid data averaged over 18-49yos, the mean would be quite a bit below 5. So, I agree the numbers look very similar.

I’ve been out of the loop due to the madness that working in the NHS after a cabinet reshuffle has become.
 

But, at risk of dragging the thread back to actual covid plotting.. have you all seen the rate of change map on the grauniad today? The SW of England looks ‘interesting’ following BANES being top of the LTLA list this week. Is this where the new(er) variant is? If so I predict a national incident in about, ooh, a week?

I'm not going to downvote, but I can tell you from personal experience of my brother and a close friend that long Covid most certainly is not "in the mind"! I wish you could have known these people and what they went through over 12-15 months...you wouldn't be saying that if you had.

I don't expect you to believe me or change your opinion on this. I'm just posting this in support of any other long Covid sufferers who might not enjoy reading your post.

You may politely suggest whatever you like, as long as you don’t mind me politely suggesting you do some research and don’t make denigrating and patronising assertions about people’s suffering based on thin air.. absence of evidence vs. Evidence of absence and all…

Oof, I hadn't, not paying enough attention. That does look bad. Attached image for anyone who can't navigate their website.

I wonder if it couldn't be partly caused by people going to be re tested who had had a positive LFT/negative PCR combination over the last few weeks? I think I read that the problems there mostly affected the south west... seems a bit unlikely to explain it all though.

(I thought from Bruxists link that there were higher%s of AY4.2 in Scotland? In which case it's unlikely to be caused by that. May have misunderstood though.)

It's because of retesting all the likely false negatives from the dodgy lab rather than anything else.

The SW of England stood out on the last plot 18 update buried somewhere mid-thread as well.  Latest update below.  The far right of this plot is as provisional as ever, and I'm not sure the growth is as over as it looks in this provisional zone.  I think there's some noise going on with the hospitalisations - I consider the leading edge of that a lot more provisional than cases.

I haven't looked at the geographic data over the variant, that is one obvious candidate for a strong regional change.  

Another is the issue (scandal) over the dodgy testing lab that is thought to have given 43,000 false negative results largely in the SW.    This will create the impression of rise by having removed around 1,500 cases/day from the data for some time establish a lower baseline, and could cause a subsequent "false" (in terms of indicating new inflections/day) high as those people were being asked to re-test and some will still test positive.

Of course, if the variant happened to be establishing in an area with poor testing - and by extension poor feedthrough to sequencing - that would be bad.

I'm not sure it needs everywhere else to follow the apparent trend of the SW to get to that point within a couple of weeks - at least in terms of locked in consequences - if the current rising trend (with baked in demographic shift in the wrong direction) doesn't end.

Edit: Too slow to type that up, see reply from mik82 above - but I think the false negatives bias the rise as well as the re-tested positives, and would do so (to a lesser degree) even in the absence of re-tests.

Oh, was that all down there? I hadn’t realised.. as I say I’ve been out of the loop

Have we been busy forming a single directory company with no history and no central accreditation to take a £120m contract for RT-qPCR testing have we sir?  Suits you sir.  Donations go in this box sir.  Suits you sir.

Do you accept BTC?

Yes - and had a big enough effect that loads of people locally spotted the disparity between symptoms and +ve LFT and the PCR negatives.

The good news I guess is its a (hopefully) isolated lab incident, rather than something that sidestepped the PCR.

Anecdotally lot sof people being asked to re-test are not bothering - the infections are now weeks ago in some cases.

Seems entirely reasonable tbh! I wouldn’t bother in those circumstances.

If you are already past the date that would have been the end of your isolation period had you originally tested positive (still 10 days from symptoms beginning I think?), then it seems reasonable not to do it.

Edit: minimike beat me to it

Ok, so given 5 mins reading of news reports, it seems they’re estimating 43000 false negatives, of which ‘a few thousand’ were expected to still be active infections (failures occurred from early sept apparently). So let’s assume 5000, of which most are SW maybe (test centre was in Wolverhampton and other areas are also mentioned). 
 

so say 4000 false negatives which could be retested in SW. of which some fraction don’t bother.. so maybe 2/3000 cases to add across the region? 
 

that doesn’t account for the majority of the rise.. also that map looks suspiciously ‘radial’ to me. I’ll hold my breath until next week I think. 

The rise is not just about the addition of cases now, but a return to normal from the depression of the baseline beforehand caused by then-missing positives.

My take was that they think there are ~43,000 false negatives out of ~400,000 samples - as if the lab (*) was reporting no positives.

This is over a 35 day period, giving a baseline depressed by ~1,200 cases/day if true.    If mostly applied to the daily cases in the SW, that is going to create a significant impression of a rise in cases if it is suddenly rectified by switching labs, even without people being sent for re-testing.

It’s funny how different people look at these things; I looked at it and thought "artefact" although occurring as it does by a coastline doesn't help.  Not saying I’m any less wrong than you, or any more right!  What we need here is some AI to give us an unbiased and implicitly trustworthy judgement.  In the absence of AI, I’ll see if I can fire up my rate constant vs time map code…

Especially if you're going near the South West...

I hope there are people intensively investigating this to understand exactly what is going on, the worst possible outcome could be the rise of a potent variant being masked by confusion resulting from the testing clusterfudge.  Once again we go back to waiting for another week of data.

(*) There was a lab, right, not just an intern typing '0' in to an Excel spreadsheet a lot?  Right?  I mean, at this point I wouldn't mind if the SFO were smashing down literal doors to check, assuming I have the correct understanding of the situation from the media

Cases in the south west seem to be roughly 3000 per day more (very roughly, doubled) compared to last week.

I think that seems more than the 43000 figure would explain (at least, it is certainly more than your 1200/day estimate). But then, I'm not sure how they came to the 43000 figure or how confident they are it isn't even higher?

I guess we'll see if it drops back over the next few days.

yes of course, just filling in the local picture.

Indeed, but we're going from perhaps -1200/day (missing positives) to perhaps +1000/day (added positives from retests) for a few days.

Reporting is pretty light on details, isn't it?  With order of 400,000 tests through the lab in total and recent positivity rates it can't be much higher, unless other labs have had similar issues.  As another poster pointed out on the thread on this [1], it basically equates to the lab returning no positives, so it can't get much worse.  

I'd be very interested to hear from those who work in the testing program (I know you're out there!) if any advisory notices have gone out to all labs as a result of lessons learnt from this (e.g. bad batch(es) of reagents, new failure mode found on an instrument etc), I rather suspect not.

That's the hope.

I would like to see the time series data of tests/day sent to this lab so that we could understand where the missing positives fall over that time period; I have an entirely unfounded suspicion that the lab was just ramping up online and so they may be biassed towards the end.  Thats smacks of the kind of fairy tale we tell to ourselves as false comfort however.... !

Edit: If it really 1,200 missing positive tests/day that suddenly came online, that could be significant in terms of the behaviour of the national level data and perhaps why the recent turn to growth has been more sustained than we have seen from any other period of higher rate constant in recent times.  It would have needed the switch-on of proper testing to land at just the perfect moment to balance infections turning to decay, an effect that couldn't last more than a week and would be running out by now.  Another fairy story?

Worth a dig I think in to the regional level demographic data to see if the unusual (for recent months) growth of cases in all ages is in any way associated with the south west.  

[1] https://www.ukhillwalking.com/forums/off_belay/43000_incorrect_pcr_tests-74019...

Can anyone help please!

Can you link me to a chart showing the percentage of total daily recorded cases by age bands (for a recent day)?

Have found on ONS site estimated percentage increase in cases by age band, but that's not what I'm after.

Thanks.

There's a heat map here (England only)

https://coronavirus.data.gov.uk/details/cases?areaType=nation&areaName=...

I've not seen such a plot elsewhere, it's cropped up on some of these threads as a relative frequency (different linear scaling to a percentage) as Plot P1.C [1] - it might be making a comeback in thread #49 as things are changing there quite a bit...

If you use the "Download" button at the bottom left of the heatmap mik82 linked, that includes absolute daily case numbers as well as the population normalised rates shown in the heat map.  It's not in the most inspired format, mind you, but it has everything you need to calculate what you want...

[1] https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_46-...

Thanks, that's very helpful.

Thanks.

It does seem that I have not missed an obvious summary of what I'm after.

I tried the downloads...but couldn't make much of them!

Thanks anyway.

And I'll keep looking.

Another couple of days of data for the English rate constant plots.

Cases are doing an impression of heading for decay; they might even show decay by tomorrow looking at the provisional window.  Let's hope that's not because another 43,000 cases have been lost somewhere.  

No real developments in the less up-to-date demographic data. Perhaps the behaviour in the rate constant in children is lagging adults slightly suggesting the balance of blame lies outside of schools, perhaps not.  Could just be a vertical offset looking like a time shift, there's not enough features to really tell.

These are fair points. However there won’t be that much vaccine fade in the 40-50 group yet. I’m 40 and I had my second early June - that was ahead of most people in my age group. So I fear the % will increase with time. The other point is it’s not just about hospitalisations - it’s also Long Covid or a couple of weeks in bed (mild symptoms in medical speak but that would be 2 weeks out of my life plus recovery time and 2 weeks of lost economic output as well).

Nor am I asking for a booster now. However it would be nice to have one in 6 months’ time or  at least before best autumn. Plenty of time to scale up production. What I’d like to see is ongoing boosters for everyone in the world. Of course first doses for everyone in the world would be nice for a start… It’s just the lack of political will to make it happen. Rishi spent £300bn on furlough. Rightly so but are we really saying he can’t throw in another £10bn to get the ball rolling on vaccines for poorer countries and shame the US etc into doing more?

But the results are very good. It’s just that it seems that the immune system response fades over time. So it can be boosted to ‘very good’ again. It’s just common sense! Nor do we need to boost with the same vaccines. There are studies looking at mix n match strategies. 

The USA has pledged to deliver 5.87 times as much vaccine to low-income countries as the UK in 2022. On what basis are you intending to shame someone?

Thanks for your cases per day plot; just what I was after.

That’s great, the numbers are pretty small though, in the scheme of things. The richer countries need to do more and manufacturing capacity needs to be increased further. 

Great to see numbers stabilising (this also comes through by eye on the headline numbers). I fear we may have reached a new case baseline - 40-50k rather than the previous 25-40k. With an adverse demographic shift as you say. I actually wonder whether the weather effect is now about as bad as it will get. It’s already too chilly for prolonged outdoor socialising (less so the last two days, more so today!). Half term this week and next would help to moderate hopefully. I would expect the next significant upsurge in December due to pre Xmas socialising, including large corporate parties.

Having some good discussion over the CFR plots prompted me to do them for age for the England data.

As always, it's subject to the proviso that cases do not equal infections, and that the relationship between them can be flexible.  But I think the UK has been relatively consistent over this time, no more than a change of ~30% perhaps.

This is done using the UK dashboard's demographic case and deaths data.  Cases data is deweekended.  CFRs are then calculated using 7-, 14-, 21- and 28- day lags from the cases and deaths data, and the result is filtered with a 7-day moving average.  The colour bands show the minimum and maximum CFR values across the various lags, and so give a reasonable bound for a "true" longitudinally determined CFR.  When the number of deaths is very low, the trace is censored as it gets very noisy.

Two plots of recent months, one with a linear y-axis which helps clearly show individual risk, and one with a logarithmic y-axis which clearly shows the exponential increase in fatality risk with age.

Two plots of the last year, both with logarithmic y-axes.  One the second one I've manually traced black lines back a year from the current CFRs.  This nicely shows how the vaccines have reduced individual risk by a factor of ~10x (smiler to the conclusion from the noddy all cause mortality plots), and how they effectively make people ten years younger in terms of fatality rate.

Also one extra plot I did for visualising the input data - it's a time series heat map of cases in a teal colour and deaths in red.  How dramatically hospitalisations and deaths could reduce if a relatively small number of cases were prevented; it was good to hear the health secretary tell people to open windows in his briefing today, but energy poverty and winter is the reality for too many people.  In-room HEPA filters with a bit of guidance on their location seem like an obvious step here, Government could afford one for each of the most vulnerable million or so households for less than the cost of a private, uncertified Covid testing lab that apparently looses 43,000 cases.  

Re SW spike

BBC points west had a long sequence on this this evening - assume it will be on iPlayer.

looks like over half the cases detected this week were school age.

it’s been several weeks of people who were doing the right thing and getting tested when ill being punted back into circulation - so locally the R rate will have been much higher, and there was no way to notice the rise in cases as the tests were wrong - it’s only now we can see the impact. Not the missing cases coming to light, but the results of several cycles of transmission coming to light.

recall also the SW has been the best performing part of England - so has a fairly high proportion of younger folk with no prior exposure. Happily we also have solid vaccination rates in the oldies.

The lab sounds proper shonky - apparently already under investigation for some rum dealings over paid for PCR tests for travellers before this debacle came to light.

Thought it worth highlighting this Dispatches episode from last week, which points out real problem areas where things could be improved in the NHS. The most shocking point is the estimate of the costs of legal action on medical negligence. Just beyond eye watering (so much so it needs More or Less fact check). The proposed solution is to follow the way medical negligence is dealt with in Sweden.  It's relevant to this thread for two reasons. Firstly because as those who remain at work will on average be more tired and ill than usual from the cumulative effects of the pandemic so they will make more mistakes and that bill goes up....money that should be spent on care, recruitment, estate and clearing backlogs. Secondly the return to target cultures Javid is pushing makes this worse.

https://www.channel4.com/programmes/clapped-out-is-the-nhs-broken-dispatche...

It's anecdotal, I'll admit, but I know quite a few people who had symptoms and positive lateral flow tests, took a PCR which returned a negative result, had another positive lateral flow test, and decided to self-isolate anyway and assumed they had it. I'm not sure the increase in the SW will be entirely down to the false-negative PCRs.

Something sure is going on.... a big spread from the maps yesterday and Cheltenham, Stroud, Tewskbury all up 400% plus on the week on the maps.(data.gov.uk and Guardian which comes from that)

aye, I know a few like that, but also lots that trusted the PCR and went back to work and school.

If it is just the testing, then we* should be able to work out what the impact of the current testing regieme and isolation based on the changes in the SW from whenever the lab went wrong.

*by we, I of course mean wintertree

This may be it.. if a few thousand (or even hundred) highly infectious people were falsely reassured and went about their business, with the lack of distancing and masks, every time they entered an office/bar/school/… they seeded a super spreader event. Like the worst possible scenario. So maybe it’s not just the retests, but also the (local) carnage that resulted from the false negatives?

Either that or there’s another new variant lurking in there and we’re DOOOOOMED. I doubt that, the sequencing is pretty extensive and thorough in the UK labs… oh. Wait.

yes - thast my expectation - a lot of people have not been getting re-tested, or will be beyond the point at which a PCR will pick them up

So, in the grab bag we've got....

• Lower baseline during period of failed tests, then a rise from baseline returning to normal (oder of +1400/day rise?)
• Additional re-tests landing later on (order +1000 test/day for a while?)
• Additional spread that occurred as a result of people falsely getting negative PCR results (order of ????/day rise)
• History of lower spread in the area leaving less infection acquired immunity

The SW is still standing out on plot 18 - I think the apparent turn to decay is more an artefact of the "weekend effect"  when updating this plot away from a Friday/Saturday.  I'v coloured it's trace red, interestingly it's had stand-out high growth and decay pretty consistently over the least two months, although clearly this spike is on another level.  So far there's nothing exceptional about the hospitalisation data for the SW, and if this peak represents a real change to infections, that should start landing about now.

Do we know if this lab was processing pillar 1 samples?

Ah, the emotional roller coaster of interpreting increasingly fractured data.

In reply to Dr S. at work:

I'm not touching it with a barge pole, there are more unknowns than meaningful data points I think, and so I could produce a fit supporting more or less any conclusion.  I'll wait to see what others more skilled in the arts and with access to more longitudinal data conclude.

In reply to Misha:

Another day of growth in the week-on-week plot but ever decreasing rate constants still mean very large daily growth given the high baseline.  We wait and see how this converts to hospitalisations, but I do wish Javid had gone beyond asking people to wear masks and open windows in his entry in the trolling competition, er sorry government briefing, last night.  I was more worried again this evening to hear talk on the radio priming us for 100,000 cases/day soon enough - as if three's a demographic shift baked in that's really bad news for healthcare.  Still, the last time they primed us for 200,000 cases/day it turns out they had it well wrong, the football ended and cases took a nose dive.  Fingers crossed...

Perfect day today - still morning, Jack Frost had painted swirls on the car roof, ice on the windscreen.  Sadly I spent most of it looking out of the lab window at blue skies.

Thanks, that’s interesting about the SW. The trough wasn’t particularly more pronounced than other regions  - just a bit deeper and later. The current peak is something else though. My money would be on false negative people turning into super spreaders. Or the Bristol variant. One thing worth noting is any variants would spread pretty quickly now if they have a significant transmissibility advantage over Delta, given hardly any restrictions left / followed in England.

Yes, pleasant today in the sunshine. Went for a walk and the canalside bars were basking in the sun but hardly anyone inside or out mid afternoon. That’s the thing, with it being cold once the sun goes down and the days being short, I think most socialising would happen indoors. 

The SW. It seems bizarre I asked on here only 11 days ago if anyone had a theory - it feels like longer. At the time I'd experienced a week of anecdote - but an awful lot of anecdote, too much to be ignored. (I've got kids at schools and colleges, it's the Cotswolds so all the schools mix socially, and my kids' mum is a teacher at another school - a proper brew, in short. Same goes for many of my peers across the region.)

I hope it's just that lab. Stroud is red at the moment, like most of the Severn areas. But I'm not feeling 100% relieved that that is all it is. I don't know why.

Ah, I'm rambling. Been a long day digging out subfloor, mending and raising up joist-ends, reboarding. My back hurts - floors are heavy when you lift an end an inch - who'd have thought?

And thanks for these discussions. I may lurk, but I've read all of them. Night night. 

Yup, you got those anecdotes right.  Some more updates today - seems there's been confusion over the dates of affected tests.

These are rambling threads.

Anything interesting under the floor?  When we got our old floor out we got down to the old concrete base of the then-cow shed, and it still stank of ammonia and all the other nasties 60 years later.  Getting that out was a foul job.

I would have thought there would be plenty of room for the weather effect to worsen further.

There's a big difference between time spent/activities done outdoors (or indoors with windows open) when the temperature is 10-15° and it's light vs when it's ~0° and dark.

I think we saw noticeable spikes/drops whenever the weather changed throughout last winter.

Agreed.

Changing the subject Indie SAGE has a very extensive look at the numbers this week including the impact of the Wolverhampton lab failures (a clear uncharacteristic decline in the SW that should have rang alarm bells) and the need to speed up boosters alongside other measures to cut spread. Also a ripple plot (from Mainwood) showing the time for kids infections to cause a ripple in their parents age group and later on their grandparents age group (wintertree got there first again with his shadows).

youtube.com/watch?v=X7DCWpsyUFU&

I'll copy the slides when I can access them. 

In reply 

Latest ONS covid insights:

https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/con...

The flawed wonder that is humanity:

"Between 6 and 17 October 2021, 39% of adults said they had always or often maintained social distancing when meeting with people outside their household.

This compares with 84% who believed it was important or very important in slowing the spread of coronavirus.'

For reasons I don't understand, the SW often has more extreme rises and falls and what I see in their data doesn't stand out compared to some other periods.  

Alarm bells in the central data aggregation system should have been screaming over one input source (lab) with positivity about 10% lower than others.  ("Now, warning lights are flashing down at quality control")

Starmer was on the radio yesterday talking about the gulf between where boosters are and where we need them to be.  This seems like a really clear, obvious thing to hold the government to that has the most immediate potential to make a significant difference.  

I think the previously rather academic discussions over the past couple of weeks over case rates, death rates and CFRs around Europe are starting to become relevant to the situation on the ground; a freight train called Winter is sweeping across the continent and change is coming everywhere perhaps.  The German health department today is messaging over a coming winter wave in their media.  Lots to get people thinking about tomorrow...

Edit to your second post:

Yet, despite the continuing drop of restrictions by the population, we're still seeing no ability for sustained exponential growth in cases; each burst of growth ratchets the baseline up but that's all; never runaway or (exponentially) rapid growth.  

Things could be a lot worse, and in a sense its comforting to think that we have these measures available to us to reduce our rate constants if we need to - remaining so close to stagnation as they do, it shouldn't take much to change that.

It really does look unusual in the plot in the Indie SAGE presentation. They have produced a series of recommendations following the lab problem:

https://www.independentsage.org/statement-on-covid-19-testing-at-immensa-he...

I'd add my dented optimism on the UK pandemic front is still just a bit over half full. For the world (where it matters more), I'm well below half empty in the next months. Also for those hundreds of UK families dealing with death and long covid daily, and our overstretched and exhausted NHS, a perfectly feasible rachet down rather than an unnecessary rachet up would have been very welcome....

I've put a screenshot in from their presentation below with two green arrows added by me.

Things often make sense in retrospect in the data, identifying meaning in real time is much harder.  

I would argue for example that during the failure period, case rates for the SW are generally in the lower range of the regions, in keeping with the rest of the time period, and that whilst there is an oddball low (second arrow), it is no more extreme than the oddball high a while earlier (other arrow).  

The trick is to be smart in real time, not in retrospect (the later is easy).  With reference to being smart in real time, I think there is an immediate lesson for PHE here....

The measures seem reasonable.  One that I do not see there and which would have picked this up within days is monitoring the positivity of each lab returning data to PHE central and flagging for manual investigation any with a positivity more than, say, three standard deviations from the mean over a weekly rolling average.  The actual threshold would need to be chosen with reference to the actual data, and might need adjusting for periods of regional differences.  But a lab returning a positivity of close to 0% when national positivity is around 10% should stand out like a saw thumb immediately.

An almost unique sharp change occurs in SW data around Sept 7th... it's a bit buried under the other curves but it's there. Yes, it's easier to see that with hindsight. 

I've posted already that the internal QA should have been way way more obvious.

To be fair if it’s a dry, sunny and still day in mid winter, more people will head out, especially at weekends, so you have a point. 

Or your flawed logic, the others may not have met with other people......

On the boosters point - it’s the usual ‘blame the people’. There isn’t enough publicity including clear implications, indeed the new vaccines minister has gone to ground. The call up seems patchy due to system issues - have read potentially couple of million people have been missed so far. And the roll out is disorganised - GPs aren’t doing it or at least not all who were doing the initial roll out are still involved. Hence in smaller towns there is nowhere local doing boosters (that’s the case where my parents live). 

My understanding is one of the reasons the sequencing takes time is there’s lots of quality control. Not so with the PCR tests perhaps. It’s understandable that PCR results are needed a lot quicker but as you say some basic monitoring of outputs isn’t hard to implement. 

BoJo or Javid said the other day it’s fine, we have 6-7k spare beds. Occupancy has gone up by 1k in a week, with more backed in given cases and demographic shift.

They just don’t learn from past mistakes… I predict a hasty shift to Plan B by mid November when they realise that a one week half term ‘firebreak’ hasn’t helped. 

Hmmm... not read the report and its predecessors then to show that's not the case.

I thought you could book your booster jab on the nhs online site as long as you were past the 6 month period.

The previous vaccine minister was on top of his brief and by all accounts was good ( one of the reasons for his promotion),……the current one looks really appallingly second rate.

Err no, if Ihad I wouldn't need to read your interpretation.

You can once you are 6 months plus one week, for some reason. That's only been the case for a couple of days though.

On the contrary the new one is world leading..... globally.

https://twitter.com/BestForBritain/status/1451147208087191552

Exactly what I mean! Blatantly useless. 

Oh . Did not know that.

I also  think the campaign to get people double vaccinated has drifted off .

something has lost its way as a campaign 

Re your interest in weather correlations: https://www.nature.com/articles/s43588-021-00136-6

Excellent, thanks.  That's going to need reading on the large monitor, if I can find it under the piles of stuff...

Skim reading it, one line jumped out:

The problem of co-linearity in climate factors has challenged the search for environmental drivers of influenza in the past, and very similar issues now apply to COVID-19

Spot on.