UKC

Friday Night Covid Plotting #47

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 wintertree 09 Oct 2021

Post 1 - Four Nations Plots

Thread no 47.  After the last 18 months, I'm surprised I can still count in to the double digits.

The four nations plots have an up-tick in cases for all nations in the last couple of days; it's too recent to drop through to plot 9x, which measures the rate constants over a longer time period.

This is very synchronised and feels like a weather effect to me - it corresponds to the vile few days around October 4th.  We'll know by next week if this is sustained growth or not, but I'm leaning towards "not".

The general feeling I have is that we've seen - multiple times - over the last 6 weeks that there's the potential for decay in symptomatic cases, but that it's very fragile - to changes in restrictions, to schools reopening, to crap weather.  We're just not seeing the sustained decay that would deliver the respite our healthcare systems and people increasingly need.  We're also never seeing runaway growth, just this never ending hinterland of high daily numbers and the looming approach of winter.  Given how clearly cases respond to changes lately I get the feeling basic control measures (masks, more WFH, better enforcement over ventilation) could bring about sustained decay, so it's comforting to think that's probably there "in reserve".  Indeed, this last week has heard some nosies out of government that they might be considering some of this. 

Link to previous thread: https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_46-739797

Post edited at 21:27

 wintertree 09 Oct 2021

Post 2 - England Ⅰ

Cases are back to growing this week; over the last month they’ve been up and down like a yoyo, until now there’s always been some clear, identifiable explanation for it; the next post digs in to the demographics of this latest rise; the causality is not so clear to me this time.  Perhaps weather.

Hospital admissions are just starting to rise; this is likely the result of the limited growth in cases in adults aged around 35-50 that immediately followed the much larger growth in cases in school aged children.  Hospital occupancy has probably gone back to rising, having had quite a large decrease over the last couple of weeks.  I think it needs a few more days of data to see if deaths are rising, but they’re likely to given the hospitalisation changes.


 wintertree 09 Oct 2021

Post 3 - England Ⅱ

The week-on-week rate constant plot shows five days of growth in top level cases; these are low rate in exponential terms, but as the absolute number of cases is so high (~30,000/day) they still translate to large numeric growth (about +500 cases/day added each day at the moment).

The demographic week-on-week rate constant plots stops a few days earlier due to reporting lag.  In this plot, the last big growth peak in under 15s has ended and turned to decay, and the smaller, subsequent peak in adults (that I take to be lagged household transmission downstream of school infections) had also turned to decay.   Over the last couple of days both have swung around back towards growth with no lag between them; this to me feels more like the typical weather related modulation on the rate constant we see; certainly those days were stand-out miserable, cold, windy and wet - so if I’m not barking up totally the wrong tree in my interpretation this growth should not be sustained for more than a few more days in the top level data (and a few more again in the lagged demographic data).  The growth is almost all in adults in this simple breakdown.

Plot D1.C is more concerning; this breaks the growth down by the 5-year age bands.  It uses the exponential fitting method to measure rate constants; this is a bit less immediate (more lagged in analysis) than the week-on-week method but works well for highly broken down data with lower numbers.  Here, the strongest growth (most vivid orange on the far right of the rate constant plot) is in adults aged 65 and over.  I can think of two different interpretations to this:

  1. This is down the chains of infection of the parents, themselves downstream of the school burst.
  2. This is the age range with the closest potential to growth, and so the first tipped over by the rotten weather.

There are pros and cons to both interpretations, I’m leaning towards (2) for various reasons that I’ll come to below.

The bad news with this development is that compared to the last few rising phases in cases over the last ~6 weeks, this one is likely to have more impact on hospitals and individual health.

The good news with this plot - astounding really - is that there is still no sign of any university outbreaks; well past the time they were showing up last year.  Last week I’d said I was unsure why growth in school ages ended - was it reaching immunity thresholds, or was it a combination of disruption from control measures and a good weather?  I’m now leaning towards thresholds being reached; if it was reactive control measures and weather I’d expect to see the next cycle of growth beginning.  So, hopefully in younger people of both school and university age, we’re getting to the point there just isn’t the potential for sustained growth in symptomatic infections.  

It's increasingly worrying to me that cases in older people aren't going in to continuous decay; it seems we're realising that potential in younger people, but the immune system - like most of the subsystems in our bodies - gets worse with age.   Helpfully, the booster program is kicking off.  I've been happy to see signs coming out of the government that they're considering bringing back some control measures; with the uncertainty over the looming winter respiratory season quite apart from Covid and the unyielding pressure of Covid on healthcare, something may yet have to give.

Edit: No plot 18 this week for the English regions as the dashboard API keeps timing out on me.  I'll try in a day or two.

Post edited at 21:46

 wintertree 09 Oct 2021

Post 4 - Scotland Ⅰ

The cases plot 6s has a little up-tick in the trend line, I would say this is just down to noise in the data, but the week-on-week rate constant plot in the next post supports a turn to growth.

Likewise plot 7.1s for hospital admissions has a bigger uptick, which again appears to be a single data point; that one is a bit more concerning as it’s a bit more stand-out of the usual noise levels there’s no reason to expect a rise yet given the lags from cases to admissions.  Hopefully it’s just a blip that passes with more data, although hospital occupancy in 7.2s has stopped reducing; for reasons I don’t understand it’s not falling anything like as fast as in England despite good progress in reducing cases. 

Deaths have more than halved in the last couple of weeks which is good and better than expected from the other measures; where-as I think England has had a lot of confusion in the cases data (detailed over previous weeks) plot 9 for Scotland shows very conventional behaviour in the cases, admissions and deaths data all crossing the y=0 axis in to decay in the expected order, but now the halving time for deaths dropping more than the others.   Perhaps this is fully explained by the recent shift in cases towards school aged children in Scotland, but it seems incongruous that deaths are falling so much faster than hospital metrics.  Regardless of the cause, it's a good development.


 elsewhere 09 Oct 2021
In reply to wintertree:

Thanks!

1
 wintertree 09 Oct 2021

Post 5 - Scotland Ⅱ

The week-on-week method rate constant plot shows that cases have been heading for growth for a while and have just got there.  This is why I think the growth on the leading edge of plot 6s is real and not just a noise effect - the week-on-week method rate constant almost always behaves as if it has momentum and inertia, and it's a predictable turn to growth from the points before it.

The timing of the growth matches that of the worsening weather.  The demographics in the detail plot for the Scottish D1.c suggest its going to be adults where this growth is coming from, and perhaps younger children.   Again it’s encouraging that there’s no sign of university related explosions in ages 15-19, as with England.


 wintertree 09 Oct 2021
In reply to wintertree:

Very much a holding pattern this week.

Every pandemic ends, and the way this one ends is not making itself as clear as I'd like.

 In the last month it seems there's been a step change in how most people view the situation, and the prevalent view is now that it has ended; it has not.  

The individual risk has reduced massively (for those choosing to engage with vaccination) since the start of the pandemic - despite the increased lethality and transmissibility of Alpha/Kent and apparently of Delta on top of that - but it's still roughly an order of magnitude more lethal than life itself.  One wonders how much lower hospitalisations and deaths would be if the messaging about and understanding of the risks was more informed.

The big question for me is how much we have - or have not - switched from new cases being sustained by the ever-shrinking pool of people with no immunity to cases being sustained by re-infections and vaccine breakthrough infections; I don't think the public data (largely in PHE reports) on this is enough to really understand it.  The expectation and hope is that the severity of illness becomes less as people gain more immune history with the virus; understanding how that does or does not develop helps us understand how much worse the post-pandemic Covid is or is not going to make life.

Since I removed poster minimike's tracking device from my car, they've been failing at my "Identify the xxx" posts.  The oil rig from a couple of weeks ago was Brent Alpha, the third from the Brent oilfield to come in to our local shipyards for dismantling.  This week's photo is from last weekend - we hid out from the worst of the weather at a local aviation museum; a couple of the larger aircraft live outside; what is this, and where is the museum?

Post edited at 22:04

 J101 09 Oct 2021
In reply to wintertree:

Is that a Vulcan by any chance?

 Si dH 09 Oct 2021
In reply to J101:

I thought the same - presumably in the North East so I'm going to guess that it's the one at the museum where Sunderland airport used to be.

It surprises me how small the tyres look in that picture.

 wintertree 09 Oct 2021
In reply to J101:

> Is that a Vulcan by any chance?

It is indeed.  A sad one with no air left in any of its tyres, and with dirty water running out of its underside when it rains.

I shouldn't really like the Vulcan given its singular and awful purpose, but it's one of the most impressive aircraft I've ever seen.  

If I was offered three wishes, they'd be to fly a Vampire, a Canberra and a Vulcan.  Something I only learnt a few months ago is that NASA fly several licence built Canberras as chase planes for photographing rockets in flight and for doing earth obs stuff - mind-blowing that NASA are still flyings a British designed aircraft from the opening years of the jet age as a part of their space program.  They look pretty space age with the more modern engines and their black cowls. 

https://warbirdsnews.com/warbirds-news/nasa-martin-wb-57f-canberra-returns-skies-making-flight-41-years.html

https://www.bbc.com/future/article/20160309-why-nasa-still-flies-an-old-british-bomber-design

Post edited at 22:28

 wintertree 09 Oct 2021
In reply to Si dH:

> It surprises me how small the tyres look in that picture.

Bigger than they look but still not stand out large - but then aircraft undercarriages rarely are, having never gone through the giant-wheel nonsense of prestige automobiles.

The photo is compressed by using a wide-angle shot to get anything recognisable in the frame.  This is indeed the museum at Sunderland; like many of the smaller aviation museums it's half way to being a boneyard, and not one in an arid climate either.  Some interesting land vehicles, a great model aircraft collection and a couple of very early aircraft as well as the usual.

 J101 09 Oct 2021
In reply to wintertree

> I shouldn't really like the Vulcan given its singular and awful purpose, but it's one of the most impressive aircraft I've ever seen.  

It's a mighty feat of engineering alright, often find military planes are the most impressive (through necessity I guess). I've got a soft spot for the Mosquito, superb engineering to produce something halfway between a bomber and fighter plane that was actually useful, must finally get round to heading to the De Havilland museum soon. 

Did not know about the NASA Canberra's, just reading those links now, fascinating how they're still in use

Post edited at 22:48
 Misha 09 Oct 2021
In reply to wintertree:

Thanks as always. I think the comments in your OP are spot on. It does make you wonder where we’d be if the basic control measures were retained. We’d certainly have more headroom going into the winter. 

3
 Dave Todd 10 Oct 2021
In reply to J101:

Many years ago I was doing some computer work for BAe at Hawarden Airport - where a Mosquito (G-ASKH I believe) was based, and frequently flown from.  We used to have to drive around a wide road to get to the offices and I once met the Mosquito coming the other way - surprisingly large for a 'small' aircraft.

Now, just for synchronicity, once a week I work about 300m from the Vulcan in Washington.

In reply to wintertree:

> Very much a holding pattern this week.

> Every pandemic ends, and the way this one ends is not making itself as clear as I'd like.

> The big question for me is how much we have - or have not - switched from new cases being sustained by the ever-shrinking pool of people with no immunity to cases being sustained by re-infections and vaccine breakthrough infections; I don't think the public data (largely in PHE reports) on this is enough to really understand it.  The expectation and hope is that the severity of illness becomes less as people gain more immune history with the virus; understanding how that does or does not develop helps us understand how much worse the post-pandemic Covid is or is not going to make life.

Good posts as always.

If I’ve interpreted you correctly you’re now starting to wonder if c.30k cases a day and c.100 death is broadly what endemic Covid looks like?

Children aside, we must be very close to the point where every adult (except for those who’ve been purposely protected from Covid e.g. people in care homes) have been exposed to Covid (through vaccination or infection).

If 30k people are testing positive for Covid a day, the real number is likely to be 60k. Which is roughly 2m infections a month. Given we’ve been running at these rates for nearly 4 months now it means close to 8m people will have been infected in that time. Even if you assume a high level of that is in children there can’t be many adults left to go?

I can’t quite get my head around how else Covid hasn’t followed the curve that the modelling suggested. Are behavioural/ social factors really moderating the R rate in such a way that it remains broadly 1 over time (when set against a background of rising immunity)? After 3 months of steady case rates that’s starting to feel less and less plausible to me.

Post edited at 13:27
 Offwidth 10 Oct 2021
In reply to VSisjustascramble:

Previous exposure doesn't stop you catching it. A good friend was double jabbed and still subsequently caught it twice (with some long covid symptoms both times). In terms of good protection against serious illness and death you need to have been vaccinated twice or to have 'rolled the dice' on a previous infection.

On a different subject there are some interesting covid stats here from a new book:

https://www.theguardian.com/world/2021/oct/10/covid-by-numbers-10-key-lessons-separating-fact-from-fiction

 elsewhere 10 Oct 2021
In reply to VSisjustascramble:

60M population at 60k cases per day is 1000 days. So it's what you'd expect if immunity faded over 3 years and everyone catches it every 3 years.  ON AVERAGE.

It's in the plausible ballpark for endemic cases based on what we know so far.

A perpetual bad flu year - not a happy prospect.

 Misha 10 Oct 2021
In reply to elsewhere:

However the older / more vulnerable people could be given rolling boosters (in fact I can’t see why anyone who wants it can’t have a booster every 6-12m (if that’s what’s required), if governments around the world got their act together and expanded vaccine manufacturing capacity / worked with pharma to do so. 

In reply to elsewhere:

Indeed. That’s what I was sort of getting at and I guess we’ll know more by next spring.

It seems hard to make historic comparisons as we’ve never had a post pandemic endemic phase where large parts of the population wouldn’t have survived infection in the pandemic phase.

Not a nice when you think through the consequences.

 wintertree 10 Oct 2021
In reply to VSisjustascramble (and elswewhere & Offwidth):

> If I’ve interpreted you correctly you’re now starting to wonder if c.30k cases a day and c.100 death is broadly what endemic Covid looks like?

No.  I think the population-wide immunity picture would be very different to now in a truly endemic situation.  I'm hopeful that the phase 3 trials for Valneva haven't been wrecked by recent bizarre events, particularly the one using it as a 3rd dose.  Be very interesting to see how far that could move us on from pandemic to truly endemic as an alternative to a lot more high-risk infection.  Otherwise I think it's quite a long way to go, albeit with the worst order of magnitude behind us. 

> Even if you assume a high level of that is in children there can’t be many adults left to go?

We know the currently in-use vaccines don't offer perfect protection against catching delta, so there's both the unvaccinated and uninfected pool to exhaust, and there's people who've had the vaccine but are susceptible to catching delta.  The later have much less health risk than the former, and won't be exhausted any time soon; that's why IMO we're looking for lowering hospitalisations and a lowering infections:hospitalisations rate, rather than cases dropping per-se.   

> I can’t quite get my head around how else Covid hasn’t followed the curve that the modelling suggested

It helps if you look at the modelling as a source of noise...

> Are behavioural/ social factors really moderating the R rate in such a way that it remains broadly 1 over time (when set against a background of rising immunity)?

I think it's more been luck than judgement, as unlikely as that seems; a steady state (give or take seasonal bunching) is the inevitable result; now feels like too soon for that; it's more that every time we've had another relaxation of restrictions or return to normal, it seems to me like the evolving immunity situation stops things form running away with themselves.  

In reply to misha:

> in fact I can’t see why anyone who wants it can’t have a booster every 6-12m (if that’s what’s required

My outsider's take - the immune system seems very computational and makes all sorts of decisions on prioritisation, storage and its future speed of response, and how much it "locks in" patterns from one variant vs maintaining a flexibility to future variants.. I don't think that we're at the point someone can understand what unintended consequences something will have here until its been trialed; that's why I've been a bit surprised today that the recipients of the Novovax vaccine during clinical trials are now being offered two doses of Pfizer so that they have a recognised vaccine to enable travel etc.  That means four doses total, two of Novovax then two of Pfizer; that'll make an interesting dataset if they're tracked; at the very least I hope the medical bods get some serology data out of it...

In reply to thread:

The dashboard API seems to have taken a real kicking, eventually got the data pulled down for plot 18.  Both the recent events - hospitalisations from the previous burst of rising adult cases downstream of schools and the new rising phase cases are in the provisional zone on the far right.  Both events look pretty homogeneous nationwide, much like everything else.  It's always nice to see that the rise in cases isn't being driven by one initially small area...

Post edited at 19:52

 elsewhere 10 Oct 2021
In reply to Misha:

We are sort of at that point already - the vulnerable had their 2nd jab about 6 months ago. In theory their immunity should not have faded yet?????

 elsewhere 10 Oct 2021
In reply to wintertree:

At 100 deaths and 60k cases per day, 3 years to reach an endemic state where everyone has been infected at least once? It's not much better for a very very long time, particularly if endemic is after everyone infected more than once.

Mostly unknown but long term.

 bruxist 10 Oct 2021
In reply to wintertree:

> It's always nice to see that the rise in cases isn't being driven by one initially small area...

I'm starting to feel a little sceptical of local case rates as measured by testing. Initially this scepticism was caused by a large mismatch between my own local area's MSOA figures and my impression of the sheer number of people becoming symptomatic in the area, plus a recent uptick in admissions. Half of that's entirely subjective, of course, so might be dismissed as such were it not for the hospital figures.

Digging into the data a bit more deeply, I was surprised to see a massive difference between the ONS sub-regional analysis and the Gov.uk case rate data. Some areas are reckoned by the ONS to have a case rate eight times higher than that evidenced by testing.

Again, I'm only going on local knowledge and personal impressions in saying this, but I'm not sure that many people in my own area are getting tested anymore. Lots of reasons for this, including that it's got a very large deprived population who can't afford to be off work ill, but (again entirely anecdotally) the number of times I've heard a gruff "No, I haven't been for a test - it's just a cold" this last week has been exceptional, and not just limited to those of working age.

In reply to wintertree:

Re: Vulcan's - they were bloody loud. We used to have an airshow just over a mile away from home when I was a kid, we'd walk across the fields and sit (semi out of sight) off the end of the runway. A Vulcan doing a low pass was the loudest thing at any of the airshows. (Lightnings and Harrier's hovering tied for 2nd place)

The new RR engine contract for B-52s will keep them in service until 2050, which knowing the usual military replacement delays means a few years after that. This will mean that B-52s will have been in service for 100 years !!! 

Post edited at 21:19
 aksys 10 Oct 2021
In reply to elsewhere:

> 60M population at 60k cases per day is 1000 days. So it's what you'd expect if immunity faded over 3 years and everyone catches it every 3 years.  ON AVERAGE.

> It's in the plausible ballpark for endemic cases based on what we know so far.

> A perpetual bad flu year - not a happy prospect.

What’s even more worrying is that many people in the UK now regard this as the ‘new normal’ and have swallowed the government’s line that this level of cases is inevitable and acceptable. It’s not inevitable it’s down to crap government policy for abandoning simple restrictions to reduce the spread of the virus.

Looking at the latest 7 day cases rates/100,000 for major Western European  countries (UK 360.3, Germany 63.8, France 44.6, Italy 33.1, Spain 25.9 https://www.statista.com/statistics/1139048/coronavirus-case-rates-in-the-past-7-days-in-europe-by-country/ ) clearly shows that there is something wrong with the UK approach and that other countries have done things much better.

Post edited at 21:42
4
In reply to elsewhere:

> 60M population at 60k cases per day is 1000 days. So it's what you'd expect if immunity faded over 3 years and everyone catches it every 3 years.  ON AVERAGE.

60k cases x 1000 days = 60 million cases but that is not the same thing as a 60 million population all catching Covid exactly once.

If immunity really lasted for 3 years and was 100% effective then you'd get a continuously reducing susceptible population and the number of cases would fall over time.  In the last year the situation for Covid would be like trying to get the last top trump you've not collected yet - far more attempts needed than when you just start your collection.

If immunity isn't perfect and doesn't last for three years  the number of people catching it more than once is going to be a significant factor which means way less than the whole population get it from 60 million total infections.

Assuming the number of cases per day remains constant and everyone has the same risk the chance of not getting it at all within 1000 days is  (1 - (daily_infections / population)) ^ 1000 

1
In reply to aksys:

> Looking at the latest 7 day cases rates/100,000 for major Western European  countries (UK 360.3, Germany 63.8, France 44.6, Italy 33.1, Spain 25.9 https://www.statista.com/statistics/1139048/coronavirus-case-rates-in-the-past-7-days-in-europe-by-country/ ) clearly shows that there is something wrong with the UK approach and that other countries have done things much better.

Let's remember that Scotland's approach is not the same as England's.  We still have mask rules.

But basically I agree.  It is the same as throughout the epidemic, the Tories are taking decisions based on incomplete data, and the short term economic factors their donors and supporters understand and making the population accept the risks.   They'll claim to be geniuses if the risk taking works out and say it was unforeseeable if it doesn't.   

The big unquantified factor is long term illness: if high infection rates create a huge cohort of long term sick people the economic consequences will be vastly worse than a few months of precautions until there's enough data to act prudently.   My view is that as long as the science is making rapid progress on vaccines or drugs or equipment which reduces risk in other ways we'd be better to stay cautious because time is on our side.

2
 elsewhere 10 Oct 2021
In reply to aksys:

Agree entirely.

 elsewhere 10 Oct 2021
In reply to tom_in_edinburgh:

Well I did say ON AVERAGE. It's just an order of magnitude calculation based on zero solid knowledge of COVID in 2022-2025.

Post edited at 23:07
 wintertree 10 Oct 2021
In reply to bruxist:

Disengagement with testing has been on the cards for a while now, and with the big shift in perception over recent last months, it wouldn't be surprising of you've got a point in your observations.  I struggle a bit to square off the ONS and P1/P2 data for a bunch of reasons.  

>  the number of times I've heard a gruff "No, I haven't been for a test - it's just a cold" this last week has been exceptional, and not just limited to those of working age.

With about half of them saying "It isn't be Covid because I did an LFT and it came back negative?".

I don't think I've got any ranting left in my about the scale of misunderstanding about LFT results.  Our local university's training on self-administered LFTs never actually explained about the false negative rate or what a result means, just what to shove where and what the lines mean etc.  I despair, I really do.

In reply to elsewhere:

I think almost every assumption going in to that estimate is on the pessimistic side (infections vs cases, inhomogeneity of breakthrough infections, booster program kicking off, the potential still in the therapeutics pipeline etc.).  We won't know until we get there, but our situation keeps improving and I don't see any reason to assume that it won't keep improving going forwards (other than a bogeyman variant).

In reply to aksys:

Cases aren't on such a level footing between nations I think these days.  Different policies on testing, different demographics of infection and of vaccination etc.

>  clearly [...] shows that there is something wrong with the UK approach and that other countries have done things much better.

I disagree here.  It's not about the scale of infection, nor the scale of infection detected as cases, but about the scale of hospitalisation and deaths.  By one measure, "success" would be plenty of infection and almost no hospitalisation or deaths, with cases being down to arbitrary definitions and policy.  Some very quick estimates of the case fatality rate with a 3 week lag (case > death) in a few European nations right now:

1.4% - Spain 
0.6% - Germany
0.3% - UK

The situation is clearly a lot more complex than the daily number of cases, with the UK generally having a stand-out good CFR.

It's highly unlikely that the ratio of infections:cases is enough to possibly be behind the difference in fatality ratios for the UK and Spain for example, so I think that making an argument that we're doing much worse than other countries based on just cases is not a valid argument.

There are a lot of specific instances where the UK could be doing better, e.g....

  • Clearly communicating the scale of the risk to more vulnerable individuals (nowhere near back to pre-Covid levels) and holding their employers to account over exposure to that risk rather than lowballing it all, having senior ministers waffle bollocks about returning to offices and sticking with vague guidance
  • Giving better guidance and having better enforcement over ventilation in locations where people go to live, shop or work
  • Legally protecting the right to WFH where possible for the more vulnerable 
  • Either stopping LFTs entirely or re-naming the results to "you probably have Covid" and "maybe you have Covid but maybe not"
  • Welding ventilator windows open on busses
  • Keeping mask restrictions on high risk areas that people can't really opt out of, such as public transport and shops

If Covid is to be normalised into endemic status, the people mostly unaffected by it must get immune exposure, and those more affected by it need more protection including boosters, likely broader spectrum vaccination and consideration from others in shared space.  Feels to me like we're doing the first half but not the second half; the harm downstream of the first half is largely because we're not doing the second half.  What really - really - ****s me off here is that the second half is akin to the "focused protection" that the Great Barrington Disgrace called for; at the time it was totally unviable and unrealisab ; now that we're at the point we can open up and still protect the more vulnerable there's almost no sign of that focused protection, and the people behind the GBD have moved on to challenging the kind of mild restrictions that could deliver that enhanced protection.

In reply to Michael Hood:

> This will mean that B-52s will have been in service for 100 years !!! 

Their A-10s keep on going as well.  The B-52 is unusual for a western (non-transport) military plane in having the engines on pylons, that must make it a lot more upgradable than most bombers.   It'll be strange to watch them fly without the filthy exhaust coming out of the back of the engines.

Post edited at 23:31
In reply to elsewhere:

> Well I did say ON AVERAGE. It's just an order of magnitude calculation based on zero solid knowledge of COVID in 2022-2025.

Yes, but it's not ON AVERAGE.  There's a substantial difference between 100% of people getting it exactly once in 1,000 days and 36.7% of people getting it at least once in 1,000 days which is what the more complex formula calculates.   

I agree there's not enough solid data for an accurate prediction.   We need to see more data to have much confidence in calculations using a constant infection rate.

 George Ormerod 11 Oct 2021
In reply to wintertree:

Here in Alberta the government used the UK as the modelling input and relaxed all restrictions early July and buggered off to hide during the federal elections. This has resulted in a 4th wave, catastrophic for the health service. It seems we have lower case per capita numbers than the UK and higher full vaccination rates, but the ICU occupancy rate is six times higher. This all seems rather odd, is it the higher infections in the early poorly managed waves in the UK that have given more broad immunity?  

Having said that maybe that’s a price worth paying for a lower death toll. We’re about the same population as Scotland and have a third the deaths so far.  

 Si dH 11 Oct 2021
In reply to George Ormerod:

> Here in Alberta the government used the UK as the modelling input and relaxed all restrictions early July and buggered off to hide during the federal elections. This has resulted in a 4th wave, catastrophic for the health service. It seems we have lower case per capita numbers than the UK and higher full vaccination rates, but the ICU occupancy rate is six times higher. This all seems rather odd, is it the higher infections in the early poorly managed waves in the UK that have given more broad immunity?  

Possible explanations include: different vaccination demographics (UK did exceptionally well in vulnerable age groups); different case testing strategies (hence % cases found), different policies for putting people in ICU, different definition of ICU in the covid dashboard data (I think in UK it just means mechanical ventilation).

> Having said that maybe that’s a price worth paying for a lower death toll. We’re about the same population as Scotland and have a third the deaths so far.  

Is the current death rate lower or higher? That would give you a good indication whether the difference in ICU occupancy is 'real'.

 Si dH 11 Oct 2021
In reply to aksys:

> What’s even more worrying is that many people in the UK now regard this as the ‘new normal’ and have swallowed the government’s line that this level of cases is inevitable and acceptable.

This is precisely the line that the government have *not* taken. They have very definitely never said that their policies will result in this level of ongoing cases, and that is the biggest problem. Most people are blindly following the idea that with restrictions removed the problem will now continue to recede and by next spring covid will be in the past. This is because the government has purposefully avoided being honest with them.

> It’s not inevitable it’s down to crap government policy for abandoning simple restrictions to reduce the spread of the virus.

I broadly agree that policy has been poor, however I'm not sure whether I'd support a broad policy of stricter measures at this point, it would depend what they were. We do at some point need to return to a new normal and any discussion about ongoing restrictions should, in my opinion, be held in the context of them becoming permanent, not temporary.

There needs ideally to be a public debate and parliamentary vote about the level of permanent hospitalisations and deaths we as a society should tolerate and the nature of permanent restrictions we are willing to tolerate if necessary to achieve that level. Of course this will never happen. Of course, if they didn't turn out to be permanent, that's great...and they still might not, but it's certainly looking like a reasonably strong possibility.

In reply to Si dH:

>> There needs ideally to be a public debate and parliamentary vote about the level of permanent hospitalisations and deaths we as a society should tolerate 

This is one of the problems IMHO.  All the debate has been about cases, deaths and hospitalisations.  We know there is a substantial problem with long Covid and more acute ost Covid organ damage, we know that an ICU stay can have lingering consequences but as soon as the discussion turns to what level of precautions are needed the long term, less well quantified factors are treated as zero.  This isn't a sensible approach, we need to know what the long term effects are and factor it in to the debate.   

Post edited at 08:55
 wintertree 11 Oct 2021
In reply to George Ormerod:

> This all seems rather odd, is it the higher infections in the early poorly managed waves in the UK that have given more broad immunity?  

Si dH rassied a lot of good alternate suggestions; one thing about infection acquired immunity is that it tends to fall where it's most needed.

Along your lines of thought... Delta looks to be far more lethal than the first wave of Covid and of the Alpha/Kent wave; this is significantly masked by the greatly improved clinical care and therapeutic treatments, but treatments and clinical care only kick in when people go to hospital, so it's certainly possible that a lot of people who got infected in the first wave in the UK now have enough immunity to avoid ITU if they catch delta where-as if they were catching delta now without any prior immunity that could be very different.  It is almost impossible I think to get quantitative comparisons between the scenarios.

> Having said that maybe that’s a price worth paying for a lower death toll. We’re about the same population as Scotland and have a third the deaths so far.  

It's going to have to happen everywhere; and it's going to be harder I think the less natural spread there's been.  This in no way retrospectively justifies the early rush to have the virus spread in the UK IMO; the comparative death tolls speak for themselves, as does the total time in strong control measures.  

There's the argument that we should still be delaying the releasing of restrictions and somewhat uncontrolled spread; a counterweight to that is just how much worse the true IFR of zero-immunity delta likely is - many of the gains made in therapeutics and treatment approaches are being lost to the increased lethality of successive variants.  If (big if) getting broader immunity out there makes a significant difference, it makes for some uncomfortable decisions.  Unless there was a default option of buying 200m doses of an inactivated virus vaccine with a modern adjuvant that apparently delivers strong antigenic responses against multiple viral proteins.   

In reply to Si dH:

> There needs ideally to be a public debate and parliamentary vote about the level of permanent hospitalisations and deaths we as a society should tolerate and the nature of permanent restrictions we are willing to tolerate if necessary to achieve that level. Of course this will never happen

I agree; throughout this I would have preferred more consistent, pre-defined thresholds over control measure so that everyone knew what was going on and could do some halfway sane planning, and so that the democratic processes could have time to happen before the crisis points arise/arose.

In terms of societal discussion around permanent control measures, if we're dreaming about how it should be done, we now know that we can almost eliminate flu if we want to.  We've learnt a lot about not sending sick people to work or school.   The current death rates from Covid aren't stand-out compared to a bad winter respiratory season.  It seems Covid is probably still taking more years of life from fewer people however which changes the balance, and which is why I don't think a threshold level of deaths is appropriate for triggering control measures going forwards.  I'd like to see a proper discussion that puts seasonality of deaths at the forefront - it's not just bad for individuals, it puts healthcare under immense pressure in many winters, with politicians being loath to invest in permanent capacity for peak load.  We're not really going to know where Covid lands in all this until winter is behind us.  

In reply to tom_in_edinburgh:

Re: Long Covid; the discussion and data on this (in broad circles)  remain perpetually muddled with serious debilitating illness on one side and broad church definitions on the other.  It's not surprising that people get absolutely clobbered when catching this virus with no prior immune exposure; those days are moving in to the past and what needs understanding now are the enduring health consequences of catching Covid when endowed with prior immunity.   Early publications there are showing clear, significant improvements with vaccination but not perhaps as optimistic as one might have hoped.

Interesting things ahead I hope for therapeutics for the ME/CFS like component of long Covid and indeed for ME/CFS as well.  Some really interesting papers coming out on the immune changes associated with this.  No short cuts to getting a new treatment on the market however.

Post edited at 09:47
 oureed 11 Oct 2021
In reply to wintertree:

>  if they were catching delta now without any prior immunity that could be very different.  It is almost impossible I think to get quantitative comparisons between the scenarios.

New Zealand

 jonny taylor 11 Oct 2021
In reply to wintertree:

Better late than never?

https://content.govdelivery.com/accounts/UKHSE/bulletins/2f68b5e

("Scientists advise office CO2 monitoring to help manage COVID-19 risk" and "Ventilation tool to support COVID-19 controls")

 davidalcock 11 Oct 2021
In reply to wintertree:

Something that's started happening in the SW is a pattern of consistently positive LFTs followed by negative PCRs. Any idea what that's about? 

 aksys 11 Oct 2021
In reply to wintertree:

> I disagree here.  It's not about the scale of infection, nor the scale of infection detected as cases, but about the scale of hospitalisation and deaths.  By one measure, "success" would be plenty of infection and almost no hospitalisation or deaths, with cases being down to arbitrary definitions and policy.  Some very quick estimates of the case fatality rate with a 3 week lag (case > death) in a few European nations right now:

>1.4% - Spain 
> 0.6% - Germany
> 0.3% - UK

>The situation is clearly a lot more complex than the daily number of cases, with the UK generally having a stand-out good CFR.

I agree that it’s a complex situation and relying on one measure is likely to be misleading. For example, the difference in CFR between Spain and the UK may be partly down to there being more cases in school age children in the UK than in Spain at the moment. Spanish age demographic data can be found here;

https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov/documentos/Actualizacion_480_COVID-19.pdf

Alternatively, the NHS may now be better at treating covid patients than the Spanish health service (no evidence for this though).

Nevertheless, cases seem to have remained stubbornly high in the UK when they have fallen in similar European countries.

On a personal level this matters as my son’s school recently reported that they have already had more confirmed covid cases since the start of this term than in the whole of the previous year with inevitable disruption to education.

Post edited at 16:34
 Offwidth 11 Oct 2021
In reply to wintertree:

A CFR of 1.4% for Spain is almost certainly bs. Track the averages and after the first wave it's always been below 1% when numbers are high enough to be reliable (eg August 2021 peak CFR was about 0.5%)... if this is from current data the current case numbers are just wrong.

 wintertree 11 Oct 2021
In reply to jonny taylor:

> Better late than never?

Very useful, thanks.  Good to see some advise with HSE blessing; I'll reserve comment on the tool.

In reply to davidalcock:

> Something that's started happening in the SW is a pattern of consistently positive LFTs followed by negative PCRs. Any idea what that's about? 

I'm waiting to see what PHE (or their new acronym) have to say, but if there wasn't a significant false positive rate on LFTs, I don't see why they'd be sent for PCR confirmation; sources differ on what the false positive rate is for LFTs.  Some interesting reading on an old BBC article - I haven't followed the issue to see if an eventual explanation was derived - https://www.bbc.com/future/article/20210705-how-children-are-spoofing-covid-19-tests-with-soft-drinks - perhaps sales of FCOJ are up with the future in pork bellies going down due to the failure-to-plan-for-Brexit derived labour crisis.

In reply to aksys:

> On a personal level this matters as my son’s school recently reported that they have already had more confirmed covid cases since the start of this term than in the whole of the previous year with inevitable disruption to education.

Indeed, although rules and requirements have been changed to significantly minimise the disruption compared to what would have been expected with these case rates in an earlier term.

The problem seems to me that we have an unstated policy here (AdJS has given it an acronym in previous weeks), a policy that nobody in government is publicly willing to stand behind.  This means that the pros and cons of it aren't being clearly set out.  Clearly there are pros as well as cons to this plan.  It's very un-democratic to steamroll ahead with it all without discussion or chance for dissent...  

> Nevertheless, cases seem to have remained stubbornly high in the UK when they have fallen in similar European countries.

Yup; control measures work to lower cases, and the UK has pretty much moved on beyond control measures.  Another thread on this recently heard from various people across Europe about how much more adherence there is to control measures.

In reply to Offwidth:

> A CFR of 1.4% for Spain is almost certainly bs.  [...] current data the current case numbers are just wrong.

The CFR is never "bs", it is always exactly what it claims to be.  It is a calculation of two measurables, one of which has very flexible definitions across time and space. That was rather my point to aksys - that the case rates themselves are not a meaningful comparator between different nations, even more so now than in the past.   Hence, my suggestion that the hospitalisation and death rates are a far more important and useful basis for comparison than cases.  A sub-point is that Spain is presumably significantly under-detection infections to get such a high CFR on a 3-week lag, raising further signs that cases are not a suitable basis for comparison. 

> if this is from current data the current case numbers are just wrong.

Case numbers are never "wrong" except for reporting errors, they are what they are.  What they are is not useful for comparisons between different nations with different testing policies and engagement levels.

Worldometer numbers for Spain:

  • 7-day moving average deaths Oct 10 - 43 / day
  • 7-day moving average cases Sep 19 - 2982 / day
  • 21-day CFR = 1.44%

Given how high this CFR is, and given that Spanish cases also seem tilted towards children right now, it rather suggests that the Spanish infection>case detection ratio is much lower than it is in the UK.  Which means that aksys's original direct comparison of cases between the UK and Spain is comparing apples with oranges and is not valid, even before we start thinking about differences in demographics and immunity levels.

Post edited at 17:52
 Offwidth 11 Oct 2021
In reply to wintertree:

I'd say your calculation is not an CFR under its standard definition. You have defined some kind of rolling CFR equivalent which should be called something else to avoid confusion.

As an aside, I have the 7 day rolling  average deaths as 39 for Oct 10th in Spain (not 43) from worldometer and on October 2nd it was 33 (with cases over 4000 21 days earlier)  so your rolling 'CFR' is clearly too noisy to be meaningful. The German data has a bit of a death blip as well in the last few days. It's not just picking up cases its also how deaths are defined and how deaths and cases get attributed to specific days for the measuring systems of  different countries.

Post edited at 19:09
3
 wintertree 11 Oct 2021
In reply to Offwidth:

> I'd say your calculation is not an CFR under its standard definition. You have defined some kind of rolling CFR equivalent which should be called something else to avoid confusion.

I'm not sure there is a "standard" definition when estimating rates from the cases and deaths curves; I've seen plenty of sources using CFR as applied to these time series (vs a true, longitudinal CFR).

I gave my method and used the same method on different countries for the comparison.  With a massive day-of-week effect in most of the data sources the use of a 7-day average is pretty standard, and some interval has to be picked; 21 days is both pretty uncontentious and also specified.

You seem to be suggesting that the "rolling" component is a problem; unless the halving or doubling time is very short (less than a week, almost never seen in top level data), over a 7-day interval the data series are basically linear (Taylor series and all that), so a 7-day rolling average is an obvious, effective and unbiassing way of dealing with day-of-week sampling effects.  

The use of rolling averages bothers me not one bit; having to pick a time intervals between cases and deaths with non-longitudinal data is a much more worrisome issue and potential source of bias especially when different counties are in different phases (rising vs falling vs level) and is where any simple comparison such as mine falls short.

> As an aside, I have the 7 day rolling  average deaths as 39 for Oct 10th in Spain (not 43)

Then you are either doing something wrong or using a different Worldometer to me.  See the attached screenshot.

> so your rolling 'CFR' is clearly too noisy to be meaningful.

If I pick different dates for the comparison or different time intervals for the CFR measurement, I still find that Spain > Germany > UK in CFR.

I think you're almost wilfully missing my point which is that cases data varies so much between countries that it can't be used as a meaningful basis for comparison.  I think you've missed the point so significantly that some of your comments against my noddy CFR analysis are some of the very points I'm trying (and clearly failing) to make about cases (from which CFR derives) not being a good basis for comparison.

Yes, I could have measured the CFR for all the countries over a longer period of time and for a bunch of different intervals, and tried to get a fairer picture, but the differences are significant enough that my point stands, and I'm explicitly making the argument that cases - and by extension CFRs - are not a fair basis for comparison, and so trying to get a fairer comparison by tweaking the CFR method is almost by definition pointless.  

You said

> if this is from current data the current case numbers are just wrong

This.  This is the point.  The case numbers are not "wrong" for Spain but they don't represent infections in Spain in the same way case numbers in the UK reflect infections in the UK.  Also, case numbers don’t represent demographics which make a massive difference to the things that do matter - hospitalisations and deaths: by some views cases without hospitalisations or deaths are part of the long term solution.  

Post edited at 19:41

 Offwidth 11 Oct 2021
In reply to wintertree:

It was 39 (I checked twice) but it's 43 now.... no idea what happened and I apologise. I completely agree on your main point of apples and oranges but giving the percentage as 1.4% when in a week it has increased by over 0.5% for no obvious logical reason (so is likely some statistical blip) is sloppy statistical practice.

3
 wintertree 11 Oct 2021
In reply to Offwidth:

> sloppy statistical practice.

I hope my original rider of “some very quick estimates” conveyed to most readers that I wasn’t claiming statistical rigour. 

I don’t know how to be more up front than that.

If you want to sink some time in to doing a detailed time series analysis of the CFR over a bunch of intervals I’d welcome a more rigorous take on it.  If the Spanish data is that much all over the place it just makes the case further that cases data is not a good basis for comparison…

 kirsten 12 Oct 2021
In reply to aksys:

https://www.theguardian.com/world/2021/oct/11/covid-rates-lower-western-europe-than-central-and-eastern

Apart from the UK of course, as already mentioned. The only reason we're dropping down the Statista table linked above is because of the sharp rise in cases in E. Europe. 

1
 aksys 12 Oct 2021
In reply to kirsten:

> Apart from the UK of course, as already mentioned. The only reason we're dropping down the Statista table linked above is because of the sharp rise in cases in E. Europe. 

And perhaps the government are still guilty of ‘groupthink’?

https://www.theguardian.com/politics/2021/oct/12/covid-response-one-of-uks-worst-ever-public-health-failures

2
 Offwidth 12 Oct 2021
In reply to wintertree:

We'll have to agree to disagree on the detail. Maybe with all the excellent work you do I just expected you to notice your CFR measure shifted by about half in the last week due to filtered daily data not being reliable enough (deaths rising oddly, when 21 days before cases were still dropping in a standard looking way) to say anything more than it being about 1%.. Also if you look at the August peaks, even allowing for convolution effects, I'd expect the upper limit of this wave's CFR to be a good bit below 1% (as any missing cases would bring that measured number down).

Its not easy, as some extrapolated case information and estimated CFRs for Spain indicate (with several phases as the pandemic progressed):

https://www.nature.com/articles/s41598-021-90051-7

On a different subject.... watching " The Papers" last night on BBC News 24, today is a very bad covid press day for government across nearly all the main titles, (with highly critical reports from two select committee's assessments of the government covid response). It was funny watching the reviewer from the Express squirming.

https://www.theguardian.com/politics/2021/oct/12/covid-response-one-of-uks-worst-ever-public-health-failures

Post edited at 08:44
4
 Si dH 12 Oct 2021
In reply to Offwidth:

> On a different subject.... watching " The Papers" last night on BBC News 24, today is a very bad covid press day for government across nearly all the main titles, (with highly critical reports from two select committee's assessments of the government covid response). It was funny watching the reviewer from the Express squirming.

It's good that two select committees chaired by conservative MPs have seen fit to highlight some of the key failings as wel as successes. From the BBC digest, it seems the reports are pretty balanced. However, it is all stuff we already knew - there is no news there for anyone who has been paying attention.

On your discussion with Wintertree about CFR...it seems pointless to me to argue about week-on-week changes in the data if the obvious headline conclusion is that the data is not comparable anyway because Spain is significantly under-detecting infections. Woods, trees etc.

I admit the higher CFRs in some parts of Europe at the moment have surprised me and they do place a question over how much difference their remaining restrictions are really making. 

Post edited at 09:25
 wintertree 12 Oct 2021
In reply to Offwidth:

I think you're consistently missing my point.

I don't really know how I can put it any more precisely.

I'm not looking to do a detailed CFR analysis of any of the 3 nations for which aksys compared case rates.  I am not looking to die on a hill over what I gave as "quick estimates".  What ever consistent methodology is applied, the CFR have the same ranking with the UK much lower than Spain over recents weeks.  That is the point.  

The point of my "very quick estimates [...] right now" - was to show that the relationship between cases and deaths is by no means consistent between the different nations, and so comparing case rates as an indicator of the scale of the problem is very one sided.  (Comparing deaths is also one-sided the other way as it discounts health damage short of death, hospitalisations are probably a good middle ground but such comparative data is not so trivially available).

It is too soon to determine robust CFRs for the present moment - the paper you linked spells that out in their rational for their detailed methods as applied to past data and the inability to use them to understand the now.

Re: your Nature paper link - I still don't think you're getting my point here.  

  1. This is a retrospective analysis and very clearly says it can't be used to understand the present moment - it's looking at very different parts of the timeline to now
  2. Terminology issues CFR vs IFR
    1. I am talking about a CFR as in the Case Fatality Ratio as in the ratio of measured cases to deaths.  This is a standard, clear and well explained/used concept.  Iv'e been going out of my way to make the point that this shows cases are not comparable between nations.  
    2. The paper you link is using an Infection Fatality Rate or  IFR determined from seroprevalence and for reasons unclear to me is wrongly calling it a CFR.  They are then using their seroprevalence derived IFR to back-calculated an estimate of true infections from the deaths data.  This strikes me as on more than a little shaky ground as it is not demographic, and as analysis of the demographic cases or deaths data over time for the UK shows, the demographics are not time invariant.  They're also a highly sensitive parameter.

> I'd expect the upper limit of this wave's CFR to be a good bit below 1% (as any missing cases would bring that measured number down).

I added some bold to show where I think your'e still missing my point.

If there are more "missing cases", the CFR goes up because measured cases are lower, and the CFR is the ratio of measured cases to fatalities.  You can't "add them" in to get a lower CFR because then it's not cases.   There's a difference between IFR and CFR, and that matters.  This was part of the point I have been failing so spectacularly to get across - there are increasingly large changes in attitudes and policies to testing that differ by nation, so cases are a rotten basis for comparison.

The difference between CFR and IFR is pretty clear (unless you're a Nature editor) and has been for a long time.  No need to muddy the waters here.  

The point I was making is not that Spain is doing worse (obviously it's not, I had hoped), but that the differences in CFR are a massive red flag that cases are not comparable between countries.  I can pick different periods in time for quick estimates of CFR and get different values, but the precedence and general message remains the same.

Still, well done on. finding a paper in Nature that's about a different time period, that clearly estimates a ratio of true infections to fatalities and using that to argue about an estimate of measured cases to fatalities.  They're not the same.  That's pretty much half of the point I was trying to make.

Poor show from the editor at Nature for not pulling them up on their terminology or lack of consideration of demographics.  Par for the course with Nature.

https://en.wikipedia.org/wiki/Case_fatality_rate 

  • In epidemiology, a case fatality rate (CFR) – sometimes called case fatality risk or case-fatality ratio – is the proportion of deaths from a certain disease compared to the total number of people diagnosed with the disease for a particular period. 
  • Like the case fatality rate, the term infection fatality rate (IFR) also applies to infectious disease outbreaks, but represents the proportion of deaths among all infected individuals, including all asymptomatic and undiagnosed subjects. 

If you read the paper around the bit talking about CFRs and seroprevalence I hope it is now clear to you that what the paper erroneously calls a CFR is actually an estimate at an IFR.

Terminological confusion aside, it's also for a different time period.  I'd expect the IFR in Spain to be much lower now than in the time periods they estimated it for.

To return to aksys's original point:

> Looking at the latest 7 day cases rates/100,000 for major Western European  countries (UK 360.3, Germany 63.8, France 44.6, Italy 33.1, Spain 25.9 https://www.statista.com/statistics/1139048/coronavirus-case-rates-in-the-past-7-days-in-europe-by-country/  ) clearly shows that there is something wrong with the UK approach and that other countries have done things much better.

Let's look at this a different way, deaths per million per day:

  • 1.6 - UK
  • 1.0 - Germany
  • 0.9 - Spain
  • 0.7 - Italy
  • 0.6 - France

By this measure (where we can reasonably assume all infection is detected, unlike cases where there is massive variation in detection), the UK is still the stand out worst example, but by a factor of less than 2x vs Spain rather than the 15x difference in case rates they cited.

I think a fairer way of making their comparison is to recognise that cases are the mild end of the spectrum especially with current demographics and fatalities the harsh end; reality will be somewhere in the middle.  However you cut it, more people are being impacted by Covid in the UK than any of the other nations, that is clear. 

Comparing different nations at a fixed point in time has long been a fool's errand as all sorts of factors combine to cause infection and illness to spread in waves, and these are desynchronised between nations.

I've held off taking a view that the UK is definitively in a worse situation than the comparator nations in my bullet point list above. We have to get through winter and we don't have a time machine so we don't know how that's going to go for the different countries; expert opinion is far from monotonic in terms of how that's going to go, or what the "right" thing to do now is.  

It's very hard to take a leap of faith that what the UK is doing is right - as the news you have linked (and the fuss on UKC at the time...) shows, we were horrendously failed by our establishments at the start of the pandemic.  We've also benefitted from some very good decision making in other areas, and had a lot middle ground stuff.

I'm damned glad I'm not making the decisions on policy going in to this winter; it's not half as clear cut as it has been in the past.

Post edited at 09:36
 wintertree 12 Oct 2021
In reply to Offwidth:

> We'll have to agree to disagree on the detail

No, the detail is important.  Undersanting it is important to the understand the point I am trying and failing to make.

> Maybe with all the excellent work you do I just expected you to notice your CFR measure shifted by about half in the last week due to filtered daily data not being reliable enough (deaths rising oddly, when 21 days before cases were still dropping in a standard looking way) to say anything more than it being about 1%.. 

I made it clear mine was an instantaneous measurement.  It's clear the jump about with noise. also repeatedly stated that the difference between the CFR for Spain and for England remains significant regardless of exactly when we measure it, and that I wasn't interested in spending a lot of time on doing more detailed measurements because the quick estimate I did was there to illustrate a key point, and that said key point (cases are not a valid basis for details comparison) undermines any value in doing a more refined analysis.

Attached is Ourworldindata's CFR measurements from the data they assemble.

The case fatality rate (CFR) is the ratio between confirmed deaths and confirmed cases. Our moving-average CFR is calculated as the ratio between the 7-day-average of the number of deaths and the 7-day-average of the number of cases 10 days earlier.

They use a different time lag to my quick take (10 days vs 21 days); theirs is perhaps too short.

But, guess what?  

At any point in the last two months, their CFR for Spain is higher than that for Germany, and the CFR for Germany is higher than or equal to that for the UK.  As with my quick estimate, their CFR measurements for Spain are much higher than the UKs.

The same point stands for different measurement intervals between cases and deaths, and it stands regardless of when its made in the data.

Remember, this is a case fatality rate and so is about detected cases not true infections.  Just to spell it out, I am not talking about the ratio of true infections to deaths.

The relationship between detected cases and infections/deaths is clearly not even vaguely comparable between the nations.   Cases without illness, hospitalisation or death are part of the solution.  Severe illness, hospitalisation and death are part of the problem.   The stark differences in CFRs (by any measure) hint in various ways at the shifting balance between the problem and the solution, and sampling citing high cases as a problem may be to significantly miss out on key parts of an emerging solution.  The high hospitalisation and death rates in the UK remain, and that IMO are a much more urgent and worhy focus for questioning and concern than any of the rest of this discussion.

https://ourworldindata.org/covid-deaths

Wish I'd just linked to the OWID plot now instead of giving my quick estimates.  

Post edited at 11:50

 Offwidth 12 Oct 2021
In reply to wintertree:

I'm completely clear on your methodology and that of OWiD . I completely agree on your big picture views. I understand the point you are trying to make about 'apples and oranges' by using your measurement of CFR but I'd prefer you just stick to per capita cases. When a rolling CFR measurement like yours gives numbers that are suspiciously higher than the error limits of likely IFR/CFRs by survey samples, I think you should consider a mild 'health warning' on those figures, as a trusted commentator here, knowing this is almost certainly a misleading number arising from data issues; in a sense it's showing a problem you might want to highlight, as long as its clear the problem is obvious because actual fatality rates won't be changing in such short time-scales. The OWiD Spanish CFR is trending up, most likely due to an increasing significant proportion of people who would be covid positive but are not being tested as such, but there is noise on that trend, especially in the last week.

So I still think your 1.4% for CFR is an unfair representation of the actual situation in Spain right now, likely due to a short term over-estimation of deaths (possibly daily noise or a lump of late registrations) added to a slightly larger medium-term effect due to an increasing number of  'missing positives'. The OWiD plot also shows the same big unexplained rise in the Spanish CFR, by their measurement, in the last week. A >50% increase in CFR in a week due to a small increase in average deaths (which should have been dropping)  is clearly showing the significant effects are more than just any 'missing cases'. The OWiD plots for Spain and Germany have both been just less than the UK in the last 7 weeks so I think when such CFR plots are high, they need 'health warnings'/explanation (likely a combination of noise, late death registrations and an upward trend in missing cases right now for Spain).

ONS are very clear on the distinctions between their Infection survey and government case numbers.

https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/comparingmethodsusedinthecoronaviruscovid19infectionsurveyandnhstestandtraceengland/october2020

Post edited at 14:02
3
 elsewhere 12 Oct 2021

I've been wondering about endemic, what it means, how it results and timescales.

Maybe a good timescale is 1918 pandemic which seemed to last about 2 years and then presumably was endemic.

Endemic for the UK means the immune system of most of 70M people has been modified (hopefully making us more resistant) by infection. It can't be endemic and can't produce an immunological response in the population if it's not almost inevitable get infected at some point.

For the common cold, that must have happened to all of us as we have all been exposed to common cold viruses many times.

Not sure if immune system can be modified by a virus without infection (eg immune system successfully killing off a viral infection, possibly without any symptoms).

Developing that immune response from mostly vaccinated & mostly uninfected population now to mostly post-infected is not risk free, but the CFR is probably reduced by a factor of 10 by vaccination. An appropriate CFR is for mostly vaccinated & mostly uninfected so that means the CFR now. That's thousands or many thousands of deaths to update the immunology of most of the population. That would take years unless there's hundreds of thousands of infections (mostly undetected and asymptomatic?) per day but regardless of speed the CFR appropriate to mostly vaccinated & mostly uninfected applies as that is the starting point for most individuals.

Another timescale. I reckon it takes 25 years for a newborn to enter the population in which the common cold is endemic. I base that on lots of colds as a child and into early adulthood. Then you are one of the population for which colds are endemic and you don't get as many colds. Is that a common experience? Let's hope it doesn't take infection by 50 shades of Covid and 25 years to get any immunological benefit.

Post edited at 14:14
 wintertree 12 Oct 2021
In reply to Offwidth:

I am far from convinced that you understand.

>  but I'd prefer you just stick to per capita cases. 

My whole point is that cases - both per capita and absolute - are not comparable between nations right now.  

That.  That is the point I have been making.

I see no sign you have understood this - if you had, you wouldn't have suggester  per capita cases, which have the same problem.  If you had understood my point, you would not be asking for this.

I gave the CFRs as a way of illustrating that there is a problem using cases for comparisons about the gravity of the situation between nations.

Per capita cases are not the answer, they are as much the problem - deriving from problematic cases - as cases are.

I am mystified as to why you ask me to "stick to per capita cases" when you claim to have understood my problem.

>  When a rolling CFR measurement like yours gives numbers that are suspiciously higher than the error limits of likely IFR/CFRs by survey samples, 

Re: rolling - Everyone uses some form of averaging when dealing with massive day-of-week effects.  There's nothing unusual nor biassing about the "rolling" nature.  It's not causing the bias, it's reducing it by reducing the noise.  The main issue. of bias is in the selection of an interval from cases to deaths.   I see no sign that you have understood this.  This is where my method could introduce more bias, especially with different phases.  What I did was IMO perfectly sufficient for the argument I was making.  I see Si dH gets it...  I'm glad, I was starting to seriously question my own sanity here.

>  I think you should consider a mild 'health warning' on those figures, as a trusted commentator here, knowing this is almost certainly a misleading number arising from data issues. In this case, until this week, most likely due to an increasing significant proportion of people who would be covid positive but are not being tested as such..

As I said: "Some very quick estimates of the case fatality rate with a 3 week lag (case > death) in a few European nations right now:"

I don't know how to speak any more clearly.  

I had credited people reading with being able to recognise the difference between a CFR and an IFR.

Looking at the OWID time series analysis I have no more concerns over what I have said - I'll return to this below.

The CFR I gave was valid for the definition I gave.  I did not claim it was representative of the IFR, or of the CFR at other times.  It's not on me that you have consistently determined to misinterpret it as an IFR, nor have or would I claim it is an IFR.  The difference between the two is more or less my entire point.

> When a rolling CFR measurement like yours gives numbers that are suspiciously higher than the error limits of likely IFR/CFRs by survey samples,

IFR and CFR are two vastly different things.

Why are you comparing a CFR measurement with an IFR?  They are two totally different things.  This is central to my point.

What is a "survey sample" based CFR?  The "C" in CFR can not be determined by a survey, only by the national detection and reporting systems.

IFR and CFR are different things.

Half off point has been about the international differences between "I" and "C" in those measures.  You brought a paper on an IFR which they had mislabeled as a CFR as a rebuttal to my quick estimates.  This just further drives home that I don't think you're understanding this.

> So I still think your 1.4% for CFR is an unfair representation of the actual situation in Spain right now [...] added to a slightly larger medium-term effect due to an increasing number of  'missing positives'.

That.  That is the half of my point.  The CFR is getting larger and that is a fair representation on the changing relationship between infections and cases which you call "missing positives.

The Spanish CFR is not "bs" as you have called it, it's not wrong, it literally is what it is.  It is not the IFR, it can not be used to infer the IFR.  It tells us about cases and deaths.  This gives us a way to infer a changing relationship between infections and cases, because if that relationship was fixed, a well measured CFR would not vary.

You continue only to convince me that my whole, entire point has sailed you by.

(the other half of my point is demographics)

> The OWiD plot also shows the same big unexplained rise in the Spanish CFR, by their measurement, in the last week

Or, another way of looking at it is that the Spanish CFR (a) has been rising gradually and significantly for the last two months and (b) is very noisy.  I've made a cartoon sketch, attached.  I gave - and fully qualified - my quick estimates based on the most recent data.  You've picked a point a week or so before to counter this but actually stepping back and looking at the trend, you seem to be cherry picking and not recognising the trend.

> missing cases

Do you actually mean missing cases (data lost down the back of a sofa) or do you mean infections not detected as cases?  If the later, that is my point.  My point is that the relationship between cases and infections seems to be changing, and that this manifests in the rising CFRs.  

Here is the path to enlightenment.

  • Step 1 - recognise in the screenshot that the CFR for Spain has become 8x higher than for the UK over the last two months.  
    • Note - The quick estimate I gave look pretty valid to me in terms of the scale and ratios between the three countries on this plot; the absolute values in the OWiD are higher than mine (you might let them also know that they are a trusted source and should put a health warning on their plots???)
  • Step 2:
    • Question: Has Covid become 8x more lethal in Spain than in the UK over the last two months?
    • Answer: Almost certainly not
  • Step 3:
    • Question: Do we think recorded death figures are trustworthy for both nations?
    • Answer: Almost certainly yes
  • Step 4:
    • Question, where then can the discrepancy possibly lie?
    • Answer a: Demographics
    • Answer b: Changes to the relationship between infections and cases.

Edit to your edit:

> ONS are very clear on the distinctions between their Infection survey and government case numbers.

This has no relevance to what we are discussion as far as I can tell.  

Post edited at 14:28

 wintertree 12 Oct 2021
In reply to elsewhere:

Once you start thinking it all through... It's fascinating enough to make you want to re-train as an immunologist isn't it

>  Let's hope it doesn't take infection by 50 shades of Covid and 25 years to get any immunological benefit.

For older people who will never have the chance to experience Covid as a young person, that's a bit of an unknown as in past pandemics they didn't have the therapeutic and vaccination support we have now.  It doesn't seem unreasonable to expect therapeutics to continue to play an ongoing roll for them over at least the next few years.  On that note...

AZ are submitting a monoclonal antibody mix for emergence use authorisation in the US.  They have done work to extend the lifetime of the MABs in humans so that they last long enough to be usefully prophylactic as well as therapeutic.  One of the ways that more vulnerable people can be better protected going forwards, hopefully.  

https://www.reuters.com/business/healthcare-pharmaceuticals/astrazenecas-covid-19-drug-cocktail-meets-main-goal-late-stage-trial-2021-10-11/

https://www.medrxiv.org/content/10.1101/2021.08.30.21262666v1

In reply to Offwidth:

I think you’re completely missing Wintertree’s point.

What he’s saying makes complete sense to me.

You seem to be purposely focusing on case data to present the UK in a worse light than the current situation suggests, rather than the death data which is also worse, but only marginally so.

Either the Spanish are really rubbish at treating Covid, or they’re not recording the same % of cases we are. If we’re picking up only c.50% of cases, what are the Spanish picking up? 10%?

 Offwidth 12 Oct 2021
In reply to wintertree:

I totally agree that cases - both per capita and absolute - are not comparable between nations right now.  

I don't see the low points on the OWiD graph as cherry picking as it's on the highest recent  data levels so the least noisy and probably when people are most incentivised to be tested; so probably the closest to meaningful death rates from cases.

I think we are agreeing, except on the need for clear emphasis that these OWiD CFR changes are not real changes in probability of death from infection....that they show something else, mainly an increasing proportion of the infected not testing when CFR's increase well above 0.5% right now in western nations.

I'd prefer your stricter view on use of CFR if it was consistent but it's not, my counter- example was a Nature paper (and not the first one either). In such a world I would say estimated IFR's would be the only reliable data in terms of actual death rates; as case rates (and so CFRs strictly on positive 'test and trace' style tests) have been and still are so unreliable. We'd still need care comparing IFR's internationally, as what constitutes a covid death changes from country to country (and in some cases was changed mid-pandemic in some countries).

On your method versus OWiD. There was some evidence that time to death from symptom onset seemed to have shortened in 2020. I wonder if modelling different times to death (or more complex convolutions) reduces the current trend lines such that they are part of that estimating mechanism.  An example on median times to death changing:

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/928729/S0803_CO-CIN_-_Time_from_symptom_onset_until_death.pdf

I've not seen anything yet on such times for delta, but it is more infectious more quickly and likely a bigger risk of death.

https://theconversation.com/how-contagious-is-delta-how-long-are-you-infectious-is-it-more-deadly-a-quick-guide-to-the-latest-science-165538

2
 wintertree 12 Oct 2021
In reply to Offwidth:

> On your method versus OWiD. There was some evidence that time to death from symptom onset seemed to have shortened in 2020. I wonder if modelling different times to death (or more complex convolutions) reduces the current trend lines such that they are part of that estimating mechanism.

As I said, the change in the lab biases the result, and it does so in different directions for rising and falling phases.  I worked some examples through on here about 6 months back.  

> I think we are agreeing, except on the need for clear emphasis that these OWiD CFR changes are not real changes in probability of death from infection....that they show something else, mainly an increasing proportion of the infected not testing when CFR's increase well above 0.5% right now in western nations.

But that was literally my point and the point I have been repeating ever since.

I have never claimed CFRs to be anything other than what they are, and my whole point is that their relationship to IFRs is not universals, because the relationship between Cs and Is is not universal.

I don’t see how I could agree any more emphatically than I have consistently been doing.

I was doing this with the express intent of showing why I consider CFRs and by extension cases a useless basis for comparison.  This pretty much by definition negates looking further in to CFRs.

I’m out.

 Offwidth 12 Oct 2021
In reply to VSisjustascramble:

> Either the Spanish are really rubbish at treating Covid, or they’re not recording the same % of cases we are. If we’re picking up only c.50% of cases, what are the Spanish picking up? 10%?

It's not that simple. The UK has allowed a bigger case outbreak in school aged kids and young adults so our death rates would be lower for normalised actual infection numbers. I'd suspect we are pretty similar in the proportion of missed cases.

Id add that per capita hospitalisations and deaths from covid are a reasonable public health comparison.

Plus, I've just realised you have probably misused the data in exactly a way I was concerned about (in suggesting 10%).

Post edited at 15:29
3
 elsewhere 12 Oct 2021
In reply to wintertree:

> Once you start thinking it all through... It's fascinating enough to make you want to re-train as an immunologist isn't it

NO! I'm too thick and too lazy!

 wintertree 12 Oct 2021
In reply to thread:

Back to the UK...

The growth in cases continues in the week-on-week rate constant plot.  It looks like it might be turning the corner back to decay in the style of a classic "weather wobble".  

The two demographic plots are an uncomfortable insight in to Winter IMO.  Remember the far right of D1.c in particular is highly provisional and I expect the final values to moderate a bit from the stark orange band seen here.

  • There's no leader/follower between adults and children as we've seen over the last few months. which suggests to me infection is spreading pretty evenly, not primarily through workplaces (summer) or schools (recent schools mad growth).
  • Ages 20-30 are seeing as much growth as other bands, they had been more disengaged from spread since their mega-spike during the Euros.
  • Plenty of stronger exponential growth in older ages where hospitalisations are concentrated.

So, it looks pretty clear to me like there's still potential for positive growth in cases at all ages - all-be-it perhaps needing a standout miserable few days in a row.

If this rise doesn't break in keeping with the almost cyclical nature of cold weather periods (or for any other reasons), it'll be time to start reaching for control measures - this may be low exponential rate growth but it's on a high baseline, and it includes a bad demographic shift (hidden from a simple plot of cases) in terms of hospitalisation potential.  

Still no sign of a giant university spike in the national level demographic data.  Lots to think abut there given the lack of that as a stand-out event but the ability of cases to grow in all ages.  Harks back to some earlier discussion about what post-pandemic Covid might look like in the short term - not really truly normalised in to circulation like other long existing viruses, but a step closer.  It starts to look like our current very low level of restrictions poses a significant risk to healthcare over the winter; it's been reassuring to see some comments out of government recognising this.

Edit - in reply to Si dH:

> Thanks for the update. Think you copied in the wrong second graph?

Yes, yes I did.  Thanks; I have fixed it through this edit.  At least it was an on-topic plot and not one of the other ones from the other hobby project that's floating about on my desktop...

Post edited at 17:29

 Si dH 12 Oct 2021
In reply to wintertree:

Thanks for the update. Think you copied in the wrong second graph?

In reply to VSisjustascramble:

> Either the Spanish are really rubbish at treating Covid, or they’re not recording the same % of cases we are. If we’re picking up only c.50% of cases, what are the Spanish picking up? 10%?

Or the mask mandate (or some other environmental factor) in Spain is considerably mitigating one important source of infection (so there are fewer cases) but that source of infection usually involves lower levels of exposure (or a younger population) and therefore less serious disease.  So the cases which remain tend to be more serious and the death rate per case is higher.

The whole thing is very complex. But that doesn't mean it isn't obvious what the basic strategy should be at the moment i.e. caution and trying to limit infections.  The science and technology are improving fast so the longer we delay people catching it the better.

Post edited at 02:18
 Si dH 13 Oct 2021
In reply to tom_in_edinburgh:

Don't agree with that. If you aren't going to get a booster, I think you are better getting the virus while your immune response is strong. No new treatment is going to be more significant than that in the near future. At a national level, if you had the ability to flick a switch on when a wave of infection was to occur, you would do it when immunity was at its maximum in vulnerable populations, not wait in the hope of a technological breakthrough.

Post edited at 07:42
In reply to Si dH:

> Don't agree with that. If you aren't going to get a booster, I think you are better getting the virus while your immune response is strong. No new treatment is going to be more significant than that in the near future. At a national level, if you had the ability to flick a switch on when a wave of infection was to occur, you would do it when immunity was at its maximum in vulnerable populations, not wait in the hope of a technological breakthrough.

They've got no right to make that call.  None at all.  Their job as the government is to protect the population and that means being cautious.  We aren't soldiers, they don't get to take calculated risks or be speculative with our lives. 

The cautious approach is to try not to catch a novel and dangerous virus, to slow things down and learn as much as possible before taking difficult decisions.  What we see is a fairly continuous stream of new products coming on the market in all technical aspects: vaccines, medicines and physical protections such as masks and HEPA ventilation.   Technology will reduce the risks even further if we give it a bit longer.

The French already opened legal proceedings against a health minister.  If anybody needs prosecuted for screwing up on Covid it is the entire Tory cabinet, but our PM just p*sses off on holiday when a critical report comes out so he doesn't even need to answer questions.

Post edited at 07:58
5
 wintertree 13 Oct 2021
In reply to tom_in_edinburgh:

Another argument against stalling indefinitely is that twice now the virus has been replaced by a yet more transmissive and yet more lethal variant.  A lot of the gains made over time in transmission control measures and in therapeutics have been gobbled up by the increased nastiness of the virus. 

Stalling based on potential future technology is a risky, speculative decision.  One that gives no consideration to what the immunologists might think and one that gives no consideration to the way the virus may change in the future.

In reply to wintertree:

> Another argument against stalling indefinitely is that twice now the virus has been replaced by a yet more transmissive and yet more lethal variant.  

Nobody said indefinitely.  But right now the pace of technology improvement is rapid.  It is still early days and there is low hanging fruit.  Not just medicines, but if you go on Amazon you see a whole new category of inexpensive home HEPA units that were never there a few years ago.

> A lot of the gains made over time in transmission control measures and in therapeutics have been gobbled up by the increased nastiness of the virus. 

And people who caught one variant have caught one of the newer variants as well.  So gains from catching it don't last either. 

> Stalling based on potential future technology is a risky, speculative decision.  One that gives no consideration to what the immunologists might think and one that gives no consideration to the way the virus may change in the future.

Expecting technology gains is basic common sense.  There are a large number of medicines in development.  Every time we have this discussion there's another product announcement.

 wintertree 13 Oct 2021
In reply to tom_in_edinburgh:

> It is still early days and there is low hanging fruit.  Not just medicines, but if you go on Amazon you see a whole new category of inexpensive home HEPA units that were never there a few years ago.

Basic HEPA units have been cheap for a long time, it’s hardly new technology.  Doesn’t make much difference if people don’t use them; I’ve been running one at home at high risk periods since the start of the pandemic, most people don’t…

> And people who caught one variant have caught one of the newer variants as well.  So gains from catching it don't last either. 

I think this betrays how broken your view of the immunology is.  Am I afraid of catching OC43?  No.  Would I be afraid of catching it if I’d never had it before?  Yes.   The gains from my prior exposure back to childhood have lasted - not despite me catching it multiple times, but because of that.

Covid is being caught without a lifetime of those gains and we’re leaning heavily on medical technology to reduce the clobbering this has.

> Expecting technology gains is basic common sense. 

I’ve yet to see a call to “common sense” as anything but a warning there’s no good argument coming.

> There are a large number of medicines in development.  Every time we have this discussion there's another product announcement.

Yes, the therapeutics pipeline looks very promising.  But, as I said, a lot of the therapeutic gains have been balanced by lethality gains from the virus.  Some of the coming therapeutics like the anti viral will probably have a cat-and-mouse game of resistance (already proven in lab serial passage experiments I believe for some synthetic nucleoside compounds) and the MABs will remain very expensive for now.

When to allow spread is a difficult decision.  I see all the points you make and agree with all other than expecting substantially better vaccines, but I disagree with your one sided take.   Each side has different risks and benefits.  Speculative future stuff is on both sides of those calculations.

There are two sides, and it is not clear.

Post edited at 08:21
 Si dH 13 Oct 2021
In reply to tom_in_edinburgh:

> They've got no right to make that call.  None at all.  Their job as the government is to protect the population and that means being cautious.  We aren't soldiers, they don't get to take calculated risks or be speculative with our lives. 

Look, I don't like the Tories either. I've voted against them at every opportunity I've had and I am strongly against most of the policies they have enacted over the last 11 years. So I also resent the fact that this particular Government are taking such important decisions with such long-lasting consequences, and getting some big ones wrong. However, your statement above is ridiculous if you think about it. You are talking about exactly what we vote for a Government to do. If their decisions were purely administrative, we would just have civil servants do it. In practice almost every decision any government takes is a balance between one benefit or risk and another. Risk is inherent in all of them. Every economic decision that has upsides somewhere and downsides elsewhere carries a risk (or indeed a certainty) that those downsides carry painful consequences for some people. In the pandemic, it is all a balance of risks. Indeed if they were all calculated risks (to use your words) I'd be perfectly happy. The problem is that in the pandemic they haven't been calculated well at all because our understanding of the likely outcomes from various actions is poor (and has consistently proved to be so.) But we can't avoid taking decisions on that basis. Indeed, avoiding taking difficult decisions was what got us in to an unholy mess earlier in the pandemic. Your 'the government have no right to do something that makes me more likely to get ill' is someone else's 'the government have no right to do something that makes my business more likely to fail.' I'm afraid, in both cases, they do. Someone has to make the hard choices about when to act and how. The Government are the people who have that right, because the country voted for them.

Post edited at 09:26
1
 Offwidth 13 Oct 2021
In reply to Si dH:

I have to admit that it must seem a bit weird to non-covid obsessives that the government were wrong according to the select committees for listening to the scientists in  March but wrong for not listening to them in September. 

I do agree with your broad ideas on government public duty but see this cabinet as so flawed and the rest of government functions so criminally silent on this that this duty has become corrupted. Boris decided what he thought was best for him, not for us.

>"If you aren't going to get a booster, I think you are better getting the virus while your immune response is strong. No new treatment is going to be more significant than that in the near future."

I don't agree with this... you might turn out to be right but you might not be as well. It's not just that medicines improve, epidemic waves decline and reduce risks to more sensible levels and past pandemics do seem to end wth less lethal variants. We all make our choices for ourselves. Often our idea of real risk is poor. I think back on my choice to travel to interesting places with a downside of serious disease risks, be it from medium malaria risk to almost certain giardia infection, and I could acknowledge that maybe I was being rash. Maybe I've been rash at times when onsight leading at close to my limit or climbing quite hard for me in remote parts of Sinai. Yet some scientifically minded folk here were concerned that I went on a train double jabbed at a time when infections levels were quite low!

This pandemic really hits the poor and infirm who have little or no choice and they are in that situation beacuse society doesn't care as much as it should. This governing party are the most dishonest in this respect I've ever lived under as they loudly promise to care in their populism but act (as much as they can get away with)  in the exact opposite direction.

Post edited at 10:00
2
 wintertree 13 Oct 2021
In reply to Offwidth:

> It's not just that medicines improve, epidemic waves decline and reduce risks to more sensible levels and past pandemics do seem to end wth less lethal variants. 

Whoa there.  

I think there's a bit of a flaw in your logic here if I understand you correctly.

Do you have any actual evidence that previous pandemics of this sort have had less lethal variants emerge and displace more lethal variants?

  • It seems to me that the lethality it largely a product of the interaction of the variant and the host, and one of the major factors in the lethality is the lack of immune history of the host with the virus.  
  • This - rather obviously - changes in the course of an uncontrolled pandemic and people either die rapidly or end up with a protective level of immunity.
  • The idea that less lethal variants emerging magically ends a pandemic seems to be a fairy tale relied on by some of the denialists; certainly when challenged by an actual domain expert on here to produce evidence (not me obviously) they came up empty handed.

In other words - a pandemic ends for a reason, and that reason is that is repeated and (before modern times) absolutely awful waves of illness and death.

  • Simply holding off letting cases spread to wait as you suggest for the waves to decline is...
    • at best paradoxical - because that decline is driven by the spread you suggest holding off
    • almost certainly counter productive - because leaving it to long interferes with the mechanisms by which immunity builds up.
    • at worst dangerous - because new variants continue to emerge in the world and so far they have been becoming more lethal (even despite our improved clinical care and therapeutics), and more transmissive, and further removed from the protection conferred by our single-protein vaccines.
  • Tom's argument of waiting for better technology is completely valid, but it has risks that have to be tensioned off against the alternatives, which is what we have a government for.
  • Your argument seems to miss the entire reason pandemics always end.  If the virus doesn't spread, it doesn't end.  Vaccination can take a lot of the pain out of that, and improved therapeutics likewise, but they're not a magic shortcut past this process.

Yes, all pandemics end.  The reasons the waves decline and the risk reduces to more sensible levels is because the waves of the virus pass through people.  It doesn't just happen by itself.

Both sides of this argument have to be recognised to understand the different and often intangible risks that every government has to tension off against each other.  On that front, I note that even New Zealand is now allowing the virus to spread and is no longer pursuing their highly effective interim measure of elimination.  An incredibly unpopular move in some areas, but they're doing it.

 > This pandemic really hits the poor and infirm who have little or no choice and they are in that situation beacuse society doesn't care as much as it should. This governing party are the most dishonest in this respect I've ever lived under as they loudly promise to care in their populism but act (as much as they can get away with)  in the exact opposite direction.

I totally, 100% agree.

I think that the messaging in the past and now does not help everyone understand their risk under this; it has never been on point.  That's in some ways more unjust now because some people are clearly remaining more vulnerable.   Vulnerable workers could have much more legal protection than they do. Enforcement of reasonable control measures intended to moderate viral load could be much more thorough.  There is lots of low hanging fruit in protecting people it seems to me.

As we follow an apparent policy of deliberately letting the virus spread to build up population immunity - a critical part of the process of getting fully post pandemic - we are not sufficiently protecting those who are more vulnerable.  As I said up thread, now is the time for "focused protection" the GBD lot were keen on, and now it's time is here they've moved on to trying to undermine the mechanisms and support such protection would need.  These are people who have had private audiences with President Trump and our PM, and who have at their backs a lobbying organisation with a $5m/year budget.  It's atrocious.

Post edited at 10:25
 Offwidth 13 Oct 2021
In reply to wintertree:

I sbould probably rhetorically whoa (for the same reason I picked up on 1.4%)  but I find the hard realities of this pandemic increasingly frustrating, especially in the UK.

I'm not saying that less lethal variants will happen, I'm saying they might and other things might, which shift policy. It is possible for a less lethal variant to evolve and dominate spread and I don't need evidence when I know and you know that plenty of experts have speculated on this subject (and yes a similarly or more lethal variant might also do that). Hence, I agree it would be bloody foolish to rely on this, even if current chances looked much better than they do but who said they are relying on that?

My main point is we don't know what the future of this pandemic will bring. As such we need to take care and follow the developing science as best we can. I certainly think encouraging the vaccinated get infected is not the best scientific idea right now, as there are other big risks to that: of spread to others less sensible or too vulnerable, and even to those individuals, especially knowing double jabbed who got covid and long covid (twice in one case). We sit in a worldwide system that might spin round and bite us again, even if we become largely protected in the UK from major delta threats. 'Wait and see carefully' seems way better to me than 'vaccinated covid parties while immunity levels are high'. Human response will have some exploring all those alternatives (plus hiding from any perceived covid risk), whatever we think. I'd strongly prefer it if people played safe and took boosters. I'd also prefer it if people played safe and wore masks where feasible indoors in public and avoid badly ventilated crowded public indoor places, and maybe even not go indoors in public unless they had to.

On a world population level with modern transport spread I think we have lost the battle by vaccination alone as massive inequaity of access to vaccines in the poor countries alongside denialism, hesitancy and refusal in the west is way too significant.  It's a crazy world we live in where, in the most enlightened nations, lies on a major public health issue sit almost equally weighted next to truth in some mainstream media; it's the west's equivalent of witch doctors. So it seems obvious to me that we must try all we can to slow and mitigate this pandemic by vaccination, as the consequence of what looks like an otherwise inevitable mainly infection based herd immunity would still be terrible. Western denialism is highly emotive and does influence and lead to tragedy: right now one in six of the most critically ill hospitalised are pregnant women with two lives at risk. The bad actors, bad politicians and GBD should all be drowning in the vast quantities of blood on their hands. Yet I'd be more forgiving of the public who make mistakes given such a dishonest media system as we live with.

Post edited at 11:28
In reply to Si dH:

> Look, I don't like the Tories either. I've voted against them at every opportunity I've had and I am strongly against most of the policies they have enacted over the last 11 years. So I also resent the fact that this particular Government are taking such important decisions with such long-lasting consequences, and getting some big ones wrong. However, your statement above is ridiculous if you think about it. 

No.  My point is a moral/ethical/legal one.  The government has no right to put civilians intentionally in harms way.  Civilians don't sign up for that in the way that a soldier or cop does.   Setting out to get us infected with a dangerous disease because they have a theory that herd immunity is best or a more subtle theory about the efficacy of vaccination followed by infection is putting us in harms way.    

It is the same moral/legal principle that stops them having compulsory vaccination for the benefit of society as a whole when there is a risk to the individual being vaccinated or compulsory donation of a kidney.

Post edited at 12:17
4
In reply to tom_in_edinburgh:

Playing devils advocate here, but governments make morale decisions around healthcare outcomes all the time.

The key one is NICE’s QALY threshold which is currently between 20-30k a year.

If we assume that 600,000 people would have died from Covid and they would have lived 10 additional years had they not died, using the QALY guidance the government would have spent a maximum of 150B. Instead we’ve spent c.400B. 

It’s not fair if you catch Covid as a result of public policy, but equally it’s not fair if the Government won’t provide cancer treatment that will extend your life.

To view the state as some sort of benevolent comfort blanket that will do anything to protect its citizens is naive.

Anyway, very off topic - sorry wintertree.

1
 Si dH 13 Oct 2021
In reply to the thread:

A few thoughts on the long term state. I've had some of these things swirling in my head for a while but haven't managed to articulate them in to any sort of coherent post. Elsewhere's post prompted me to try again, but I failed, so here's a few bullet points. I'm interested what people think about any of this. I'm sure some of it can/will be refuted.

- the level of infection must eventually reach a long term equilibrium level, in the absence of significant events that change infection risk (eg a major new variant or new restrictions.) Once population immunity levels and behaviours reach a certain state, any further increase in infection rate will cause a reverse due to the increased immunity, while any reduction in infection rate will eventually lead to a rebound as immunity declines. There will be some time delay in these feedbacks, and there will still be seasonal factors as risks change with the weather and with term/holiday periods, but broadly speaking it will be a long term equilibrium.

- we don't know what that equilibrium is yet. We might already be there. If there is still a long way to go for immunity levels with booster doses or repeat infections then we might be a long way off. Hopefully the latter.

- if we reach a point that we are better-informed and we think the ongoing infection rate and resulting death rate is going to be too high, then we will probably need to reintroduce some restrictions on society if we wish to fix the problem. If we do this, we should do so with our eyes wide open that the solution may be permanent, not temporary.

- if a major new variant comes along, we don't know what differences it will make to the disease, or what the variant will be. However, we do know that it will be either more naturally transmissible or more able to evade our immune system, and will (all other things being equal) lead to higher equilibrium case numbers. It can't lead to lower case rates. Equally, higher case rates lead to a greater probability of a major new variant. Bit of a bad cycle to get in to. I'd be really interested in an educated take on why we had no new really major variants emerge for the first six months of the pandemic, several in the following six months, and none in the six months since - and what that could tell us about the future.

- I don't think it takes anything like 25 years for someone to build up a strong immune system. I think most teenagers get ill less often than most adults. Younger kids tend to get ill a lot each time they move to a new nursery setting or perhaps start a new school year, but that period fades after 1-2 months IME. For a specific pathogen, if exposed more than once I'd have thought young people would build good immunity pretty quickly. I have no expertise though and this is just a gut feel. My personal experience is that we become more vulnerable to infection again once we become parents and get exposed to high viral loads through our young kids.

- for people who are more vulnerable to severe disease from covid and will be offered booster doses, the optimum outcome seems to be keeping infection rates as low as possible, for as long as possible. The combination of artificially boosted immunity and low disease prevalence will minimise their chances of getting seriously ill.

- that's even more the case for people who are unable to mount a strong immune response to the vaccine, who are in a really difficult situation.

- a big winter wave would cause too many deaths in these groups, so some temporary measures and even restrictions are IMO still appropriate to limit any peak. Given the data we have available, it's not sensible to see a big winter wave as a good way for us to quickly achieve higher immunity levels.

- for people who won't be offered booster doses, but are vulnerable enough that it was considered worth giving them a first double vaccine dose (ie, 18-50 yos), the picture is more complicated. Ideally we would see infection rates drop very low so that we could go about our lives without significant concerns even once our antibody levels declined (AFAIK there is still inadequate understanding of T-cell effects or timescales?) However, right now the prospects of infection rates dropping that low do not look good. To me, that leaves us with a 'choice' whether, in the longer term, we would rather get the virus less often with less immunity or more often with more immunity. I don't know which is actually better, but personally, I think the difference is sufficiently unclear that it certainly isn't worth continuing to restrict one's activities in aiming for the former. (A certain level of caution to avoid high viral loads is, though, still appropriate.) [Personally, I have been consciously trying to change my mindset recently towards a state of normality and trying to lose my residual fear of catching the virus, because my head now tells me this is where I'm going to end up (especially with young kids), and changing my approach will help my mental health. I'm still wearing a mask where it doesn't make me feel like an outlier, but am taking no other precautions.]

- I think there is a significant risk that we get in to a situation where the best thing for society as a whole (even just in this demographic, never mind when considering the more vulnerable groups) is for everyone to be cautious to bring prevalence down, but that the best thing for the health of a lot of individuals, in the context of continuing high prevalence, is to get a mild dose of infection once a year. A bit of a 'tragedy of the commons' in the making?

- New treatments might come along that reduce the risk of severe disease or death. However, if that happens, they will rightfully be targeted at the vulnerable groups for whom remaining cautious is still the clear best course of action anyway.  So, such new treatments appear to make no difference to the above calculations in my mind for people under 50. They will probably still be better off getting a regular mild dose of virus and avoiding the need to ever be given such treatments, which would probably only happen if they were seriously ill in hospital.

- If a new vaccine came along that had significantly higher efficacy against infection and was offered to all groups, that could change the picture. However, I don't see the same level of excitement and investment in new vaccines that existed a year ago. Governments are just ordering huge stocks of what we already have. In that context, I don't see how we could expect to develop any new improved vaccines on the same sort of timescales that we did in 2020.

- all countries everywhere will have to go through the same set of stages that we are doing in the UK, but the infection and death rates they reach and the eventual equilibrium will vary wildly with environmental factors - climate, geography, population density, deprivation, population demographics, etc. And many countries will stop mass testing for covid long before the process is done.

- I've been taken aback by just how much we have now opened our borders up, with just a tiny number of countries now on the red list, and no amber list. I expected a loosening, but not this much. The approach of the UK to a eventual equilibrium state is going to be heavily influenced by what happens elsewhere, and at the moment most places are at least a few months behind us in the process.

Hit me...

 oureed 13 Oct 2021
In reply to wintertree:

> A lot of the gains made over time in transmission control measures and in therapeutics have been gobbled up by the increased nastiness of the virus. 

This is most certainly not the case in New Zealand. NZ makes for a good case study because of their stringent attempts to control the spread of the virus.

1
In reply to Si dH:

Yep. Strongly agree. With this and the similar take from what wintertree has been saying.
Only thing to add is that we're likely to approach the 'equilibrium'* via a few more big oscillations yet, and the short-medium term objective has to be not to let any of those overload healthcare. Beyond that, letting immunity fade significantly is a recipe for another wave. This is also why timing of boosters can be quite important especially in the short term; they can damp or drive peaks in case numbers.
Ending the pandemic phase means at certain times running case numbers as high as is tolerable. Very glad I'm not the one that has to define tolerable.

* - big air quotes on that word. It'll always be very oscillatory, seasonally if nothing else, like all these things are.

 Offwidth 13 Oct 2021
In reply to Si dH:

Even in my current sensitive state (about the way we say things) that's not setting off many alarm bells. I'd stress we are open to big unnecessary risks with the new openness of borders. I'd add long covid (and better knowledge of that) into your mix (but it's looking like another of those long term debilitating conditions where the health system will help but won't invest massively to resolve....so the wait for that on its own would likely be too long). I'd add more efforts to get vaccines to poorer countries (for humanitarian and selfish reasons).

My position on the wisdom of more UK (especially in England) caution right now is based on a collection of interactive factors including: a dangerous government with a terrible record on covid response; high case levels; high hospital stress levels; high care system stress levels; high deprivation levels; a still defective public health system under ridiculously cash strapped councils; still quite fast improving vaccination protection; higher than preferable variant risk; high levels of schooling disruption; winter coming; any mix of flu and covid making things worse than the sum of the parts; too little action on ventilation of public space (which would also help with flu);  known improved medical treatments in test phases......all in no particular ranked order, other than the first being first. Yet, I can go wish all I want as, in the UK, govenment policy and public ignorance means due caution mostly can't now happen. If things do go very badly or moderately badly wrong again we are looking at a lot more unnecessary suffering (in health and other terms) and maybe a return to some restrictions over winter. What's so sad about the UK is we could be in so much better a position if the government actually followed the science and their messaging supported that (too often the opposite happened, despite what they still claim).

International lessons abound. In recent terms look at how Japan dug themselves out of a hole (and Russia are still busy digging deeper).

https://www.theguardian.com/world/2021/oct/13/back-from-the-brink-how-japan-became-a-surprise-covid-success-story

Post edited at 13:48
1
 Si dH 13 Oct 2021
In reply to Offwidth:

> . I'd add more efforts to get vaccines to poorer countries (for humanitarian and selfish reasons).

I didn't cover the international situation at all other than our own interface with it, but yes - this. It just seems such a no-brainer that we should be ramping up deliveries abroad and donating many of our ordered doses at the moment. We have loads spare on order over/above booster requirements, I think.

The other thing I didn't mention was: why are we not spending lots of money to build our sequencing capacity faster (or are we?) - and in case our own infection rates do drop off a lot such that we had spare capacity in the medium term, are we developing relationships that would allow us to effectively offer our capability to other countries that we have lots of travel interfaces with? If not why not? Seems like another no-brainer.

Post edited at 13:51
 wintertree 13 Oct 2021
In reply to Si dH:

Don't know if you watched it back in the day, but on Babylon 5, when presented with a complex question, Ambassador Kosh would often pause for some time, and then answer "Yes".  

> Hit me...

Yes.  

Nothing like bullet pointing stuff out to get it clear in your own head.

I'm in pretty broad agreement there, to comment on a few points:

> [...] major new variant [...]

If it's major enough to sidestep the immunity built up by all that has come to pass in the last 18 months, it's going to be a new pandemic.  The good news there is that everyone is now more or less on the same page with what to do in a pandemic.  

> I'd be really interested in an educated take on why we had no new really major variants emerge for the first six months of the pandemic, several in the following six months, and none in the six months since - and what that could tell us about the future.

Yes, I've thought a fair bit on this.  I can see different possibilities, I know far too little to assign even coarse likelihoods to them.   The parallel discussion gong on in the "Origins of Covid 2" thread brought a paper and some analysis to the table that is interesting and I think in some ways reassuring (and in others rather the opposite).  Ultimately, the appearance of a new, more effective part of the virus (RBD, for example) is a very low probability stochastic effect.  So, expect the unexpected. 

> - that's even more the case for people who are unable to mount a strong immune response to the vaccine, who are in a really difficult situation.

Indeed.  Their risk will reduce as the pandemic phase of Covid passes and there's (hopefully) a lot less of it about.  The AZ MAB cocktail AZD7442 is of direct relevance here as a way to restore immune system like functions to people without functioning immune systems.  Expensive, I suspect.

> To me, that leaves us with a 'choice' whether, in the longer term, we would rather get the virus less often with less immunity or more often with more immunity. I don't know which is actually better, but personally, I think the difference is sufficiently unclear that it certainly isn't worth continuing to restrict one's activities in aiming for the former. (A certain level of caution to avoid high viral loads is, though, still appropriate.)

This is how I see it.  If you know any immunologists offline, raise the question with them.  They may just take a long pause and then say "Yes".  Totally agree on avoiding high viral loads.

> [Personally, I have been consciously trying to change my mindset recently towards a state of normality and trying to lose my residual fear of catching the virus, because my head now tells me this is where I'm going to end up (especially with young kids), and changing my approach will help my mental health. I'm still wearing a mask where it doesn't make me feel like an outlier, but am taking no other precautions.]

My fear of catching it is in general gone; I am very wary of high viral load situations, and I'm not sure I'm ever going to set foot on a bus again.  I'm still going out of my way to reduce the risk of me inadvertently transmitting the virus in places people have little choice over going, especially recognising that many high risk individuals may not be very well aware of their risk. I'm in a rapidly shrinking minority when it comes to wearing a mask in certain indoor public settings.  

>  I don't see how we could expect to develop any new improved vaccines on the same sort of timescales that we did in 2020.

Trialling them post-pandemic is a bit more fraught I think from several angles.  Re: your comments on adapted vaccines, there has been very little high level information given over the lack of apparent progress towards variant adapted vaccines.  Complex subject

>  all countries everywhere will have to go through the same set of stages that we are doing in the UK, but the infection and death rates they reach and the eventual equilibrium will vary wildly with environmental factors - climate, geography, population density, deprivation, population demographics, etc. And many countries will stop mass testing for covid long before the process is done.

Yup.  

> I think there is a significant risk that we get in to a situation where the best thing for society as a whole (even just in this demographic, never mind when considering the more vulnerable groups) is for everyone to be cautious to bring prevalence down, but that the best thing for the health of a lot of individuals, in the context of continuing high prevalence, is to get a mild dose of infection once a year. A bit of a 'tragedy of the commons' in the making?

Yes; although there are less tangible benefits to each side as well.  The homology and cross immunity between SARS-nCov-1 and -2 is on my mind; perhaps this virus has sidelined the near existential thread of another -1 outbreak that would otherwise have got out of control?  Without access to parallel timelines it's pure speculation.  

 What you say here is also applicable to the flu I think - it turns out we can basically eliminate flu, but now there's a lot of worry more people are more vulnerable to flu this year.  The middle ground between the extremes is a dangerous place to be, it seems.

Edit: My peril sensitive sunglass won't let me read your last bullet point.

Post edited at 13:54
In reply to VSisjustascramble:

> Playing devils advocate here, but governments make morale decisions around healthcare outcomes all the time.

> The key one is NICE’s QALY threshold which is currently between 20-30k a year.

> If we assume that 600,000 people would have died from Covid and they would have lived 10 additional years had they not died, using the QALY guidance the government would have spent a maximum of 150B. Instead we’ve spent c.400B. 

Deciding how much of a limited budget should be spent on treatment to help someone who has already caught a disease is ethically completely different from deciding that it would be cheaper for a healthy person to catch a disease.

The other key point is that this is a novel disease and there is high uncertainty because there's less than two years experience.  When there is uncertainty but the uncertainty will reduce over time then you need to be cautious and patient and collect data before making decisions that could end up in people dying unnecessarily.

3
 wintertree 13 Oct 2021
In reply to VSisjustascramble:

> Playing devils advocate here, but governments make morale decisions around healthcare outcomes all the time.

Absolutely.  It'd be daft to take a one sided view that only acknowledges risks of the virus and not the costs of controlling it - both direct and indirect, and both tangible and intangible.

The idea that there's a bean counting model for the value of each of our lives vs the cost of extending them is deeply uncomfortable too many, myself included.  But, it is fair and it is rational and it is necessary given our finite resources.  Would that many other decisions on state funding outside of healthcare were made with such carefully evaluated expert guidance

Where your devil's advocate falls down is in using a linear accounting model during a pandemic; the finite and exhaustible capacity of healthcare and its role in providing enabling many other pre-existing cost/benefit tradeoffs for society change the accounting, and the indirect costs of a pandemic are not a linear scaling of the indirect costs of a small outbreak.

> Anyway, very off topic

The day I complain about someone shifting a topic is the day I get banned for being the site's biggest hypocrite....

 Offwidth 13 Oct 2021
In reply to wintertree:

I agree, which is why I said above I should whoa a bit. I'm sorry.

The fact that denialists hope for one possible something in a big bunch of other bs somethings, doesn't mean that one possible something can't happen (unlike some far worse early denialists shit, like: we don't need lockdowns as only hundreds will die; and herd immunity being achieved in summer 2020 (influencing our idiot PM to ignore actual science recommending restrictions in September and kill tens of thousands more). We are all, on our side of the argument, human and caring, so, given the awful human consequences, often upset and disturbed. So I'll take criticism and apologise when I get the tone wrong and I recognise that anything I'm 'nit picking', isn't written with ill intent (albeit sometimes stuff was actually wrong: like when I called out 18 to 24 year old vaccination rates allegedly stalling at 50%).

By in the past I was referring to flu pandemics eventually resulted in less fatal variants, which arose after earlier lethal variants had caused carnage to world populations, a horrible way to produce any exit. I should have been clear on that point as well. In my defence I'm seriously angry with the gaslighting from govenment on the select committee reports, even if it was as predictable as covid exponential growth with no restrictions or immunity..

You said above: "The good news there is that everyone is now more or less on the same page with what to do in a pandemic." I see no clear evidence that's universal in our government nor in our press nor our population nor even in some Oxford profs.

You beat me to it on the reply to VSisjustascramble...this bean counting of the value of a life is necessary in an underfunded health service. However it cant apply in a pandemic when the whole system is potentially on the verge of collapse. Even in emergency mode as a society we can't go on for long without functioning hospitals. The broad costs of the response were essential but increased by implementing restrictions too late.

Post edited at 16:35
 wintertree 13 Oct 2021
In reply to Offwidth:

I decided to drop the argument and canned my post but looks like you got it.

> By in the past I was referring to flu pandemics eventually resulted in less fatal variants, which arose after earlier lethal variants had caused carnage to world populations, a horrible way to produce any exit. 

Yes, we are lucky to have better options now.  

It’s not at all clear to me that the later flu variants are less lethal, rather than that the surviving population was more robust due to a mix of the most susceptible being killed off and the rest retaining immunity that refreshes occasionally during the endemic phase.  Stop refreshing that immunity and we start to find out how lethal it really is; that as I understand it is some of the concern for this winter flu season.

> I'm seriously angry with the gaslighting from govenment on the select committee reports, 

I’m taking time out from the news.  Nothing they've not said before, and no more palatable this time around.

> nor even in some Oxford profs

Astounding the continued impunity enjoyed there.  At what price a human soul?

Post edited at 16:41
In reply to Offwidth:

> By in the past I was referring to flu pandemics eventually resulted in less fatal variants, which arose after earlier lethal variants had caused carnage to world populations, a horrible way to produce any exit. 

Did they become inherently less lethal though? Or did the populations immunity improve so less people died of it? I.e. what makes Spanish Flu harmless now - is it that the variants currently in circulation are mild compared to the original or are we’re just immune from repeated exposure?

Random thoughts whilst I’m pondering

1) if you took a harmless virus (a common cold strain e.g. a type of rhinovirus) which had a similar natural R rate to Covid-Delta and did sample PCR tests now how would their prevalence compare?

2) if you were born just after the Spanish flu epidemic and it’s endemic, there’s a fair likelihood you won’t encounter it until adulthood. Why don’t we see a longer tail of death from pandemics? Is there an epigenetic element to immunity?

In reply to wintertree:

I do like the idea that wintertree = Ambassador Kosh. But I think you are a lot more helpful than Kosh usually was.

In reply to wintertree:

I am worried that what's behind the government's current approach to the pandemic, and the coming winter, may be a willingness to let the NHS get so stressed that it has to be replaced by something that is not an NHS. Is that unduly cynical?

 wintertree 13 Oct 2021
In reply to BusyLizzie:

> I am worried that what's behind the government's current approach to the pandemic, and the coming winter, may be a willingness to let the NHS get so stressed that it has to be replaced by something that is not an NHS. Is that unduly cynical?

You're not the first poster I've seen float the idea on here, but you are I think the first who doesn't work on the front line of healthcare... 

About a month ago, there seemed to be a concerted media push over private healthcare including a (clearly Marketing department driven) survey being pushed across the media, and at least one big employer advertising private health benefits in a big recruitment drive.  Hard to tell what's deliberate and what's blatant opportuning.

When you look one of the groups behind a lot of the pushback against early lockdown and later milder restrictions in the UK, it is the "American Institute of Economic Research", a libertarian think tank that seemingly lobbies on behalf of various US business interests.  

In the past they have pushed staggering untruths against the NHS as part of their politicisation of the tragedy of Charlie Gard.  I won't link an example as I refuse to raise any of their output up the google search rankings, but it can be found.  I find the way the CG case was misrepresented in the USA as about relating to the costs of socialised healthcare, rather than the reality which was medical ethics as applied to the patient, to have been a great disgrace.  Worse still when others buy in to the lie that the decisions were about cost.

One could imagine they want more incidents where they can point to the NHS as part of their marketing narrative against socialised healthcare in the US, or one could imagine they want to quake it apart and get their benefactors a piece of the pie.  Or that someone else wants some pie.  

I don't know.  But I do know how I feel about their influence on the situation in the UK including some "academics".  I feel strongly that it is a matter of national security and should be treated as such.  

I suspect when the AIER representative walks in to the room, they ask "What do you want?" rather than "Who are you?"

 wintertree 13 Oct 2021
In reply to VSisjustascramble:

My thoughts on your main questions are "yes".

>  Is there an epigenetic element to immunity?

I'd expect such elements to only regulate the function of the progeny's immune system, rather than to pass on information on antigens etc.  

The transfer of antibodies in breast milk is one way antigen information can flow from parent to child that I would say is distinct to epigenetics.  Like MAB therapeutics/prophylactics I think these exist for a limited time only before fading away, and can't transfer the antigen information in to any of the systems that can actually replenish the expired components.

It's really interesting to speculate wildly about the future direction evolution might have taken if we'd not gone all technological on it - how far away was it from being able to encode antigen information in ways that could be passed enduringly between generations - or even passed laterally within a population, allowing immunity to spread in an established, adult population?   I doubt we're anywhere near reaching the potential of our biological building blocks.

Post edited at 19:57
In reply to wintertree:

Yes, that is indeed the sort of horrible stuff I have in mind.

 mik82 13 Oct 2021
In reply to BusyLizzie:

>I am worried that what's behind the government's current approach to the pandemic, and the coming winter, may be a willingness to let the NHS get so stressed that it has to be replaced by something that is not an NHS. Is that unduly cynical?

They're almost certainly using this as an opportunity. You only have to look at the constant negative articles about primary care, and in particular, GPs. If primary care fails then the rest of the NHS will quickly fail afterwards. and it has already been set up to be the scapegoat if this does happen - the same as the fuel crisis has been blamed on "Remainer fuel bosses" and the DVLA. 

2
 Misha 13 Oct 2021
In reply to Si dH:

You are better getting the virus while the immune response is strong - yes, if you are definitely going to get the virus and have a choice as to when you get it and you are definitely not going to get it again. Clearly this is completely unrealistic. It’s best not to get the virus at all, ever. Also fairly unrealistic perhaps. Is there a middle way with regular reinfection? That’s not realistic either as you can’t choose when you get infected (unless you go to a Covid party I suppose) and it would be playing with fire because what’s to say you don’t get a really bad case at some point - plus, if everyone adopted this strategy, we would have a never ending epidemic with continually high case rates and that would be bad news for the vulnerable.

So where does that leave us? The reality is you don’t know to what extent your immunity has waned at any point, whether that’s post vaccine or post infection. You don’t know how your body will react to the virus even if immunity has not waned. You don’t know what viral load you might get. You don’t know whether or when you might get infected again. So I think it comes down to playing on the side of caution. Most people don’t seem to be bothering though. Hardly surprising case rates are still relatively high. 

What’s missing from the discussion above is the possibility of ongoing boosters for everyone. It must be possible, if manufacturing capacity is vastly expanded. That is what the government should be focusing on. We should donate surplus orders / stocks to poorer countries but equally we should be investing in our production capacity so that going forward boosters for everyone would be a reality. Of course that’s not going to happen…

Post edited at 22:28
2
 Si dH 13 Oct 2021
In reply to Misha:

> You are better getting the virus while the immune response is strong - yes, if you are definitely going to get the virus and have a choice as to when you get it and you are definitely not going to get it again. Clearly this is completely unrealistic.

It's not about never getting it again. It's about using the virus to maintain or improve our immunity levels, using the starting hand we have from the vaccine to minimise risk of serious disease. I fully expect this to be a repeating cycle and that most of us will catch covid multiple times, unless case rates drop substantially over the next few months.

> It’s best not to get the virus at all, ever. Also fairly unrealistic perhaps. Is there a middle way with regular reinfection? That’s not realistic either as you can’t choose when you get infected (unless you go to a Covid party I suppose) and it would be playing with fire because what’s to say you don’t get a really bad case at some point - plus, if everyone adopted this strategy, we would have a never ending epidemic with continually high case rates and that would be bad news for the vulnerable.

You reduce your risk of having a really bad case by getting it while your immunity from vaccination is still strong, and then subsequently while you still have some immunity or immune system memory from previous bouts. If you minimise your risk of getting infected by taking precautions against it, your immunity eventually wanes completely and then you go out and get hit 'fresh' by the virus, you are more likely to get seriously ill. That's the whole point of what I'm saying.

> So where does that leave us? The reality is you don’t know to what extent your immunity has waned at any point, whether that’s post vaccine or post infection. You don’t know how your body will react to the virus even if immunity has not waned. You don’t know what viral load you might get. You don’t know whether or when you might get infected again. So I think it comes down to playing on the side of caution. Most people don’t seem to be bothering though. Hardly surprising case rates are still relatively high. 

I accept most of the above. But I don't accept that I 'don't know whether or when you might get infection again.' I'm afraid I think that's a naive position. It is looking fairly inevitable, especially for those of us with kids just starting school. If rates don't significantly decrease it becomes inevitable for most adults. And the problem with advising caution is that, for the reasons given above, the cautious approach is no longer obvious. It might well turn out that minimising ones risk of infection for another 12 months before eventually accepting that life must go on is a high risk strategy. A more cautious personal approach may well be to make conservative assumptions about when your immunity is likely to wane and act accordingly. I touched on your other points in my post.

> What’s missing from the discussion above is the possibility of ongoing boosters for everyone. It must be possible, if manufacturing capacity is vastly expanded. That is what the government should be focusing on. We should donate surplus orders / stocks to poorer countries but equally we should be investing in our production capacity so that going forward boosters for everyone would be a reality. Of course that’s not going to happen…

I'm not convinced this is politically deliverable as an ongoing thing to all adults and if it was, I don't think it's the best use of NHS resources or of vaccine doses. I do get the attraction and obviously I'd take a dose straight away if offered, but I'm not sure it's the decision I'd take if I was in charge.

(Up late with a two week old so apologies if anything doesn't make sense.)

Post edited at 23:17
 oureed 13 Oct 2021
In reply to VSisjustascramble:

> Did they become inherently less lethal though? Or did the populations immunity improve so less people died of it?

Vey probably an element of both. Immunity and evolution are not mutually exclusive and are neither binary nor permanent processes.

If host lethality negatively affects the reproductive potential of a virus (which it very probably will!) there will be considerable selective pressure for the virus to become less lethal. At the same time, exposure to the virus will strengthen a host's immune response (if it survives), and this will in turn increase selective pressure for immune-resistant variants to emerge.

Like the economy, these are very dynamic processes with host and virus both continually adapting to change. Vaccines, therapeutics, barriers and behavioural changes can be added to the mix.

The end result seems to be for Coronaviruses to either become very scarce (eg. MERS) or endemic and relatively benign (eg. common cold).

Post edited at 23:29
1
 Misha 13 Oct 2021
In reply to Si dH:

I get what you’re saying but I would preface it with “in theory”. We don’t actually know whether repeated infection leads to milder infection and rules out serious illness. In theory, it should do. In practice, it’s a new virus, so we don’t know yet; your susceptibility could increase with age; and you might get a heavy viral loads. So I don’t think there’s a clear cut answer. Add to this the fact that continually having a relatively high case load would strain the NHS and make life miserable for more vulnerable people.

I don’t see why ongoing boosters for everyone would be politically difficult. The cost would be immaterial in the scheme of things, while the benefits would be significant.

In terms of personal behaviour, everyone will have their own view. My take on it is doing things which are important for me (climbing indoors and out) and not doing things which aren’t important / essential (socialising but to be fair I hardly ever do that anyway, going to the office). Plus wearing a face mask in shops etc. 

 Si dH 14 Oct 2021
In reply to Misha:

> I don’t see why ongoing boosters for everyone would be politically difficult. The cost would be immaterial in the scheme of things, while the benefits would be significant.

Running the vaccine programme required the hiring of lots of venues and the time of lots of staff. The NHS' biggest problem is lack of resources (staff.) Perhaps someone well-informed could comment on this but I would anticipate providing a continuous cycling booster programme for the population would require a lot of resources they don't currently have.

Having said that, I am of the opinion we should size the NHS to do what we need in the medium term rather than try to work within current constraints. There is then the question of how to enable more NHS recruitment, which is way off-topic!

LSRH has other reasons for not doing ongoing boosters I think.

Edit to add: Ultimately though, my opinion on this is not because I don't think we should do boosters, it's because I don't think we will. The govt's stall set out, as informed by JCVI, is that over 50s are going to be get boosters, not under 50s. It took JCVI surprisingly long to reach that recommendation to do boosters to over 50s, along with some govt pressure in the press. Quite a few scientists went on record saying there should be no boosters at all until there is evidence of waning immunity in hospital admissions. So I just can't see any prospect of those of us under 50 ever getting offered booster jabs and I want to manage the risks in that context.

Post edited at 07:34
 elsewhere 14 Oct 2021
In reply to Si dH:

>  evidence of waning immunity in hospital admissions. 

That's the canary in the coal mine. 

With 700 admissions per day almost all with a known vaccination status there's loads of real world data to pick up waning immunity.

Post edited at 08:04
 Jon Read 14 Oct 2021
In reply to VSisjustascramble:

> Did they become inherently less lethal though? Or did the populations immunity improve so less people died of it? I.e. what makes Spanish Flu harmless now - is it that the variants currently in circulation are mild compared to the original or are we’re just immune from repeated exposure?

It would have killed off those most vulnerable to it in the first few years. It then, of course, became a seasonal influenza (until 1957 when it was replaced by the next pandemic strain AH2N2, which in turn became seasonal). Immunity developed through childhood exposure to seasonal influenza probably protected against the worst severity aspects of that original 1918 strain on subsequent types. I don't think there's *any* evidence that the virus evolved to be less harmful, more those that were most vulnerable through immunological naivety were unfortunately removed over time.

> Random thoughts whilst I’m pondering

> 1) if you took a harmless virus (a common cold strain e.g. a type of rhinovirus) which had a similar natural R rate to Covid-Delta and did sample PCR tests now how would their prevalence compare?

Take a look: Figure 37a vs 37b. Difficult to compare the numbers testing +ve because they're somewhat different populations, but the % of tests that are positive (positivity) are currently comparable between SARS-CoV-2 and RSV.

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1023910/Weekly_Flu_and_COVID-19_report_w40_v2.pdf

> 2) if you were born just after the Spanish flu epidemic and it’s endemic, there’s a fair likelihood you won’t encounter it until adulthood. Why don’t we see a longer tail of death from pandemics? Is there an epigenetic element to immunity?

You would see influenza much earlier than adulthood, most likely the first winter you attend school or day-care. Rule of thumb: the higher the R0 of a virus, the earlier in life you are likely to first be infected. Again, the lower excess deaths in 1921-1930 (which is about the only way we can attempt to measure the mortality for flu then) may just be because everyone that was going to die from it already had.

 kirsten 14 Oct 2021
In reply to Si dH:

Let’s see what they say re boosters come early Dec, they don’t have to think about the under 50s until then anyway. 

https://www.theguardian.com/world/2021/oct/14/covid-booster-shots-important-to-stop-infection-finds-english-study

Post edited at 08:10
 Jon Read 14 Oct 2021
In reply to oureed:

Just to pick up on a couple of your points...

> If host lethality negatively affects the reproductive potential of a virus (which it very probably will!) there will be considerable selective pressure for the virus to become less lethal.

I think this is a fallacy, perpetuated unfortunately by some media-friendly scientists. You just have to consider how anthrax spreads on the Serengeti, or consider the impact of safe funeral behaviours on the West African Ebola epidemic to realise that viruses can do quite well through killing their hosts in the right circumstances. Also, simplistic theoretical predictions of pathogen evolution tend not to survive well when confronted with real world modern human behaviour.

> The end result seems to be for Coronaviruses to either become very scarce (eg. MERS) or endemic and relatively benign (eg. common cold).

MERS hadn't really shown potential to spread between humans well outside of specific circumstances (unprepared healthcare settings), which is why we haven't so far seen a MERS pandemic. It's mostly spill over from the animal reservoirs, so the scarcity has more to do with that reservoir and the interface than immunity in humans.

 wintertree 14 Oct 2021
In reply to Jon Read:

I’m glad you came along to make that post Jon. It’s funny how this point comes up time and again without any actual evidence.

Media friendly scientists have a few things to answer for; I was pleased to see that another one recently acknowledged their early comment - that covid was mostly killing those close to death anyway - was in fact wrong.  Makes you wonder why they say these things to journalists without any evidence at their backs.

The pre symptomatic aspect of covid and timeline of infections shows to me how lethality can be somewhat decoupled from ability to spread.  The slower it kills, the more the lethality decouples from transmission.  As I was thinking last night when touring the local ash trees

Post edited at 08:17

 oureed 14 Oct 2021
In reply to Jon Read:

> I think this is a fallacy, perpetuated unfortunately by some media-friendly scientists.

So you disagree with some scientists. This is unsurprising, scientists very often disagree about some very fundamental concepts. I recently listened in on a conversation between 2 researchers who had opposing theories about the use of a drug. Both were talking about their specialism, both following the science.

Edit: The use of 'media-friendly' to delegitimise someone's opinion is interesting. Our most media-friendly scientists are undoubtedly professors Gilbert, Whitty and Ferguson! 

> You just have to consider how anthrax spreads on the Serengeti, or consider the impact of safe funeral behaviours on the West African Ebola epidemic to realise that viruses can do quite well through killing their hosts in the right circumstances.

These comparisons don't tell us much about a highly transmissible respiratory virus provoking relatively low mortality rates in active people. Anthrax is not contagious, Ebola most often spreads via body fluids. It's unsurprising they can be successful while killing their hosts. Not so your average Coronavirus, whose preferred environment is a teeming crowd in a tightly-packed room.

> Also, simplistic theoretical predictions of pathogen evolution tend not to survive well when confronted with real world modern human behaviour.

My whole post was about the complexity of the system. Wintertree, VS and yourself are arguing for a more binary understanding of how pandemics end. 

> MERS hadn't really shown potential to spread between humans well outside of specific circumstances (unprepared healthcare settings), which is why we haven't so far seen a MERS pandemic.

Indeed, low transmissibility and high lethality is not a winning combination!

Post edited at 09:11
3
 Jon Read 14 Oct 2021
In reply to oureed:

> So you disagree with some scientists. This is unsurprising, scientists very often disagree about some very fundamental concepts. I recently listened in on a conversation between 2 researchers who had opposing theories about the use of a drug. Both were talking about their specialism, both following the science.

> Edit: The use of 'media-friendly' to delegitimise someone's opinion is interesting. Our most media-friendly scientists are undoubtedly professors Gilbert, Whitty and Ferguson! 

Perhaps media-friendly was the wrong phrase; replace with "some scientists in the media". The final arbiter for disagreement is good-quality evidence, which to my mind is lacking for the assertion that premature death of a pathogen's host is selected against.

> These comparisons don't tell us much about a highly transmissible respiratory virus provoking relatively low mortality rates in active people. Anthrax is not contagious, Ebola most often spreads via body fluids. It's unsurprising they can be successful while killing their hosts. Not so your average Coronavirus, whose preferred environment is a teeming crowd in a tightly-packed room.

Some of those scientists in the media used to say (pre-2014) that Ebola outbreaks would always be self-limiting and never cause a big outbreak *because* it killed the host too swiftly for it's own good. To me this is a classic example of [edit to complete sentence] a poor understanding of evolutionary dynamics in a real world setting.

> My whole post was about the complexity of the system. Wintertree, VS and yourself are arguing for a more binary understanding of how pandemics end. 

I'm not sure I'm arguing for any binary understanding (whatever that means).

Post edited at 09:40
 oureed 14 Oct 2021
In reply to Jon Read:

> I'm not sure I'm arguing for any binary understanding (whatever that means).

Fair enough, the conversation before you entered seemed to broadly focus on - Will Covid end because of improved host immunity (in the red corner you have WT and VS) or because of the virus evolving to become more transmissible but less incapacitating to its host (in the blue corner, Offwidth)? I was saying it'll probably be a combination of both + some other factors.

Personally I don't think Covid-19 is virulent enough for this aspect to exert a huge amount of selective pressure. Many people have caught and transmitted the virus while not getting particularly ill themselves. However, increased transmissibility certainly seems to be the case with the most recent variants.

 wintertree 14 Oct 2021
In reply to Jon Read:

> The final arbiter for disagreement is good-quality evidence, which to my mind is lacking for the assertion that premature death of a pathogen's host is selected against.

Agreed.

> I'm not sure I'm arguing for any binary understanding (whatever that means).

I don't think that you are, nor do I think that I am, nor do I think that VS is.

The problem is, we have here a poster who has  a repeatedly demonstrated  inability to digest peer reviewed evidence, a repeatedly demonstrated tendency to apply the wrong maths to the wrong data and to call it the wrong thing, a habit of lecturing us about "basis [sic] biology stuff regarding evolution" and our "woeful lack of knowledge about evolution".  All of their fallacies, "mistakes" and bad math always - every single time - come out in favour of Covid being less serious than it demonstrably is.  If this was a string of genuine errors and inabilities, I'd have more luck winning my 6-horse accumulator than producing a set of views as one sided as theirs have been. 

When all else fails, they end up wishing a painful death by untreated cancer on others, apparently with the intent of deliberately provoking a ban so that they can then come back with a delusional fantasy where they're subject to persecution in the Orwellian society that is UKC.

Of course, it's hard to actually hold them to account for what they've said in the past, because they apparently deliberately provoke bans so their identity and messaging can change with the times whilst maintaining it's distance off to one consistent side.  They've never been kind enough to furnish a list of their previous identities.

Further engagement is only likely to drag the thread down in to more of the same.

 oureed 14 Oct 2021
In reply to Jon Read:

>  The final arbiter for disagreement is good-quality evidence, which to my mind is lacking for the assertion that premature death of a pathogen's host is selected against.

Improvements in genome sequencing technology should soon provide more clarity. This wasn't available for the 20th century's major respiratory pandemics.

1
 wintertree 14 Oct 2021
In reply to Si dH:

> So I just can't see any prospect of those of us under 50 ever getting offered booster jabs and I want to manage the risks in that context.

Never say never.

I'm too young for the "free" flu vaccine, but I can rock up at a pharmacy and pay for it, no proscription required.  I've never done so before, but I'm seriously considering it for this winter.

I've seen no policy or forwards looking comment from government on if or when vaccines are going to be made available on a paid-for basis to those below the age that get it for free, but that doesn't seem beyond the bounds of reason far enough down the line.  I can see arguments for and against making this option available.  

Alternatively, I don't know how long for you, but I haven't got to avoid dying for that much longer to reach 50 myself...

 wintertree 14 Oct 2021
In reply to thread:

Last night update to the data was nice in that it shows the rate constant heading back for decay.  Always a bit provisional on the far right so it might go up some more with the next update.

So - good in that there's still no appetite for unbounded exponential growth in cases, bad in that we're running at a near steady state with a high level of cases and a demographic shift going on behind the scenes towards the more susceptible.  There's been lots of good discussion on what could be driving this over the past threads; the answer lies in the longitudinal healthcare data that we don't have proper access to.  There are some SAGE documents that come up occasionally which give scattered glimpses of it and might be informative.

I have a new theory about the structure in the rate constant plots - turn off the annotations and it looks like a mountain range in profile, perhaps with some bathymetry in the regions of deeper decay, and a bit of a tectonic fault when England stopped winning football matches in the Euros.


 Jon Read 14 Oct 2021
In reply to oureed:

> Improvements in genome sequencing technology should soon provide more clarity. This wasn't available for the 20th century's major respiratory pandemics.

How exactly? Plenty of sequencing has gone on in the past 20 years.

If (and it's a big if) you could translate a genome into a predictive measure of clinical severity and risk of death, sequencing might provide evidence of selection. You'd probably want gain of function studies for this

Post edited at 10:26
 Offwidth 14 Oct 2021
In reply to BusyLizzie:

Things don't look very happy this morning on the news between GP representatives and the minister.

https://www.bbc.co.uk/news/health-58904557

One of the BBC's regular GPs made the point that there is no ready supply of locums they can turn to and in some senses things improved in the pandemic, as just before you might need to wait weeks for an appointment (because of the GP shortage) but with phone and online appointments initial GP contact had been speeded up to about 2 days.

Roy Lilley recently hammered the minister about the proposal to sort out NHS management (the minster proposed removing trust leaders who don't meet targets... the same idiotic top-down pressures that led to the Mid Staffs tragedy).

https://myemail.constantcontact.com/Fair-game.html?soid=1102665899193&aid=UnPKLFW9XC8

He also had a real go at 'policy by the Daily Telegraph' (and the party conference speech as being vacuous nonsense .. but I can't find that link)

https://myemail.constantcontact.com/Telegraph.html?soid=1102665899193&aid=ekeyntwI8NM

So yes, I think something is going on.

2
 wintertree 14 Oct 2021
In reply to Jon Read:

> If (and it's a big if) 

No fair - you answered your question with an edit when I was about to throw some buzzwords about AI and deep learning in there.  

>  You'd probably want gain of function studies for this 

I was thinking about a program to delete all immune memory of OC43 from volunteers and see what happens.  That could settle a lot of questions.  After many goes, I've come up with a method that the biologists aren't outright laughing at, although quite aside from the cost and the timescales of the development program, there's the ethical side to consider.  Perhaps I should out-source it somewhere a bit more, how shall I say, amenable over such things?

 oureed 14 Oct 2021
In reply to Jon Read:

> If (and it's a big if) you could translate a genome into a predictive measure of clinical severity and risk of death

I wasn't thinking of anything predictive, more retroactively identifying different strains and investigating their virulence/transmissibility. The 1918 'Spanish Flu' pandemic is just that, in 2021 we have identified multiple Covid-19 variants and have a much clearer picture of how the virus has evolved.

Hold the press:  just read that researchers have identified different virus strains from the lungs of people who died from influenza in 1918/19. That's what I call retroactive! 

1
 Jon Read 14 Oct 2021
In reply to oureed:

Yeah, but you need to understand the phenotypic consequence of the genome don't you? Otherwise, what's the sequencing for? Just to demonstrate the strain composition in the population is changing?

 oureed 14 Oct 2021
In reply to Jon Read:

> Yeah, but you need to understand the phenotypic consequence of the genome don't you? 

Indeed, that's why I added "...and investigating their virulence/transmissibility".

1
 Offwidth 14 Oct 2021
In reply to oureed:

Wintertree was right I needed to be more careful lest someone misrepresent what I wanted to say and use it to encourage misinformation. My 'corner' is we don't know how this pandemic ends and we need to be careful right now in England (more than our government is encouraging us to be). I do not believe pandemics will all end in less lethal variants as I'd need incredibly clear evidence to believe that. On balance I think the 1918 flu probably did, as later flare-ups in protected isolated populations were less serious than the main waves were in others nearby (eg in Samoa). https://en.wikipedia.org/wiki/Spanish_flu ..... I did point out to wintertree we didn't need to evidence the less lethal variants theory as we both knew some scientists publicly postulate that. In terms of evolution acting against lethality, as others pointed out, Ebola famously survives despite being incredibly effective at killing infected hosts.

Anyhow, well done for getting me to bite...like wintertree I'll go back to ignoring your posts on these Friday might threads and would advise others do the same. Happy to debate on other threads but sadly I find you consistently unhelpful here. I wish you could be open about previous profiles (if only privately by email) and engage more honestly so that I would change my position.

 wintertree 14 Oct 2021
In reply to Offwidth:

> Things don't look very happy this morning on the news between GP representatives and the minister.

There's a few "involved" posters who I think are sitting on most of their thoughts re: primary care.  I've been hoping to see a thread pop up on the issue; I have little to contribute other than an interest in listening to what people have to say.

 oureed 14 Oct 2021
In reply to Offwidth:

I agree, Wintertree and VS were focused on defending one side of the debate. Your responses were more nuanced. 

> I wish you could be open about previous profiles 

Here's a clue, I've never wished untreated cancer on anyone, despite Wt's assurances to the contrary!

Post edited at 11:49
3
 Offwidth 14 Oct 2021
In reply to wintertree:

I genuinely believe this latest initiative will make things worse. The pandemic forced change to phone and online appointments and if we go back to the old way of mostly face-to-face appointments the demand will certainly exceed capacity very quickly and push more people to an already overstrained A&E. Primary Care clusters delivering vaccination won't be helping ease demand on their services elsewhere either. We just don't have anything like the number of GPs we need.

Medium term one practical reform I'd like to see is a primary care unit at every major A&E with linked triage.

 Misha 14 Oct 2021
In reply to Si dH:

You are probably right that boosters won’t be offered to under 50s unless there’s evidence of significantly waning immunity (and if there isn’t then no real need to be particularly cautious). We just don’t know yet.

I suspect a lot of the reticence about boosters is due to lack of supply in poorer countries. That needs to be addressed through massively upscaling vaccine production.

It might not be necessary to do in perpetuity, just until incidence is driven down to a sufficiently low level and/or highly effective therapeutics are available.

Agree re sizing the NHS to meet the challenge. At the end of the day, administering vaccines doesn’t require a doctor or nurse level qualification. They can recruit people for that specific role and give them whatever training is required - which isn’t years of nursing or medical schooling. Admin staff would be even easier to train.

As ever, it comes down to political will. Now if someone could point out to BoJo that better health outcomes are part of levelling up… Actually, he’s on record as saying that cancer survival rates don’t matter because it’s all about wages. Ah well…

 Misha 14 Oct 2021
In reply to wintertree:

Cases still going up today. I can’t judge the rate constant by eye but it’s not exponential as far as I can see, so that’s a start. However any increase on the current baseline is bad news for hospitalisations and occupancy. Hopefully the growth will peter out, particularly given the better weather in the second half of last week. If it is indeed weather related, doesn’t bode well given the forecast. Can’t stop wondering - when is it going to burn through and what’s the reinfection rate by demographic? 

In reply to Misha:

> I suspect a lot of the reticence about boosters is due to lack of supply in poorer countries. That needs to be addressed through massively upscaling vaccine production.

Rich countries buying boosters at full price means continued profit for Covid vaccine producers which means continued investment in vaccine R&D and production and more supply of vaccine.   

If anything, there's a risk that if rich countries don't do boosters and stop buying vaccine once their populations have had two doses that pharma will start moving resources away from Covid.  This would also mean that if we need mass immunisation again because of a new variant there would be a longer spin-up time.

3
 Si dH 15 Oct 2021
In reply to wintertree:

So in the last two days we have news that LFTs may be 80% accurate after all and that one of the labs is producing lots of false negative PCRs. Excellent news for understanding the data!!

 Offwidth 15 Oct 2021
In reply to Si dH:

I see that as more misuse of statistics. 80% at peak viral load and if done correctly is worse than I expected.

1
 wintertree 15 Oct 2021
In reply to Misha:

> Cases still going up today. I can’t judge the rate constant by eye but it’s not exponential as far as I can see, so that’s a start. 

Yup; another very low exponential rate constant but a substantial growth in actual cases as the baseline is high, and the demographic of cases is getting older - that means the growth is likely much worse than it looks in terms of consequences.

Nick Triggle was describing this as well today on the rolling BBC page - he was suggesting we might be reaching an approximate steady state.

I'm not so sure about the steady state - this would be driven by people getting (re)infected at the rate they become susceptible, give or take some quasi-periodic bunching up over the timescale of weeks from the weather and other effects. 

Edit: Now I think about it, it's really complicated how this would manifest; the rate constants would end up wobbling around zero in a "steady state" situation, and the key information then lives not in the rate constants but in the cases data broken down by age bin and normalised to the population size of each bin; we'd expect to see that value go up with age.  So, if we were to look for a shift to this state, we'd be looking for a rate constant that wobbles around zero, with a bit more growth in older ages to begin with until a new demographic profile is established.  But there's still so much stuff going on around schools it's all very conflated. 

I don't think a "steady state" driven by immunity fading would hit so uniformly across almost all ages as this rise in rate constants is doing, because the gradual and slow fade of immunity will be relativity faster in the older, and they also had their injections further back in time, so I'd expect the emergence of the "steady state" to be age-dependant and this latest rise is pretty age-independent.  

It feels to me like there's just more potential for transmission but only in really crap weather (or with football matches piling people in to the pubs), and the conditions for that never last for long.

> If it is indeed weather related, doesn’t bode well given the forecast. Can’t stop wondering - when is it going to burn through and what’s the reinfection rate by demographic? 

I'm excitedly looking forwards to our first frost very soon, and perhaps low altitude snow before the end of October.  This turn in the data could be the first hints of seasonality really kicking in, and yes I don't think it bodes particularly well.

In reply to Si dH:

> So in the last two days we have news that LFTs may be 80% accurate after all and that one of the labs is producing lots of false negative PCRs. Excellent news for understanding the data!!

Poster "davidalcock" was on the ball with this earlier in the thread; it's all gone a bit mad hasn't it...  It's good to read that the LFTs are more accurate for the people most likely to spread the virus, it means their lower accuracy elsewhere combined with the lack of understanding about what a result means is somewhat less problematic. 

In reply to tom_in_edinburgh:

Don't do it.  Don't make me reach for the Picard Facepalm memes again, please.

Post edited at 11:33
 Offwidth 15 Oct 2021
In reply to wintertree:

The amazing turnaround in vacinantion levels in Australia's two hardest hit states.

https://www.theguardian.com/australia-news/2021/oct/15/a-phenomenal-turnaround-how-australia-is-vaccinating-its-way-to-freedom

1
In reply to wintertree:

> I'm not so sure about the steady state - this would be driven by people getting (re)infected at the rate they become susceptible, give or take some quasi-periodic bunching up over the timescale of weeks from the weather and other effects. 

> Edit: Now I think about it, it's really complicated how this would manifest; the rate constants would end up wobbling around zero in a "steady state" situation, and the key information then lives not in the rate constants but in the cases data broken down by age bin and normalised to the population size of each bin; we'd expect to see that value go up with age.  So, if we were to look for a shift to this state, we'd be looking for a rate constant that wobbles around zero, with a bit more growth in older ages to begin with until a new demographic profile is established.  But there's still so much stuff going on around schools it's all very conflated. 

> I don't think a "steady state" driven by immunity fading would hit so uniformly across almost all ages as this rise in rate constants is doing, because the gradual and slow fade of immunity will be relativity faster in the older, and they also had their injections further back in time, so I'd expect the emergence of the "steady state" to be age-dependant and this latest rise is pretty age-independent.  

It’s probably worth noting that reinfection would be moderated by the different levels of social interaction the different age groups have.

Whilst you might expect that immunity would wane fastest in the elderly, that might not translate into cases if they’re still being cautious or would have less social interactions even if they’d gone back to pre-Covid behaviour.

It’s going to be pretty hard to make sense of whether reinfections are driving cases because the the wide disparities in behaviour - the young are back partying and snogging each other and the old are tucked away, wearing masks and generally are being more cautious.

 Offwidth 15 Oct 2021
In reply to VSisjustascramble:

Latest ONS stats including Wales being at the highest infection levels yet and England increasing; highest levels in school age kids.

https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/15october2021

Post edited at 13:08
 wintertree 15 Oct 2021
In reply to VSisjustascramble:

> It’s going to be pretty hard to make sense of 

It's getting much, much harder to make sense of any of it; so many more factors can influence the difference between growth and decay vs early pandemic phases. 

In reply to wintertree:

> In reply to tom_in_edinburgh:

> Don't do it.  Don't make me reach for the Picard Facepalm memes again, please.

It makes no difference how many memes you post.  Big companies are motivated by money.  You take the high-profit business away which annual boosters in rich nations would create and eventually they will move people onto other programs and stop investing in production.

4
 wintertree 15 Oct 2021
In reply to tom_in_edinburgh:

> It makes no difference how many memes you post.

It makes no difference how much rational content anyone posts either, and the meme are less effort.

> Rich countries buying boosters at full price means continued profit for Covid vaccine producers which means continued investment in vaccine R&D 

It's worth pointing out that in many cases the cost and risk of the R&D that got us several vaccines early on had not been shouldered by the vaccine producers.

> You take the high-profit business

Some vaccine producers are working on a non-profit basis I hear, with for example the holders of the Oxford IP having given free access to the IP for the duration of the pandemic phase.  Those are the people who did the R&D, and they were commendably happy to not profit from it during the crisis.  I don't think all the manufactures of vaccines are in this for high profits either.

The argument that we need to buy boosters in the UK to sustain the profit of big pharma so that they're ready to save us from the next pandemic is pure misinformed nonsense on so many levels I don't even know where to begin.

Probably with the idea that doses (boosters or otherwise) should be given according to expert medical judgment on what is medically best for us, and in many ways as our situation in the UK continues to improve, what is best for us is that there are no other regions of the world with Covid running uncontrolled in large populations without any pre-existing immunity.

If we need to keep reserve expertise, supply chain and manufacturing capability online in the UK to spool up production of another vaccine in the future there are far more appropriate ways to ensure that than ordering boosters for ourselves regardless of what we should be doing with them.

In reply to wintertree:

You need to get your head out of academic science and think about the real world. 

Sure there was lots of R&D long before the pandemic but big pharma have spent at least billions and probably tens of billions and moved tens of thousands of highly skilled employees onto this project and built many new facilities.   That's based on dollars.  The dollars go away, the focus will go somewhere else.

1
 wintertree 15 Oct 2021
In reply to tom_in_edinburgh:

> You need to get your head out of academic science and think about the real world. 

You need to stop jumping to diametrically wrong conclusions.  

> Sure there was lots of R&D long before the pandemic

R&D.

> but big pharma have spent at least billions and probably tens of billions and moved tens of thousands of highly skilled employees onto this project and built many new facilities.

Production.

You are arguing that by placing more production orders than we need, R&D will continue better than otherwise.  

I am arguing that R&D happens because we choose to fund R&D (or not).   Two very different views, an d it's got nothing to do with my head apparently being stuck in academic science. 

>  That's based on dollars.  The dollars go away, the focus will go somewhere else.

You have missed my point.

The money big firms spent scaling up production came from government orders placed with them to scale up production.

If we want to maintain a reserve capacity for national security reasons against future pandemics, this should be done openly with contracts for such, not by placing orders for and then giving boosters other than in accordance with medical advice.

One way we can maintain that capacity is by paying for doses to be produced here and shipped to developing nations.  I'd be all for that, other than ugly jingoistic politics, helping close out the pandemic globally is in our enlightened self interest.

 Offwidth 15 Oct 2021
In reply to tom_in_edinburgh:

As someone who has at times defended you here, I simply think you are wrong on this, so some links to expert evidence backing up your views would be welcome (in case we've missed something).

In reply to Offwidth:

> As someone who has at times defended you here, I simply think you are wrong on this, so some links to expert evidence backing up your views would be welcome (in case we've missed something).

It is blatantly obvious that a company which invests and assigns high value staff based on the expectation of a stream of large orders for regular boosters is going to reassign its resources if there's no stream of orders.

You don't need 'expert evidence' to expect that management in billion dollar companies will make decisions based on revenue predictions.   If you were CEO of Pfizer and you were expecting orders for say 1 billion booster doses a year at $20 a dose from rich countries and that didn't materialise would it affect where you allocated resources?

Also there's a difference between R and D.  D is harder and more expensive than R but people who do R in universities don't give the people who do D industry fair credit for their skills.

Post edited at 14:32
3
 Offwidth 15 Oct 2021
In reply to wintertree:

https://www.theguardian.com/world/2021/oct/15/covid-how-did-error-over-wrong-pcr-test-results-in-uk-happen

Chief exec "Quality is paramount for us. We have proudly analysed more than 2.5m samples for NHS test and trace,"

Only nearly 2% wrong then!

UKHSA say this is an isolated incident well we should bl**dy well hope so.

Expert commentator on the BBC says the mind boggles how this could have happened under the quality systems that should be in place and given this has happened it would be wise to ensure there are no similar problems elsewhere.

In reply to wintertree:

> If we want to maintain a reserve capacity for national security reasons against future pandemics, this should be done openly with contracts for such, not by placing orders for and then giving boosters other than in accordance with medical advice.

Tom’s idea is tosh, but whilst I’m normally a massive advocate of private sector involvement, I think any future rapid vaccine prototyping and production capacity has to be maintained by the government.

I can just see a scenario where one of the big pharma companies are awarded a contract to maintain a fully functioning factory with the latest technology - all very well and good. A few spending review cycles later, budgets are cut, the pharma option is deemed to expensive and it gets given to someone else. In 50 years time, when we need it, it turns out we’ve just been paying for a big barn in a field with a couple of Bunsen burners in it.

In reply to Offwidth:

> Expert commentator on the BBC says the mind boggles how this could have happened under the quality systems that should be in place and given this has happened it would be wise to ensure there are no similar problems elsewhere.

"Government records show that Immensa, which was founded in May 2020 just months after the start of the pandemic, has been awarded contracts for Covid testing by the Department of Health valued at £181 million."

Call me cynical but...

And also, just look at UK cases compared with the rest of Europe.  The Tories are running an experiment on us.

https://twitter.com/jdpoc/status/1448725804406476802

2
 wintertree 15 Oct 2021
In reply to VSisjustascramble:

> A few spending review cycles later, 

A discussion I've been having offline.

Anticipating and pre-funding infrastructure for every possible disaster is something of a fool's errand with our limited resources, and even trying to do it for a single high risk disaster isn't going to remain a priority for long after the last instance of that disaster was passed.

There are other ways to prepare for unlikely and even unknowable future disasters - and it comes down to having a healthy, strong, robust society where things aren't pared back to the limits of sustainability in good times, and where there are broad and deep capabilities in industry and academia so that there is an expert base there to draw on whatever problem emerges, and where there is a healthy, trust and respect based relationship between government and scientific institutions, and where the standard of democracy and government are high.  If we did a health check for the nation for the nation against these things, it would not be good.

>  In 50 years time, when we need it, it turns out we’ve just been paying for a big barn in a field with a couple of Bunsen burners in it.

And a giant stash of the world's most expense but sub-standard PPE that other countries keep making us take back off the "recycling" barges?

> but whilst I’m normally a massive advocate of private sector involvement, I think any future rapid vaccine prototyping and production capacity has to be maintained by the government.

Could be a boondoggle for the contract holders until/unless it's needed.  I'd be happy to see thriving industry and academic research in relevant areas and a rapid response plan to use those if or when the next pandemic lands.  But then, it turns out we had a lot of plans and scenario modelling that got thrown out of the window in preference to winging it when this pandemic landed.   The source of our woes is much more central to our national existence.

 wintertree 15 Oct 2021
In reply to tom_in_edinburgh:

>  just look at UK cases compared with the rest of Europe

We did, extensively, up thread.  There were some persistent misunderstandings.

At the risk of repeating an entire half of this thread, the "deaths" version of that plot you linked is astoundingly different.  

That tweet has the usual hallmarks of cherry picking to make a political point - one measure presented in isolation of all others and over a carefully picked, limited time window when we know that the trajectory of the disease is desynchronised between different nations.

Some scientists would make the case that it's highly encouraging that the UK is having less than one fifteenth of the people die per detected case of Covid than some of the countries on that plot.  

> The Tories are running an experiment on us.

Be honest, Tom.

Every country on that plot is in the same experiment, and each is testing a different strategy.  The strategy being tested within the UK is an outlier for those nations.  It's not the first time we've been an outlier, and sometimes we've been an outlier in a bad way (deaths in the first year) and sometimes we've been an outlier in a good way (roll out of vaccination).

Using the least important measure in terms of immediate health outcomes (cases vs hospitalisations or deaths) and ignoring the context of having the largest measured spread of low impact infections (e.g. by CFR), and using a cherry picked time window to do so, and ignoring much other context is just bullshit.  

Like a lot of your anti-Tory comments Tom, I think it detracts attention away from real issues where there's broad agreement that people are being failed by being exposed to elevated risk in the UK.  

Post edited at 14:58
 Offwidth 15 Oct 2021
In reply to tom_in_edinburgh:

Its blatantly obvious to me we are talking about something else here. Government intervention in markets, for emergency public health reasons, was huge: well over $10 billion in the US alone went to research vaccines, develop this work and kick start production. For Pfizer BioNTech they started with a half $billion from Germany, with billions in advance payment from various govenments, and as I see it their profits are pretty much guarenteed medium term based mainly on public initial investment. The priority should remain public health, with a worldwide focus, until this pandemic is over.

https://en.wikipedia.org/wiki/Operation_Warp_Speed

In reply to Offwidth:

> Its blatantly obvious to me we are talking about something else here. Government intervention in markets, for emergency public health reasons, was huge: well over $10 billion in the US alone went to research vaccines, develop this work and kick start production. For Pfizer BioNTech they started with a half $billion from Germany, with billions in advance payment from various govenments, and as I see it their profits are pretty much guarenteed medium term based mainly on public initial investment. The priority should remain public health, with a worldwide focus, until this pandemic is over.

They did all that, they delivered in spades with highly effective, high quality vaccines in large quantities and they did it very quickly.  Compared with other aspects of the response the vaccine guy's work was exemplary.

But they are businesses and management are going to react differently when they see an ongoing highly profitable $20 billion a year revenue stream for boosters and when they don't. 

In reply to wintertree:

> >  just look at UK cases compared with the rest of Europe

> At the risk of repeating an entire half of this thread, the "deaths" version of that plot you linked is astoundingly different.  

The situation is very simple:

a. the cautious approach is keep Covid rates low until you are sure.  There are more potential consequences of catching Covid than death with 28 days of a test.  The death metric completely ignores the most frequent negative outcomes such as long Covid.

b. it isn't doing an experiment to not catch a virus.  It's an experiment to let people catch it because you have a theory it might be better for them.  And actually the Tories aren't doing it because they think it is better for us if we catch it, they are doing it because it is in the short term financial interest of Tory donors and the idiots who voted for Brexit are p*ssed off with wearing masks.

c. the theory that we are safer if we catch it is just that: a theory.  It may well be true.  The next step is a properly set up experiment to see if it is true.  Not letting the disease run riot.  The situation is the same as in January, the theory that it was better to have a long gap between doses turned out to be true, but a competent government would have held infection rates down, tested the theory with a controlled experiment and then switched policy.

3
 wintertree 15 Oct 2021
In reply to tom_in_edinburgh:

> The situation is very simple:

Disagree.

> The situation is the same as in January, the theory that it was better to have a long gap between doses turned out to be true, but a competent government would have held infection rates down, tested the theory with a controlled experiment and then switched policy.

By which time tens of thousands of more people could likely have been dead.  As well as lives directly saved, against the then dominant variant it took a massive chunk out of transmission and in doing so doubtless saved many more lives.

They couldn't have "held" rates down as they weren't down, they were sky high.  Yes, things never should have been allowed to get that bad, and clear, demonstrable bad decision making in the form of ignoring clear, well presented scientific advice lies behind that.

Still, we were where we were and your take did not and does not recognise that.

It's very easy to delude oneself in to thinking something is simple if the alternatives aren't also thought through.  Then, one realises it's not simple.

Back in January you were making endless highly political attacks on the shortening of the dose.  Actual immunologists were quietly confident it seems, because what you call "just a theory" is rooted in a lot of sound science.

If nothing else, reflecting on that should give you pause for thought that the situation is more complex than the way you present it, and that possibly it is not always a case of a Tory bogeyman acting in their own direct interest.

> and actually the Tories aren't doing it because they think it is better for us if we catch it, they are doing it because it is in the short term financial interest of Tory donors and the idiots who voted for Brexit are p*ssed off with wearing masks.

Okay, that's that then.

Post edited at 16:13
 Offwidth 15 Oct 2021
In reply to tom_in_edinburgh:

You're inventing a scale of problem that simply doesn't exit based on a product who's R&D was largely funded by someone else and where that particular funding source for R&D won't dry up as long as we are still threatened by a pandemic.

As for Boris & co bashing (it's more him I see as the bigger problem in covid response than toryism) there are plenty of very serious concrete things we can blame them for in advance of cynical guesswork of hidden motives (justified though that cynicism might sometimes be).

Post edited at 16:19
 jimtitt 15 Oct 2021
In reply to Offwidth:

> Its blatantly obvious to me we are talking about something else here. Government intervention in markets, for emergency public health reasons, was huge: well over $10 billion in the US alone went to research vaccines, develop this work and kick start production. For Pfizer BioNTech they started with a half $billion from Germany, with billions in advance payment from various govenments, and as I see it their profits are pretty much guarenteed medium term based mainly on public initial investment. The priority should remain public health, with a worldwide focus, until this pandemic is over.

Hmm. Biontec actually started with a decade of privately funded research into a completely different field (cancer) which conveniently could be used to develop an effective vaccine against a problem which wasn't on the radar. The money was to pay for a specific vaccine to be developed and the tie-up with Pfizer to develop the production. That's still where the private investment is still going, the use of MRNA for other applications and as Covid fades that's where it will continue to go, Tom isn't as far of the mark as you think.

 wintertree 15 Oct 2021
In reply to Misha:

> Cases still going up today. I can’t judge the rate constant by eye but it’s not exponential as far as I can see, so that’s a start. However any increase on the current baseline is bad news for hospitalisations and occupancy

Still going up again today. Not much sign of the hoped for petering out (growth has in Scotland where there's been a similar wobble in the rate constants, but not south of the border).

The update to the demographic rate constants plot is very worrying - in exponential terms, the growth is fastest in adults over 65 - and that is starting to be true outside of the highly provisional leading edge on this plot (the last 7 days or so of data).  

There's a really interesting way of looking at the data - if you imagine shining a torch on it from the left to the right, the big growth spikes from schools in ages 5-15 and then 40-55 in month 9 look to be casting shadows to their right - as if there is less capacity for exponential growth in these ages that is resisting the urge to grow.  This hints at quite a lot, not least considering advancing the timescales on the booster program for over 50s...

In terms of higher rate growth in older adults, and looking at where hospital stats are, now is probably a good time for some clear, consistent messaging on the risks from the government and a return of mandatory masks at least in shops and public transport, as well as a strong advisory to more vulnerable older adults to avoid indoor socialising and dining as much as possible.

I'd be very interested in a comparison of daily case rates in inbound travellers and non travellers, but this is falling too soon in the data to be a result of the culling of the red list about a week ago.

Edit:  I was thinking a bit more about the "shadows".  One way of conceptualising the change in rate constant is that there's the effect of common factors which, over the last few months, have largely been policy and weather, and then there's stuff contained within specific demographics such as schools.  The new plot below is the English rate constant plot for cases (left), and the same data when a baseline estimate assumed to be less effected by things like schools - this is the average rate constant, per day, across all bands aged 55+.  Data in age 55+ is more or less structureless noise to my eye, suggesting there isn't much age dependant stuff there making it a not-awful estimate of the baseline.  I look at this and can interpret quite a lot in the features in younger ages, but it's all a bit whimsical perhaps so I'll leave other people to do their own Rorschach tests with it.  Still, no sign of university outbreaks....

Edit 2: I like this plot so much I made a larger one.  I'm not sure the baseline subtraction works so well earlier in the year - more vaccine related changes and more adoption of measures by older people I think.  Then total case rates were so low that the data drifts to noise within individual bands for a while.  One thing to jump out at me from this is the dramatic change in apparent household infection from the return to schools in the spring and the late summer.  

Post edited at 17:05

 Misha 15 Oct 2021
In reply to wintertree:

Yes, a complicated pattern. As you say, steady state seems unlikely to switch on over just a few weeks given the vaccination drive took months and in principle older people’s immunity would fade quicker. Lots of other factors at play - weather, schools, residual unvaccinated cohort who haven’t yet been infected. Really need case data by vaccination and infection status to make sense of it.

If it’s still rising to any significant extent in a week’s time, I’d be surprised and getting concerned. Hospitalisations are already rising, though still below levels seen in August and early September. 

 Misha 15 Oct 2021
In reply to tom_in_edinburgh:

I don’t think there’s any danger of Big Pharma stopping vaccine production. My point is it should be expanded significantly. That should be funded and directed by the relevant governments if need be. The legislative framework is already there in the US (wartime production act, something like that). 

In reply to wintertree:

Quite. Planning for “black-swan” type events is all but impossible. “Civilian” / well rounded societal capacity is key. 

However on that basis we were arguably one of the better prepared countries going in to the pandemic. I suppose you can argue that scientific capabilities have been degraded in recent years, but we’re still up there in terms of scientific ability/ quality. Despite this, it seems clear that the idea of herd immunity (without a vaccine) was pushed by the leading scientific minds in the early days of the pandemic.

60 years ago that would have probably been fine - censor the newspapers, roll out the propaganda and 600k deaths later we’re out of the woods, but today that’s all but impossible.

Maybe a more integrated approach is needed today? Should PR and media comms people also play a role on future SAGE committees?

Slightly off topic… but I used to work with a company who had the contract for supplying large scale morgue capacity for the MoD (think more capacity than you could ever imagine their being a need for). Of course as expected, like you or I don’t play the lottery expecting to win, they didn’t play another type of lottery expecting to loose…

 wintertree 15 Oct 2021
In reply to VSisjustascramble:

Accidental rant alert, it's been a while...

> However on that basis we were arguably one of the better prepared countries going in to the pandemic.

I agree.  Early on many would try and excuse away our reposes by drawing comparisons to other countries that did almost as badly, but in my view we should hold ourselves to the same standards as we hold our children and students etc - expect them to try their best within their abilities and the rest will follow; IMO as much as it's trendy to bash Britain in many ways, our scientific and medical capability remains world class and in some areas world leading.  Some of the other nations to fail badly were also very strong in these areas, and should be asking the same sort of questions, not using each other's failures to deflect criticism.

> I suppose you can argue that scientific capabilities have been degraded in recent years, but we’re still up there in terms of scientific ability/ quality.

I don't think the problem lies in our scientific or medical pillars, which are still strong despite the various forces eroding their foundations, but in their intersection with government.  IMO, science and government policy have been on a degrading pathway for my whole adult lifetime, stand out bad examples perhaps around the Blair government's case for war in Iraq and drugs policy when it comes to governments of every colour.

I also specifically think in this pandemic modelling has had too strong a sway over SAGE.  In a pandemic, the unknowns are massive and effectively unknowable until months of carnage have passed and so there is little role for modelling compared to a good, old fashioned strong public health response.  By the time we actually know enough for detailed modelling to be particularly useful, the time has passed where it's of much actual use.  There's a funny thing happens though when you present a technically very impressive model to people who aren't domain expects in modelling or the subject field - they believe it unquestionably because it's got some much clever stuff behind it (*).  It's very easy for group think to emerge.  I don't think my commentary on this has changed much since the first months of the pandemic.  To mis-quote Idris Elba from Hobbs and Shaw, "Modelling, Schmodelling".  Implementing modelling is a very powerful way to get highly numerically and scientifically literate people in to the field being modelled, the process of doing it is a great driver of interdisciplinary interaction and learning, and modelling is a great way to understand which parameters are more important than others - there are many ways like this where modelling is a powerful addition to the toolkit, but in none of them does it accurately predict the future.  I'd argue that as well as negative aspects associated with it being taken too factually by policy makers, the clear and obvious deficiencies of modelling against developing reality have been used to try and undermine "experts" in a far wider sphere than modelling.

I had high hopes for independent SAGE when it emerged as a less constrained counterweight, but all too often they seem to drift towards political points separate to their highly on-point and well derived public health points.  

IMO, the worlds of politics and science are far too far divided, there's little common ground, common language or shared understanding, and science can't cross the increasing gulf to politics without, well, not being science any more.  So, politics has to move or the mother of all bridges has to be built.  I think looking at the wider political developments in the last 15 years, improving the role of rational, evidence based decision making in politics is the way to narrow the gap, and is of benefit to decisions beyond those where science is a major cornerstone.

> Despite this, it seems clear that the idea of herd immunity (without a vaccine) was pushed by the leading scientific minds in the early days of the pandemic.

I wouldn't say "the", I would say "some", and I wouldn't say "leading" so much as "prominent" - distinctions that are clear within science but don't cross the boundary well in to politics perhaps.  I regret not having taken the opportunity presented me early in my career to go and be a scientific assistant to an MP for 6 months; I'm not sure I would have lasted but at least I'd have some actual, real world insight in to the other side.  Alternatively I'd have been out on my ear in a few days...

> Maybe a more integrated approach is needed today?

As above, I think the problem is an increasing drift of politics away from rational, evidence based decision making and that as science can't abandon those principles and remain a scientific force, politics has to swerve. 

> Should PR and media comms people also play a role on future SAGE committees?

No role for them in the committee action, but roles in helping scientists avoid being misrepresented and in communicating their findings onwards clearly, concisely and precisely. A marketing department of sorts.  But IMO a well functioning democratic system should not need that level of help to bridge the gap, because they should be applying the same inquisitive, evidence based thinking to everything, not just science.

(*) - well, not just modelling but any super-clever black box with impressive looking outputs.  People just trust them and suspend disbelief.  Sometimes used to con people but almost worse is when it leads to genuine, well meaning work being over-trusted and over-applied.  A bit too off-topic for UKC but I've been glued to Ars' coverage of Elizabeth Holmes' trial re: Theranos.

Post edited at 20:18
In reply to wintertree:

> By which time tens of thousands of more people could likely have been dead.  As well as lives directly saved, against the then dominant variant it took a massive chunk out of transmission and in doing so doubtless saved many more lives.

> They couldn't have "held" rates down as they weren't down, they were sky high.  Yes, things never should have been allowed to get that bad, and clear, demonstrable bad decision making in the form of ignoring clear, well presented scientific advice lies behind that.

We don't actually disagree here.  I am not arguing that they did the wrong thing in January after the sh*t was allowed to hit the fan.  I am arguing that the sh*t should not have been allowed to hit the fan in the first place by taking action much sooner.  If you look at the EU countries it is very clear it was totally possible to stop the sh*t hitting the fan and the result of keeping a lid on was much lower death rates over the course of the pandemic than in the UK.  

2
In reply to Misha:

> I don’t think there’s any danger of Big Pharma stopping vaccine production. My point is it should be expanded significantly. That should be funded and directed by the relevant governments if need be. The legislative framework is already there in the US (wartime production act, something like that). 

I don't disagree that vaccine production should be expanded.

My point is that it is naive to think that not giving boosters in the west is a positive thing for vaccine supply and development of new vaccines, it is socialist zero-sum thinking assuming there's a fixed quantity of something to be distributed fairly rather than that if more money goes in more vaccine will be made.   

The market for full-price boosters in rich countries will generate tens of billions of dollars of revenue at good profit for vaccine makers and that cash flow will mean more resource going into their vaccine programs and more vaccine being made.   

2
 Si dH 16 Oct 2021
In reply to tom_in_edinburgh:

There are other ways to ensure more money goes in to vaccine production than buying boosters. It would be straightforward to set up a system whereby the same money was spent on the same number of doses but they were then distributed to unvaccinated people through Covax, rather than to people who are already double vaccinated in developed countries and who have strong immune responses. The countries needing the vaccines could contribute what they could afford and the rest of the cost be made up by developed countries who are already well vaccinated. There are good reasons for them to do this, it just needs the political will. It's already happening to an extent, just not yet enough (or quickly enough.)

There are also other more innovative ways of using funding to encourage r&d. (I agree with you about the r and the d.)

Edit to add, if you are worried about encouraging r&d, you also have to guard against the risk that people like Pfizer, Moderna etc sit on their haunches and just cash in on the work they have already done. There isn't such a strong driver to develop a new vaccine if everyone is happy to buy existing products for the foreseeable.

Post edited at 08:49
In reply to Si dH:

Personally, I'm not interested in rolling the dice on getting long Covid and being off work for weeks or more.  If I'm not working I'm not getting paid.   My guess is even at the national level the economics of boosters will make a lot of sense.

In reply to Si dH:

> Edit to add, if you are worried about encouraging r&d, you also have to guard against the risk that people like Pfizer, Moderna etc sit on their haunches and just cash in on the work they have already done. There isn't such a strong driver to develop a new vaccine if everyone is happy to buy existing products for the foreseeable.

There's the normal capitalist driver of a lucrative market crowded with competitors and good money to be made from increasing market share.

2
 Si dH 16 Oct 2021
In reply to tom_in_edinburgh:

> There's the normal capitalist driver of a lucrative market crowded with competitors and good money to be made from increasing market share.

Not really. None of the western world wants anything other than Pfizer, Moderna, AZ or J&J, and most want nothing other than Pfizer or Moderna. The rest of the world is sewn up by China or Russia, or too poor to pay the high prices you are talking about anyway. And lastly, many of the countries that want Pfizer or Moderna have already committed to order more than they need. So really, I don't think there is much market left to play for. Anyway, off topic.

Post edited at 14:15
 wintertree 16 Oct 2021
In reply to Offwidth:

So, I went and did a quick comparison of CFRs in the end.

Quick conclusion - I reject pretty much your entire criticism of my quick analysis and my points, and I wish I'd gone and done the plots rather than arguing the case in words.   Would have been quicker, simpler and more definitive.

Plots and interpretation below.

I measure a case fatality rate calculated from detected cases and reported deaths as collated by Ourwolrdindata for various nations.

This is not, and can not be used to infer, the infection fatality ratetaken as the ratio of true deaths to true infections.  We reasonably expect most deaths to be detected, and much less than all infections, so it is almost certain that the IFR is less than the CFR.

The real case fatality rate would be determined from longitudinal medical records, to which I have not access.  So, the best I can reasonably do is to estimate a lag from case detection to death and use that.     

To wit, the cases are divided in to the deaths with 7-,  14-, 21- and 28- day lags to consider a range of possibilities for the lag.  Some will under-estimate and some will over-estimate compared to a proper longitudinal analysis, and the direction they are biassed in will depend on if deaths are in a rising or falling phase.  Careful squinting at turning points in the input data corresponding to crossing points in these plots can help to identify the least biassing lag.  I can reasonably assume the "true", longitudinal CFR falls within the range of these measurements.  I say this is reasonable because the shortest and longest lags fall either side of typical values reported in the literature.  (Although I do wonder about long-tail effects after a big collapsing wave; that doesn't apply with the 28-days measure in the UK but I haven't looked in to the cutoffs elsewhere; nevertheless I don't think it's a big factor now). 

The analysis is done with a 7-day box filter in the input time series and a 7-day box filter on the output CFR as well. 

  • You have several times raised issue with the use of a 7-day rolling average as if that is a biassing factor.  As I've said before it's basically required; a symmetric kernel is used for balance.  The second plot shows what happens if you don't do it - it seems many other nations have more extreme day-of-week effects than the UK.  It's basically impossible to analyse the data without it.  I've included a screenshot of OWiD's take on this analysis which also uses a 7-day filter...

Looking at these plots I entirely stand by my quick estimate of a 1.4% CFR for the leading edge of the Spanish data with the lag I gave.  Short term variation in the data absolutely was not biassing things towards this one value, it is part of a much longer term trend that extends well beyond the range of the box filters used.  It's almost as if I'd eyeball the plots to make sure I was happy doing the analysis before I did it and gave it...  Nah, that'd never happen... 

The final two plots show the bounding ranges from the different lags for each nation as a shaded region.  This is not a CI, but as I said we can reasonably expect a "true" CFR to fall somewhere within the bounds of the range of time lags I used.  

From this plot:

  • Is is clear that the CFR for the UK using any reasonable lag is lower than that for Germany, and the CFR for Germany lower than that for Spain.
  • It is clear that the UK has a stand-out low CFR
  • It is clear that the CFR for Spain has been rising for the last two months 

Interpreting this for meaning about the different countries is hard, as there are both demographic differences and differences in infection > case detection rates between nations, and they conflate.

  • My feeling is that the demographics of the recent school associated spread in the UK is pushing our CFR and IFR down but I haven't deep dived into international demographic data.
  • My feeling is that the only likely way Spain can get rising CFRs in the region of 1.5% is through detecting an ever smaller fraction of infections as cases, and that this high and rising CFR does not represent such a high or such a rising IFR.

The one interpretation that is very, very clear to me and that was my very clear original point is that this noddy analysis of CFRs between different nations, sprinkled with some reasonable assumptions, shows that it is entirely unreasonable and unfair to compare daily case numbers or per-capita case rates between different nations.

Gawking at this plot one thing that hasn't been discussed before is the ma-hoo-sive CFR in Germany a few months ago (~5%).  

  • This is why I added the rather ugly plot also showing daily cases - the only reasonable assumption seems to be that the infection > case detection rate plummeted through the floor for a while when case rates were very low.  Tempting to just lump that in the giant over-stuffed box called "Behavioural voodoo" but I've not been following the news enough to write off other factors.  
  • Looking at the cases and deaths per 1m data for the UK and German on OWiD's data explorer around July 8th 2021, death rates were similar in both nations, but cases were 50 times higher in the UK. I suspect this was almost entirely down to testing and not demographics back then.
  • I was so staggered by the disconnect (especially for Germany) that I went and checked Worldometer case numbers to make sure OWiD wasn't garbled.   
  • Kind of drives home my original point of the dangers of pointing at high cases in one county vs another in isolation of less hazardous and more relevant metrics.
  • I really don't understand what could have been going on in Germany; the OWiD page suggests they were performing ~3x as many tests per positive case, at that point you almost have to be going out of your way to test people who don't have Covid....  Bamboozling.

"Don't ask, don't tell" is no way to do public health.

Post edited at 18:01

 Offwidth 16 Oct 2021
In reply to wintertree:

I have to take my hat off.

However also on OWiD you get this graph (as distinct from their moving average CFR graph)

https://ourworldindata.org/grapher/covid-cfr-exemplars

With this warning note clearly on the main CFR graph (which covers my main point about avoiding misunderstanding):

"During an outbreak of a pandemic the CFR is a poor measure of the mortality risk of the disease."

 Misha 16 Oct 2021
In reply to tom_in_edinburgh:

You are assuming that lower income countries are buying the same vaccines for a lower price. I’m not sure that’s actually the case, except perhaps with AZ. 

 wintertree 16 Oct 2021
In reply to Offwidth:

> With this warning note clearly on the main CFR graph (which covers my main point about avoiding misunderstanding):

> "During an outbreak of a pandemic the CFR is a poor measure of the mortality risk of the disease."

Yes.

That rider has an equivalence with the entire point of my first CFR post.

CFR is a poor measure of mortality rates (a) because cases are a poor measure of infections, and (b) because of the need to account for demographics.

That was why I used the CFR as a way of illustrating that top level cases don’t account for variations in demographics or variations in infection detection rates.  I was literally making the point that it is not fair or bias free to compare cases or CFRs between different places.

I still think perhaps you’ve taken entirely the wrong point from my post and jumped in to correct a misrepresentation that was never there.  I defined it clearly, I used it specifically to illustrate the issues around cases (and by obvious extension CFRs) when compared between nations, and I never claimed it was a measure of actual mortality risk.

CFR is what links cases and fatalities, and as we can reasonably assume fatalities to be accurate for the nations discussed, CFR is the most appropriate tool to illustrate how comparing cases internationally can be highly misleading.

> However also on OWiD you get this graph (as distinct from their moving average CFR graph)

I suspect that graph is basically total bollocks.  The methodology isn’t given but it appears going back to the JH source to be deaths/cases for the total pandemic.  As almost nowhere was detecting most infections for the first wave, and as mortality has changed dramatically with variants, repurposed and now new therapeutics, improved clinical care and vaccination, whole-duration CFR is a number of basically no meaning at all, and is regardless of total irrelevance to the point I was making about the present time.  Perhaps I’m missing something critical, please do illuminate me.

Post edited at 20:15
 Offwidth 16 Oct 2021
In reply to wintertree:

I think you misunderstood me. My original point was the CFR for Spain for this wave is nothing like 1.4%. I've just calculated it for Spain from Worldometer (easier for me) by dividing total cases from the begining of July until 21 days ago and dividing that into total deaths from July 22nd until now and the CFR for the August (onwards) wave comes out as 0.5%, might be worth checking but it's what I expected.

You never did anything wrong with your calculations and what you have done since has pulled out some really interesting points. I love the error band style graphs.

In reply to Misha:

> You are assuming that lower income countries are buying the same vaccines for a lower price. I’m not sure that’s actually the case, except perhaps with AZ. 

I'm just assuming that if Pfizer et al can sell vaccine at a good profit for boosters to rich countries then they'll make more vaccine and take the extra profit.  

2
 Si dH 16 Oct 2021
In reply to wintertree:

Maybe the Germans were sending their test tubes to the Wolverhampton lab over the summer?

 Offwidth 17 Oct 2021

In reply

I finally re-found one of the old Heneghan pieces of misinformation showing how rolling CFR calculations have been misused:

https://www.cebm.net/covid-19/european-case-fatality-rates-beyond-lockdown-and-the-uks-outlier-status/

OWiD give a good outline of the various issues with the different mortality measures but unfortunately don't have anything on their rolling CFR graphs, which need the most care of all.

https://ourworldindata.org/covid-mortality-risk

Post edited at 06:50
1
 Offwidth 17 Oct 2021
 wintertree 17 Oct 2021
In reply to Offwidth:

Anything can be misused if it’s presented with a deliberately wrong or cherry picked context.

You appear to still be hell bent presenting a rolling CFR as a dangerous concept.

It is what it is.  I have presented it for what it is and have specifically used it to hi-light that one of the measures it derives from (and hence it itself) is in no way a rational basis for comparison between nations.

The CEBM people have misused just about every measure and method, but you don’t use their garbage to argue against other things they have misused.

Despite it clear presentation of what I was doing, it seems you confused this with both the whole pandemic CFR (a garbage measure if ever there was one - OWiD should not be scraping that data daily to turn in to a time series and plot IMO) and the IFR and are just going to keep digging.

 Offwidth 17 Oct 2021
In reply to wintertree:

I am interested in urging suitable caution where things can be misused or lead to misinformation; the Heneghan link just shows why CFR moving averages hit a nerve with me (I knew there was something I'd spotted in the past but couldn't pin it down until this am). I've said several times now your calculations are fine, way more obviously so now with the masses of extra information provided and that I like the new plot, which shows something odd is going on with a significant proportion of 'missing cases' in Germany in June).

I've consistently called out the CEBM misinformation during covid.

Mortality rates are important but tricky beasts to calculate. Cross pandemic and cross wave CFRs give useful upper bounds for IFRs.

I've also shown my calculation that the CFR in Spain for the recent wave is 0.5% (and the same method gives 0.3% for the UK and 0.7% for Germany). IFRs will be lower still (probably similar).

Post edited at 08:28

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