UKH

Post 1 - International Plots 

Everything about this week’s update feels a little futile, as it’s likely Omicron is gong to swerve everyone of in new directions very soon.  So, this week's updates are in a bit of a limbo-land; one the Leveller's sang about many decades ago [1]

A lot of Europe is under stricter control measures than the UK, mostly driven it seems by their poorer immunological situation.

• Those stricter control measures should slow the rise to prominence of Omicron for them, whilst their poorer immunological situations will make the consequences of that rise worse. 
• No idea where is less badly placed to face Omicron down, not interested in political axe grinding over it either.

For the plots below, France and South Africa both had an atypical zero-cases report for the most recent day; I've curtailed their data back a day but treat their leading edge as a bit more provisional.  I put in the "sanity checking" plot I use to look at sampling artefacts and potentially bias on the trendline from the OurWorldInData source.  This is not suitable for comparing absolute numbers between nations, just looking at trends and glitchy data. 

On the phase-space plot, much like last week, a lot of countries are curving round towards decay in cases, due to the lockdowns forced on them by insufficient immunity to moderate delta during winter.  Perhaps counter-intuitively this means omicron is going to affect their future less than ours - it can't escape from immunity that isn't there.  Another way of looking at it is that omicron might make the UK's situation more like that of Europe, nullifying some (but not all) of the advantage of us having more immunity where it matters.  

The effect of lockdowns are showing on the actual and extrapolated/locked-in deaths on the international plot as the extrapolated growth in both measures reduces (red and purple arrows get shorter) or turn to decay in a few instances.

Some observations - likely to be made less relevant shortly by Omicron

• Hungary seems to have maxed out without control measures; the first European nation to exit the pandemic phase the brutal way?
• Germany seems pretty keen on getting as many people through hospital as possible given their rise to the top; deaths haven't stoped rising yet but the growth is slowing.  Looks like they're going to see about 4x the maximum death rate the UK did during the delta area.
• France is still growing a lot; won't be long before their peak death rate exceeds that of Germany unless they change things.
• The lockdown in Austria seems particularly effective.  
• No sign of a nordic advantage for Norway or Finals

Almost every European nation is now showing an actual or extrapolated death rate exceeding the peak of the UK in the post-delta era. 

• As I’ve said many times before, the extrapolation is a way of contextualising the present, folding in case rates, their growth/decay behaviour and case fatality rates.  It’s not a forecast.  Particularly relevant today as perhaps Omicron is going to tear everything up and re-write the rules.

South Africa - as with last week it clips the top left corner of the main plot, needing it’s own zoomed out version…

• Take the extrapolated deaths for South Africa with a pinch of salt, as Omicron is likely to have a much lower CFR than the recent one being extrapolated from.  This is because it's probably reinfecting people who weren’t catching Covid on exposure pre-omicron, adding a lot of mild infections to the pool, which will lower the CFR even if the number of fatal cases stays level or increases.  A key point I return to in another post.  Spoiler alert: This probably isn’t good news.
• The doubling time appears to be slackening off, but then again Our World in Data is now suggesting that their are just 3.9 tests per detected case, meaning a positivity of 26% which strongly suggests testing is no longer reliable or able to accurately track the spread of infection.
• OWiD’s weekly hospital admissions data for SA shows an increase of ~2.7x over the last week, which corresponds to a doubling time of ~5 days.  I don’t think the recent rise in cases is yet fully embodied in this data.  Whilst more lagged than cases, it may be a less unreliable measure.

The big rise in the USA hasn't been sustained, but the more I look at their data the more messed up it seems; given how bizarrely political it's all getting over there it's hard to know what to make of it [2].

Link to previous thread:  https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_55-...

[1]  youtube.com/watch?v=fob8Dl3eMnQ&

[2] https://arstechnica.com/science/2021/12/missouri-tells-health-depts-to-stop...

Post 2 - Four Nations Plots

A note on UK dashboard data, and Omicron and reinfections.

• ONS data has shown re-infections to be a pretty small effect pre-Omicron, but with various different reasons to think it’s escaping from immunity-against-infection, re-infections could reasonably be expected to rise significantly.
• It seems re-infections are fully omitted from the UK government dashboard - who are now working on this as a priority.  There’s a rider on one of the datasets in the “England” page but this is otherwise not covered in the documentation; it’s discussed in a couple of tweet’s linked to from the currently running Omicron thread [1]
• About 16% of the UK's population count as an infection so will not as I understand it currently be reported on by the dashboard if they get re-infected by Omicron.  How consistent individual exposer risk factors are could significantly change how much this biasses the dashboard cases data down.

Same old, same old for all four nations' top level cases plots.  Holding on at around the same level, with demographic changes going on under the hood going off data for England and Scotland.

It'll be interesting to see what happens next; a lot of precautionary behaviour seems to be happening in advance of increased restrictions, inspired by the media coverage and unusually precautions government messaging over Omicron.  Perhaps this will send cases in to decay for a while before Omicron breaks through and drives growth; I wouldn't bet on it...

Plot 9 is interesting - the rate constants were really hammered down close to decay in the last growth period and cold spell; looking at the demographic data and the recent trends I think this was probably it for delta - barely capable of growing in the worst of the winter weather and finally at the point we could consider ourselves truly out of the pandemic phase.  Hopefully that leaves us well places for the acceleration that Omicron is likely to bring.

[1] https://www.ukhillwalking.com/forums/off_belay/omicron_overtakes_delta_in_scot...?

Post 3 - Thoughts on Omicron Severity

Long rambling post alert.  I kept going to do the washing up and retreating to the keyboard.   More words came out than intended.  

There’s a lot been said in the press and elsewhere about the possibility of Omicron being a less serious variant.   We really won't know until another month or more has come to pass - it takes time for lags to play out, for data to be gathered and professionally analysed, and for results to make it through to publicly released SAGE minutes etc.  In the mean time, my best understanding - I'll be delighted if it's blown out of the water by evidence the new variant is intrinsically less lethal. 

If it was genuinely less intrinsically lethal than delta - and sufficiently so to balance its faster spread - it could be a Hail Mary at ending all this.  Unless evidence emerges of this (I've seen none so far, and no properly qualified and referenced expert opinion minded that way) it's a nice fairy tale.  Fairy tales can come true, but you'd never bet your life on that happening.

The first issue is that what’s happening in South Africa does not translate well to us - they have a much smaller fraction of people aged over 70 than us, and about 40% of our hospitalisations come from that age range they almost don't have.  Going of excess deaths they have also lost a lot of people vulnerable to hospitalisations; about 0.5% of their (demographically much less vulnerable) population.  As well as significantly shrinking their pool of most vulnerable people, there is likely a lot of infection granted immunity population wide that is moderating the severity of Omicron.  As covered in the first post, hospital admissions are doubling rapidly in SA, information that wasn't out there when the first pronouncements of lower severity emerged...

The second issue is around what’s different about Omicron.

• It’s likely causing a lot of very mild Covid because it’s infecting a whole bunch of people who had so much immunity that they didn’t catch Delta at all when exposed to it.   
  • All that immunity means when they get Omicron it's mild.
  • So, for those people, exposure to Omicron is worse than exposure toDdelta.  That doesn’t bode well for people who were going to become very poorly on exposure to Delta.
• At the top level, if you take some cases that would be serious under either Delta or Omicron, and add a bunch more that would only exist under Omicron, then clearly the severity averaged over Omicron cases is lower than for Delta, yet there is more total illness because Omicron has infected more people (however mildly the additional people are infected)

I’ve made a cartoon plot that gives my thoughts here; I hope it’s clear - if not, please ask.  It’s a visualisation of what would happen if tomorrow everyone was exposed to delta  (left side) or to a variant that escapes antibody protection but not T-cell protection (right).  It represents - in a fuzzy, cartoon, non-quantified, over-simplified way the outcomes we'd see if everyone was exposed to delta (left) or a variant that evades immunity-against-infection (right) in one fell swoop.

It builds open some immunology simplified to the point I can understand it (so grossly over-simplified...).

Stating at the bottom of the two plots where consequences are mild…

• Antibodies float around in our body in the blood and spaces outside of our cells (Sort of like Jack Putter in interspace), where they sitck to whole, large parts of invading pathogens, tagging them for distraction and for some parts of Covid “neutralising” them - physically blocking them up so they can’t connect to a human cell and infect it.
• Having lots of the right kind of antibodies means someone who is exposed to Delta does not get an infection because the virus gets stuck to antibodies, and can’t bind to their cells to start the infection process.
• Only a small amount of the genetic code for Omicron has changed from Delta, but the way protein chains made from the genetic code bend in to functional, 3d shapes mean those small changes make bigger changes to the physical shape (and other properties) of the spike protein, so that that neutralising antibodies from current vaccines and from Alpha and Delta infections and current vaccines seems to be much worse at neutralising it, because they physically don’t fit it any more. 
  • My bad analogy is how a key and the barrel of a 12-pin tumber lock fit together when their shapes match, but how changing just 1 of the 12 pins means a key won’t engage at all.
• So, with Omicron, neutralising antibodies from previous variants and vaccines work much less well, and far fewer people escape infection upon exposure,
  • We get a bunch of people with asymptomatic and mildly symptomatic infection upon exposure to Omicron who wouldn’t have been infected by Delta. 
  • This is why there’s likely going to be lots of non-serious Omicron about. 
  • This in itself isn’t a problem - indeed, it's part of the way humans and this kind of virus seem to peaceably coexist after the initial pandemic phase.

Now, we get to people whose antibody response isn’t enough to send the virus particles from a Delta infection packing.

• Antibodies may have neutralised some virus reducing the scale of their initial infection and giving the body more time to respond to it, but now the virus is inside cells in large numbers and having the cells build new copies of the virus.
• This process buggers up the cells, damaging parts of our bodies, and for people with no antibody response at all (never exposed to Covid or vaccination), this goes on unchecked until the point the immune system kicks in to overdrive and turns on the host’s body - that “immune dysreguation” being one of the lethality mechanisms of Covid.
• The point the virus is being copied in large numbers is the regime of our T-cells.  These patrol the body and look at what our cells are making, with small fragments of the stuff being built inside cells being presented on their surface for inspection by T-cells.
  •  If a T-cell sees stuff it recognises as foreign presented by a cell, it decides the cell has been subverted bty an invader and goes all Judge Dredd on the subverted host cell, leaving the remains for a clean up crew.  This is part of what ends a viral infection.
• For people who’ve got no prior immunity, it’s the severe tissue damage caused by the virus that belatedly wakes up the T-cells and tells them to learn about the invaders.  For people with prior immunity, T-cells lie in wait, primed to respond to any new viral replication.
• The T-cell’s learning process is based on pattern matching against very small fragments of the virus’ genetic material.  This is a key difference to antibodies, as for T-cells  only a few of these fragments are changed by the mutations - most remain the same.  Early data suggests that many of the fragments the vaccines train against are unchanged by Omicron, which could be anticipated by looking at the number and locations of mutations, the length of the genetic code and the length of the templates used.
  • My naff analogy is imaging if you took the lock I mentioned and smashed it in to lots of small bits; most of those would be the same before and after the length of one pin was changed (corresponding to the omicron mutations).  So, if you try and identify the lock based matching a bunch of the fragments, the changed pin length doesn’t matter.

So, that’s the basis for my cartoon diagram - antibodies (which are broken by Omicron) prevent infection towards the bottom, and T-cells moderate severe infection towards the top.

The big effect of Omicron escaping neutralising antibodies is that there’s a lot more infection in the least susceptible people, where their immunity was so good it kept Delta out entirely.  However their strong immunity means there’s going to be barely any hospitalisation or death in these people now catching Omicron (I’ve assumed 0 more which can’t be pessimistic - so it must be optimistic to some degree..).

Most people aren’t very susceptible to severe illness in the first place, and of those that are many of them have T-cell immunity to moderate the health consequences, and this isn’t broken by Omicron.  This is why the faction of people being hospitalised, going to intensive care (ITU) and dying doesn’t change in this over-simplistic model. The mechanisms that deal with severe infection aren't changed much by Omicron, and people who had so much immunity they couldn't catch Delta are generally going to have plenty to keep them out of hospital even if Omicron gets in to them.

(I wouldn’t’ be surprised if Omicron turns out to be a bit more intrinsically lethal; much of its mutation is optimising a part of the spike protein called the RBD, and previous variations optimising this have turned out to be more lethal)

So, if total hospitalisations, ITU admissions and deaths don’t change, and there’s a bunch of super-mild cold-like Covid about, what’s the problem?

Over the last few months, these measures have been running about level in the UK, and hospitals can cope with that.  I’ve been looking to Europe more in recent weeks to illustrate how the stand-out high levels of immunity in the UK where it’s needed have allowed us to have far fewer restrictions than Europe - much of which is now resorting to lockdowns.   Omicron is likely to press a big reset button on part of that immunity (immunity against transmitting and catching the virus) that will see cases spreading rapidly

• For those with things in their favour (some mix of age, health factors, past vaccination and infection inducing immunity) this should be no big deal.
• But the very high levels of infection mean the hospitalisations, ITU admissions and deaths - that were coming anyway - are going to come a lot faster. Because those people are exposed to the much higher prevalence of Omicron in those who are catching it in lieu of not catching Delta. 
  • Which healthcare just can’t take.

In terms of the deaths, we could perhaps spit them crudely in to two cohorts:

• It seems like most of the people going in to ITU (and so  those dying there) are now unvaccinated individuals.  Given the ONS antibody surveys, past modelling papers and the recent LSHTM modelling paper comparing the UK immune levels to Europe, this cohort can’t be that large; but with the uncertainty in population numbers leading to big uncertainties in the size of this cohort, it’s hard to know how bit it is.  One things’s for certain, it’s smaller by the day - by hook or by crook.
• There’s a set of deaths that happen in hospital but not in ITU; this is mostly people over 80 or so where ITU admission does not help them; many of these will be people who are fully vaccinated but who are still vulnerable to Covid.  In part, this is because vaccination in old age is not the same as a lifetime of being periodically re-infected by what would then have been a mild cold, and in part because vulnerability to infection and illness goes hand in hand with old age.  Shielding trough periods of high prevalence will help here, and as the years go by, younger people who were immunogloically exposed earlier in life will become older people and will be more robust than people who got their first exposure to the virus or vaccine in the last 18 months.  The improving therapeutics will help here too; we wait to see how the various MABs hold up against Omicron; that a 3rd dose produces sufficient immune response is a promising sign that more of the existing antibodies is a useful tihing.

So, that’s my best understanding - for a lot of people Omicron will be a lot less lethal than their last bout of infection, or a hypothetical infection they didn’t get before they were vaccinated.  For the most susceptible pools of people, lethality is currently unknown and I think it reasonable to expect it to be in the same ballpark as Alpha and Delta.

So, the main effect of Omicron is to accelerate the process whereby these people go in to, and come out of hospital.  We’ve already seen winter accelerate that process across Europe and the answers to this are well known now - reduce close contact between people by messaging and control measures that may or may not fall short of lockdown.  Help the most vulnerable to reduce their exposure risk as much as practicable.  Get people to engage with vaccination.

Longsufferingropeholder posted this Twitter link a few hours ago to a thread in The Pub which is another take on this - https://mobile.twitter.com/nataliexdean/status/1468988174693289994

More concise!  Often takes a lot more time to be more concise and precise, and I've got washing up to do.  That's my excuse and I'm sticking to it.

Post 4 - England 1

Top level cases look to be falling by my trendline and by week-on-week measures (next post).

All other measures are turning to rise.  No obvious sign of Omicron bursting through at the top level yet (I.e. cases going up, lots).

I’ve said for a couple of weeks I thought we were going to hit rising hospitalisations as the decay in ages 65+ tailed off (the gain from the boosters having been realised) and with cases in ages 15-64 rising quite a lot.   The next post looks at this, it’s presumably why the downstream measures are rising - cases have been rising for a long time without them rising, and that's not a process that could carryon indefinitely, there's only so much demographic rearrangement of cases that can go on.

Post 5 - England 2

PCR cases are showing a turn to decay with the most recent 2 days showing actual decay. 

• The curve looks really ugly and jagged; in part I think this is down to the biassing effects of disruption from Storm Arwen, as shown by the purple annotation.

I’ve added a plot showing cases in three demographic bands; this shows how much cases have risen in ages 15-65 recently.   This is where vaccination starts to fall below very high uptake, and to date about 40% of hospital admissions have come from people aged under 65.  3rd doses are going in to people aged 40 - 65 pretty rapidly now.

I’ve added a scribbled-on version of the demographic rate constant plot D1.c. 

• Some may find this level of scrabbling in the data rather fanciful!  
• This shows the general structure of rising and falling rate constants from the weather effects, with various rising and falling events in schools and as reflected in parental ages annotated, and where the 3rd doses have kicked in.
• The way I see the 3rd dose is that they dramatically lower the number of people getting infected, but don't send cases in to endless decay (there will always be some level in an endemic situation, and we are in winter).  So, the blue decay from them in the heatmap can't last forever, eventually normal control over rate constants is resumed - seasonality, variants, short term weather, big events etc.    This forms a descending diagonal because of the age-based ordering of when people became eligible for a 3rd dose under the 6-month rule.  With the omicron acceleration of the rollout I don't expect the diagonal to continue.
• Notably missing from this plot have been undergraduate age outbreaks with the start of the autumn term, rather suggesting very high levels of immunity there (given the exceptional 3-day doubling times seen at some universities pre-vaccination...).   Now, however, we see that the most intense recent growth is back around these ages, encircled "O?" on the plot.  Could be the first hints of Omicron in the data, or perhaps it’s the spiring of Christmas flowing through young adults…

Plot 18 builds on trends from the last couple of weeks with London having more consistent growth in cases, leading growth in hospitalisations and more growth in deaths when other regions mostly had decay.  It’s starting to feel pretty significantly different to other areas now; it would be interesting to step back and look at cases/100k for each of the regions and see how big the disparity is by that measure.  The map of cases/100k on the dashboard was not illuminating.

Post 6 - Scotland 1

Scotland continues to show cases holding roughly level and all other measures falling which has been the trend for 5 weeks or so.  I haven’t had a chance to run off the demographic plots for Scotland, but a glance at “Weekly Case Rate by Age Group” from Travelling Tabby [1] suggests this is an ongoing demographic shift to younger ages from 3rd doses hammering down infection in the 65+ group.  Younger adults are also seeing a turn to rise as with England; hard to be so clear though due to the boneheaded demographic bins used for the Scottish data.

Interesting divergence from England in terms of hospital admissions and deaths; I can't pull the devil out of the demographic detail given the coarse age bins in the Scottish data.

[1] https://www.travellingtabby.com/scotland-coronavirus-tracker/

Post 7 - Wrap Up

Not much sign of Omicron in the data I've plotted for the UK or much of Europe, but the documents being made public that are going in to SAGE, the early modelling outputs, the early serology studies and so on all point in one direction.

I hope it represents nothing worse than an acceleration of the inevitable, requiring more control measures for a period to preserve healthcare by resisting that acceleration.

I know the news has been coming as a blow to the hopes of a lot of people recently.  The increased restrictions are a rain of blows to a lot of people in a lot of ways.  

My positive take on this - don't give in to despair over this - I hope this is just an accelerating force on our journey to the inevitable.  Left unchecked, this force would overwhelm healthcare, so we have to slam some brakes on to resist it and maintain a sustainable pace forwards out of this.

In this sense, it does not represent a set-back to our way out of this, but it does mean that we're going to have to endure more restrictions as we continue to make progress.

Hopefully.

Something that's come up a few times on various threads is that some people who enjoy following these threads don't follow one or two of the plots.  If that's the case, please do ask; they've all been explained in the midsts of time but the explanations aren't well referenced each week.  Please do ask - and if I've not explained it well in the past for you I won't be offended if you ask for "anyone other than wintertree" to explain them.  Several people regularly posting on here can I expect give excellent descriptions in very different ways to me.

Many thanks.

Europe: https://www.ecdc.europa.eu/en/news-events/epidemiological-update-omicron-va...

Sure it’s not showing itself? 

Oh, it’s cropping up everywhere but there’s not much sign of it in the data I’ve plotted was what I mean - all top level stuff for Europe and pretty high level stuff for the UK.  

Going to be a while before it dominates top level cases for some places.  

Thanks. Sort of a calm before the storm situation (not really a calm but relatively speaking it will be). 

I suspect London’s rise is due to relatively low vaccination rates and most people using public transport to get around.

Agree with this.

I think you should cut your case data a day earlier again, it gives a slightly false impression of decay imo, but otherwise good update, thanks as usual

Re: your question on London case rates per 100k, see below. These are regional average rates over the last 7 days. London is in the middle now. It was significantly below the rest for several months and has now caught up. I think this is not unrelated to the behaviour of rate constants in younger adults: there may be a bit of cause and effect in both directions. There is also more Omicron there than everywhere else.

(New variant technical report is out by the way, a good collation of existing information but nothing ground-breakingly new.)

I wonder if I'll someday forgive myself for posting all these Twitter links, but here's another apposite one: 

https://mobile.twitter.com/UncleJo46902375/status/1469560014717304839

Only other point I have is that testing rates are anything but down in South Africa. Doesn't look like saturated testing capacity.

Look at it like you're the brave one who goes out for us into the character-limited wilderness to hunt for food, weeding out the poisonous plants. Like the Ray Mears of social media.

Almost spot on analogy. But instead of a lonely wilderness, imagine a crowd of bear gryllss drinking their own piss and bathing in animal crap.

Yes, I'm begrudgingly coming round to pairing back the plots 6-8 by another day.  Will do for next week onwards.

If some growth is happening later (now) in London, that's a powerful way to speed up the rise to prominence of Omicron.  Almost as good as a Steps concert...

Edit: since I posted this a BBC story is out - one third of London cases are now the new variant - https://www.bbc.co.uk/news/uk-59627188

In reply to Longsufferingropeholder:

Thanks for the deep delve in to Twitter, nice to just get the gems...

Tests are rising in SA [1] but cases are rising faster, so the tests-per-case is dropping [2].  Positivity is 26% which is well above the WHO recommendation of below 5% (IIRC), and it's rising.  Massive red flag on cases data IMO.

Also, I put the US in to these plots.  Some bonkers stuff going on over there with testing.  Hear no evil, see no evil?

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

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

It seems to me that had Omicron not come along, then we'd be starting to think that (in the UK at least) we'd just about got to the endemic phase with Delta. Omicron has of course blasted that wide apart.

But, it has shown a way to get to the endemic phase, even though the disruption, illness and death in that endemic phase looked likely to be more than we'd like.

It also shows what fouls up getting to (or remaining in) the endemic phase - variants.

So to get to the endemic phase we need a long enough period of time without new "superior" variants. But it seems to me that whenever such a variant does come along, it will take us out of the endemic phase and back into pandemic (basically a new pandemic).

Is this the Brave New World we can expect? (or were we already there with ~10 year intervals)

And if future pandemics are inevitable, how do we increase the time between pandemics?

Very interesting reading as ever. Long overdue question for you Wintertree, is the ‘rate constant’ the same thing as the R number?

Thanks

"Get Christmas Done"...?

I'm counting down to Christmas cancellation...

Related but different concepts.

R number:

• This is an epidemiological concept
• The "R number" or "Reproduction number" is the average number of people 1 infected person will go on to infect.
  •  In itself that doesn't tell us how fast infection levels will grow or decay, because it doesn't tell us over what time period that 1 person will go on to infect R more people.   (If they infect two people within an hour of being infected the virus will spread faster than if they infect two people a year after being infected)
  • If R is between 0 and 1, infection is decaying.
  • If R is more than 1, infection is spreading.   
• Knowing R is really useful to determining the appropriate level of control measures, because if R=3 (say), you have to reduce people's transmissive close contacts by a factor of over 3 to get R less than 1 and send infections in to decay.  
• Actually determining R is hard because so many things factor in to it.
• As a concept, R only applies to true infection, it can be related to detected cases but it's hard to relate to downstream measures such as hospitalisation or death

Rate constant:

• This is a generic mathematical concept that can be applied to any time series data, and that has particularly handy relevance to disease models, even after the exponential growth (early pandemic) phase has ended.
• It's the constant r in the exponential equation describing the growth of some variable y with time t. 
  • y = e^(r * t)
  • A positive value of r corresponds to growth and a value of R>1.
  • A negative value of r corresponds to decay and a value of R<1.
• The rate constant tells us about the fractional change in cases from one day to the next, in a way that is normalised so as not to depend on the absolute number of cases.  
  • An alternative measure would be the change in cases as a fraction of the absolute number of cases, but the rate constant is a better fit to the exponential mechanic of the spread mechanism,
• The rate constant can be directly translated in to a doubling time (how long it takes the measure to double) or a halving time (how long it takes the measure to halve) with a reciprocal axis - as on a bunch of my plots.
  • The end stage of a simple pandemic is similar to an exponential decay; way more complicate with vaccination and variants but the rate constant applies just as well to decay as to growth.
• The rate constant can be applied to all measures (cases, hospitalisations, deaths)
  • If there was a fixed conversion rate from each stage to the next with a fixed lag, we would see the same rate constants for each measure, just delayed by the lag.  
  • This I find particularly useful for interpretation on plot 9 etc - even with conversion rates changing due to shifting demographics etc, the staging in time of crossing over between growth and decay is reasonably consistent.
• The rate constant is not so useful for informing the amount of reduction in social contact needed, compared to R.  
• The R number can be estimated from the rate constant if you also know parameters like how long the infectious process takes from one person to their downstream contacts; uncertainty on that measure means estimates of R made from cess data tend to have big error bars.
  • Those big error bars can obscure perfectly real and well measured changes in the spread, because the error comes from a relatively static parameter (the generation time) not the dynamic one (changes in cases) 

It's a case of horses for courses really.  I find the rate constant works well as it measures directly from cases, hospitalisations and deaths, and so it can to a limited degree be run forwards to understand what they're going to do in the near future - especially with the weather link to the rate constant holding up pretty well.

Even after the pandemic phase, the relationship between R and r remains intact, and the concept of R is very much still behind the mechanic of disease spread in an endemic phase, which is one of the reasons the rate consent is still useful.  As the short term weather effects, seasonality across Europe and historic data on flu seasonality show, cases are not constant in an endemic phase but bunch up in winter, due to seasonal fluctuations in R and hence r. 

The Royal Society have a document that covers R vs r in some detail:

https://royalsociety.org/-/media/policy/projects/set-c/set-covid-19-R-estim...

In Germany they quote precise values for R by empirically defining R=Mn/Mn-4 where M is some measure or measures 4 days apart.

Choice of 4 day timescale just needs to be roughly right. 

It means they can quote small changes in R and local variations of R to usefully inform the public. I think the German method is not necessarily more accurate but is much more informative, responsive and useful compared to UK values such as 1.0+-0.2. 

https://www.medrxiv.org/content/10.1101/2021.03.29.21254581v1

I suppose it's effectively a rate constant with units of 96 hours rather than 24 hours on your rate constant plots.

Now that's just confusing!  

Sounds like they fixed the timescale of infectiousness then it no longer accurately relates to the epidemiological R number but gives the same scale-free representation of change in the spread behaviour not clouded by the errorbars applied to the UK estimates of R.  So it's an R-like number for people who are interested in the behaviour of cases and downstream measures, not for people who are interested in scoping control measures.

It's more like an R value with a forcibly fixed generation time; this is closely linked to the rate constant r.

If c[x] is cases on day x, and ln is the natural logarithm, then:

• Rᵢ = c[x+4]/c[x]
• r = ln (c[x+4]/c[x]) / 4
• r = ln (Rᵢ) / 4

The big change between R and their Rᵢ on the one hand and the rate constant r on the other is  the asymmetry in the former (0 to 1 is decay, more than 1 is growth) and the symmetry in the later (r<0 is decay, r>1 is growth).

This shows in the asymptotes, ever faster spread sees R and Rᵢ tend to infinity, where-as ever faster decay sees them tend to 0.  For r, it tends to ± infinity in a symmetric way with ever faster spread or decay. 

It's that symmetry that allows for really nice dual y-axes with a second halving and doubling time axis to aid in interpretation, and it makes for more intuitive and representative phase space plots (aka Lissajou figures) IMO, and it's a more natural basis for the mechanic which really shows in the weather passband analysis - something that an experienced eye can spot in a raw plot of temperature and r vs time, but that's a lot less clear in R vs time, and something that is trivially revealed with a linear regression in the passband when using r but that would need more involved maths with R or Rᵢ.  I'd probably not have spotted it with plots of R; I'm a great believer in putting data in visual form that gives people's intuition the best chance.   Again, different people are different and horses for courses etc.

(In the week-on-week plots I measure r over a 7-day period with r = ln (c[x+7]/c[x]) / 7; this works so well because the multiplicative scaling effect that day-of-week sampling bias in case numbers has is very consistent over the timescale of weeks; for that reason I'd be wary of anything using 4 days, unless it also does a 7-day moving average before that to null the day-of-week effects, at which point the effective window used for the measurement is 7+4 = 11 days, meaning it gives some value representative of the average over the last 11 days; less current than a week-on-week or 7-day method.  In terms of getting the most immediate data possible there's a lot to be said for tuning methods to the whack-a-doodle noise statistics of the data sources; if I went back to the start I'd have used week-on-week methods for everything...)

The reason delta was still going to be a big problem with hospital overloads this winter was more about everything else that was alongside delta and its infection control.

Here's the latest news of part of that everything else...

https://www.theguardian.com/society/2021/dec/12/number-of-healthy-patients-...

The NHS has very little slack.

Just looked at today's data, and in particular the map of infection rates. Does anybody have an explanation for the clear disparity between the rates for those areas north of the Humber - Mersey line (central lowlands of Scotland excepted) and those to the south of that line?

Far clearer than R determined from a range of different models with a large number of ill-defined or largely unknown parameters.

It's a responsive, local, informative and precise measure of the important stuff for decision making.

Appropriate for a new disease when the best information at the time is a roughly known timescale.

I agree, 7 days is a good choice of timescale.

The UK wide 3rd dose rate for yesterday is the second highest yet and the highest for weeks (there was a single stand-out high day back in November for some reason).  It's a pretty impressive number (half a million in a day) compared to first and second doses as well.

Last week I noted that when the rules changed to allow booking a 3rd dose on a 3-month gaps that the booking system was full of gaps - unused capacity - and it's great to see that rapidly being taken up.   

The plot below shows the number of doses/day given by date.  I've joined the dots for each day of the week which helps to separate the massive day-of-week dependancy in the data from the time progression.  I've made the lines bold for the Thursday and Saturday dose rates since the rules changed.  Both have a much better week-on-week increase than the average rate over the last month.  Friday had an increase, but not such a good one.

Hopefully we'll see similar increases in the days to come, rising the 3rd dose rate considerably.

With early data shaping up that three doses may be enough to prevent the majority of people catching this new variant, as well as the vulnerable being directly protected by their doses, all doses given will indirectly protect them by slowing the spread and pushing more risk in to the future.  In the mean time, other people can choose to access vaccination, and there's a small fraction of the older cohorts who have had 2 doses who haven't yet had their third.  A point raised on the last thread is that for some of these people, accessing the 3rd dose capacity we have may not be simple. 

Oh, that is stark isn't it!  I'm minded to do a plot of cases/100k for the English regions and the other home nations and see what it looks like.  Perhaps that'll have a clue.   I'm sure their must be one out there (I try to to duplicate other people's plots...) but I have't found it.  Anyone?

If there's a lot more Omicron in London their could be some geographic spread effect going on like with Alpha; I'd assume it would be much more distributed and blossom out from many locations like Delta.   Should dust of my map code...

In reply to elsewhere:

Sure, agree with all your points.

I just mean introducing a new number called Rᵢ that isn't really much like R is very confusing. I don't mean it's confusing in the way they're using it, just that the nomenclature is getting more confused....  

Gets muddled if new variants alter the generational time...  Something that's been mooted for Omicron and is being investigated...

I tend to think it doesn't matter. Would you make different decisions Omicron had R=2 over 2 days rather than R=4 over 4 days?

It makes the whole thing intractable when both are circulating

Ta-Da!

Some anecdata: Just back from the booster. It was a full house. Booked yesterday, the first moment I was able. Got the last slot for today. They were battering through faster than even in the 1st dose days. They had a whiteboard saying 2248 people jabbed yesterday at the one centre. It was super slick and they were processing a *lot* of people.

I'm sure offwidth will be along soon with a guardian link that tells us it's not good enough and explains that that's someone else's fault, and definitely the public aren't at all part of the problem for not coming forward quick enough, and that each vaccination should be delivered on a velvet pillow, and someone else needs to be blamed and you should all be very upset about it, but.....  all indications show we're really trucking. Booking open to 30s now. Get on it.

I met some of that "lack of slack" 3 weeks ago waiting in an ambulance outside A&E for over an hour; was told that this was not uncommon. I was already aware of the situation but actually seeing it certainly drives it home.

All the "efficiency savings" over the last however many years have removed the slack. Now we have a situation where we need the slack and we haven't got it. But it's clear that everything backs up into A&E and then into "parked" ambulances which then means appalling ambulance response times (because they're sitting there waiting to discharge their patient when they should be going to the next call) which means some people are dying unnecessarily because of this.

When will the UK wake up to the fact that if we want world class healthcare, then we need to have world class funding levels of said healthcare, which means increasing taxes. But no, we as a nation can't contemplate that.

I'm going to a drop in clinic tomorrow first thing, only announced on Friday. Clearly a big push -Scotland

That post aged well didn't it

That intractable transition period is going to be ancient history within a week.

There are not calibrated control measures that can be doubled or halved rather than suck it and see or previous experience of legal changes, politics of compliance, public mood/fear and human behaviour.

I thought LSRH was suffering a similar objecting to me - adding another measured called a R (just like R and r) makes if all very confusing, but perhaps they meant variants…

There’s a reason I go with “exponential rate constant” and not ‘r’….  (Well, two, as it’s hard-wired to k in my brain).

Coincidentally earlier today I looked at the week 49 flu and covid surveillance report as I was looking for any data it had on ITU for that other thread. I noticed it had the attached graph and map (the latter being better scaled than the dashboard to see differences in the current situation.)

There were also equivalent graphs for pillar 1 and 2 positivity by region. Similar, but interestingly (?) not identical trends to those for cases per 100k.

https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveill...

(Edit - these figures from the week 49 report, covering data up to week 48, which ended 05/12 ie one week ago)

Over half a million today was excellent but that was only the average target we should have been at for weeks. We need to beat that every day just to meet the original January target. There won't be any lack of people wanting jabs for December, given the announcement just now from Boris ... let's see if the system has the right facility in the right place at the right time. I know some people who work in the service from near top to bottom, so I'm slightly pessimistic for good reasons. The first phase of vaccination was world class, this one isn't it's good but not as good as it could be and currently well behind the trend for the target.

Do we?

Updated 3 doses plot below for the UK.  

The government target is "All eligible adults in England aged 18 and over will be offered a COVID-19 booster vaccine by the end of January."

I've represented eligible adults by sliding the 2nd dose curve three months to the right on this plot as an indication of those eligible.  As LSRH pointed out last week, this is an over-estimate as some people who are eligible will have died.  

I've extrapolated the last week's booster rate forwards to the 31st of January.  It comes within a gnats whisker of hitting the eligible line, and the rate is still increasing - we only have 3 of 7 days of the week embodying the new booking rate now more demand is created (by dropping down to 90 days) for the signifiant slack capacity in the system.

Not as a numbers game it isn't, it's right on target and I suspect with a few more days growth in the booster numbers it'll be ahead of target.  Looping back to your first comment (quoted above), you're claiming the daily numbers are too low; that simply isn't the case.

I had a lot more time for the argument you made last week, which as I understood it is that there is a relatively small but highly vulnerable group of people who are struggling to access the vaccinations being offered, and that we're not taking the mountain to Muhammad this time around.  I haven't seen other people's data or discussion on this publicly, but the demographic analysis I did on time-to-target for the oldest ages (all be it conflated by the issue of people from the eligible curve dying that LSRH mentioned) shows the current rate in all older age bands as being ahead of the target [1].  I haven't looked at the second derivative of the demographic doses; don't know if they're speeding up or slowing down, but a first order projection isn't raising red flags here.

The last two rounds of vaccination showed two points where the rate slowed markedly (i.e. the lines became less steep).  The first was when 1st doses were slowed down to make capacity for the 2nd doses coming due, and the second is less explained but seems to be demand limited (which could include an impedance mismatch linking up between supply and demand) .  Will be interesting to see how it pans out this time... 

[1] https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_55-...

I think next week is the week I'd have called it for England, at least without Omicron...

We are, but that problem gets less bad each year.  The pool of people without any proper immunity only ever gets smaller, and that's a significant contributor to current hospital problems.  As the remaining population ages, with people exiting at the top and new ones entering at the bottom, the average age at which people of any given age were first exposed to any variant of this virus (by infection or vaccination) is constantly decreasing, and this should go on to reduce the severity of infection for older people.  That's why other circulating coronaviruses only cause colds it seems.

It will - new variants will sweep through the population, but, they shouldn't break T-cell protection so as they sweep through they'll be waves of a common cold rather than a killer virus

In terms of threats, I think the amount we're f*cking up ecosystems and the climate, we're going to unleash a lot more pestilence than just Covid,

Stop breaking the world.  Invest in public health.  Integrate science and scientists in to government and decision making.  Take a sledgehammer to the component of academia that sees dangerously subverted or delusional people given grand platforms.  Encourage a diverse range of blue skies research in the life sciences as well as application driven stuff.  Make sure primary and secondary education is turning out people who can think for themselves over rote learning.  Set the security services loose on the people subverting things with misinformation.  Continue the rational, evidence-driven work of JCVI that preserves public trust in vaccination in the face of rampant political point scoring.  Make tackling absolute and relative poverty a key priority combined with moving to society that values inclusive social welfare far more - critical to avoid future automation moving us further towards dystopia. 

At the same time we realise we can't have governments awarding people with no trading history what so ever £100m contracts to run testing labs for things the NHS could do with better QA if given the money instead?

That is really interesting, thanks.  Something of a ring of fire beyond the London orbital.  I'm definitely going to have to resurrect my maps code; the download that used is long gone...

Re: the surveillance reports - I'd forgotten they had the /100k regional plots.  It does look from that like London is balancing the books - which is interesting, if it was having some growth coming as the balance to a period of low cases, and Omicron was in the right place at the right time (the centre of the growth), that could accelerate its rise to prominence over its natural potential.  That's another straw to grasp at for a few days...

I'd quite like a few days consulting work inside UKHSA to prattle on at them about the idea of a more automated pipeline for making the graphs than Excel and copy + paste, and to work with them on that...

Target now end December apparently 

https://www.theguardian.com/politics/2021/dec/12/uk-booster-jab-rollout-to-...

I'm in the ring of fire. It's everywhere... lots of people getting positive tests. Had to go to the test centre today for the first time in the whole pandemic because my son had a fever. His best friend from school is positive, so I'm fairly sure it's finally here. Lucky for me, I had my booster almost 3 weeks ago.

Sure, since things were not working as well as they wanted they moved the goalposts last week: the target until them was evey adult booster  jabbed by the end of jan and they said themselves their target was an average of half a million a day.  

Yes your dotted line is a different shape to the other lines and it will accelerate for a bit but still, the line includes about 15% first and second jabs... as currently we have 34% done on booster/ third jabs by my calculations of 67 ONS population.... let alone NIMs (we passed 20 million a week ago).

Vulnerable people stuck at home waiting to be boosted are only a few percent but that's hundreds of thousands of frightened people ( ditto in care homes). I think you are overestimating double jabbed people who have died since spring if you think that makes a big difference outside the over 90s (who I think have pretty much been completed booster wise).

​​​​​​

I almost wondered out loud in my last post if we'd see 1m / day.

Someone high up has seen the light.  Can you see the light?  youtube.com/watch?v=rIklz5_o3QQ&

Edit: If that goal can be hit it's seriously impressive; there's some tension coming out of the rate constants with schools and workplaces closing over Christmas, if we can get a 3rd dose in to all eligible adults by end-December before that tension returns then it's hopefully going to be almost as if Omicron didn't happen. The third dose is hopefully going to increase health protection for all regardless of variant, which is going to further reduce the healthcare pressure from the more vulnerable and vaccinated people; and the [unvaccinated and never infected] pool is going to evaporate at some point soon.   By the pestilent gods themselves it's going to be a fantastic spring in 2022.

In reply to Offwidth:

And, numerically speaking, we're on target for the pre-goalpost shift, with that projected rate expected to increase significantly over the next few days as more of that slack capacity is filled up by the revised booking criteria...  Let alone new capacity still coming online...  Let alone: see above

"All adults" is not a permissible goal, because of the 3-month gap from second 2nd dose; any adult who hasn't had their second dose yet can't possibly get their 3rd under current criteria for another 3 months minimum.

No, no it does not.  Pro tip: read the legend - it says "Dose 3".  Hit - that does not include dose 1 and dose 2.  Dose 1 is in the curve labelled "Dose 1" and dose 2 is in the curve labelled "Dose 2".  Shocking, I know.

The main reason for the difference in shape is that the dose 1 curve had to slow down to accommodate 2nd doses spooling up, and second doses had to slow down when that kink in 1st doses hit the number of 2nd doses coming due; an effect not relevant to 3rd doses.

Please show me where I said it makes a big difference.

What I actually said was " As LSRH pointed out last week, this is an over-estimate as some people who are eligible will have died."

I didn't say a big difference.  Last week I gave an estimate of around 1% for the oldest ages.

We seem to be continuing a pattern of you replying to things I've not said (or, in this case, plotted...).

What’s your thinking on when Omicron will start making a noticeable impact on case numbers? I mean noticeable by eye as rapid growth beyond what we’ve seen through the mini peaks of the last few months.
 

I guess it depends how much Omicron there is currently. 1,000 cases ported today. Presumably that’s from sequencing, so about a week from case reported date. If they picked up 50%, that’s 2k a week ago. 8k now. 32k in a week. Which suggests we’ll see the numbers grow significantly this week. I’m probably way off on the specifics but my point is the numbers aren’t yet snowballing abut they must do soon. 

It's all gone a bit bonkers hasn't it; the last few weeks so many contacts have Covid.  I'm starting to get paranoid that I've not caught it; I wonder if I've had an asymptomatic case or if my habit of opening windows, only dining outdoors and running a HEPA filter on my work desk has made the difference.  

Hope your lad bounces back fine - wish I'd got my first exposure as a kid - and happily for you that the dropping of isolation requirements on close contacts is coming form Tuesday - https://www.bbc.co.uk/news/uk-59628609

Best wishes to all in the plague household.

Hard to say because I think precautionary measures (mandatory and public-led) are taking a chunk out of the spread of delta (and omicron), so it's already impacting in an indirect sense.  

One third of London cases was today's news report; rapid doubling times at a local level have never held up for long at any point in this pandemic, irrespective of imposed control measures or boots-on-the-ground public health work.

Then we've got the accelerating 3rd dose program.

So many variables I don't even have a hunch on what's coming.  

Things.  Things Will Happen.

One of the Twittererers, 'John_actuary', puts it at a 94% ceiling on the 80+ age group. Remember, they got their 1st doses about a year ago now so it's not just 3 months of attrition in that bar on the chart.

You’re describing my dog walks. 

Deaths between 1st and 2nd dose should be embodied in the 2nd dose curve so that’s the one to baseline from, but yes it gets very brutal at the very top.   

It’s tempting to apply the all cause mortality data to adjust the demographic baselines, but when I think about it, alarm bells go of telling me I don’t know enough to do it right.

The BBC reporting is annoying me tonight; I don’t know if it’s them or the PM’s language (haven’t watched the briefing), but talk of offering “all adults” a booster by the end of December is nonsense.   For people without two doses there isn’t time between now and the end of December to give them 2 doses, let alone 3, on the minimum approved spacing. The missing word is “eligible”.  

On that note, I definitely think it’s worth offering unvaccinated people their first two doses on a 3-week gap instead of a 12-week gap; sure it’s significantly less effective after week 16 in terms of protection level, but between weeks 4 and 16 it’s a heck of a lot better, and that’s the time period that the freight train named Omicron is coming through.

Quite. Ticking timebomb. I think in a way cases have to go up significantly for people to take notice, to the extent they haven’t already. 100k would be a significant number I suspect.

Yeah, so it's 9 months (or 10.5??), give or take.

It's not going to be night and day, but if we're fortunate to be in the position where we start talking about saturation at 94% uptake in that age group, it'll be reassuring to remember this exchange.

ETA:

I tried almost this for the 'with not of' sums. It's flaky. The numbers are really not available in the format you need and it's not trivial even to have a guess. 

http://www.bandolier.org.uk/booth/Risk/dyingage.html is the most convenient set of numbers I found but not sure how trustworthy that is.

Curse you. I woke up with a maths based nightmare ... first in years... and can't get back to sleep. Yes I made some errors interpreting your graph and was wrong. I apologise. Anyway it's always nicer to be patronised when I deserve it. You keep plotting trends and I will keep talking to people actually involved.

I wasn't wrong about Boris promising an average of half a million jabs a day when the booster campaign started (;and that we are well behind that). I'm not wrong about the time consuming vulnerable at home and masses more people with limited time and travel ability. I'm not wrong this phase has been plucking more low hanging fruit earlier than before. Just ask yourself: for what possible reason did the first U- turn happen (on dropping the target of all eligible adults done by January), if things were going so swimmingly well?

I guess the BBC report gets muddled given Boris misreads roo much from his autocue. He is just expected to be economical with the truth. Those nice scientist people get to pick up the pieces after all his covid speeches...the other one which might cause some chaos is an unqualified "some places might be offering walk-ins". I bet centre managers, and their security, on venues that only take booked slots loved that one. What's a few hundred pissed off disappointed amongst friends? I'm certainly glad that has been clipped out of the BBC replay.

20 million jabs (of course minus the one in fifty currently infected ...and those infected in the next week... who can't be done until January) in what remains in December is going to need well beyond skilled logistics and good luck. Especially when no one locally who has to 'turn the tanker' even knew about this until last night. Especially when it's in a completely opposite direction to what SAGE and UKHSA leaks said was needed. Twenty days including that little thing called xmas hols. Blitz spirit and a man in red with magic reindeers will be called on I guess!?

Things will happen. We will very soon see what those things are. Smells to me partly like a dead cat desperation thing from a cornered PM clawing to hang on to power.

I'm glad some more resources and flexiblility will come instead of top down bullying and refusal of sensible local advice on practical improvements (it certainly can't even close to happen any other way) as locally a few areas were really struggling in some centres at peak time due to problems, including a lack of key staff. At least we had the army .....in my county, from the word in the street, this included two whole jabbers who couldn't work when the worst staff shortages were, nor do anything outside big centres.. I must have just made all this paragraph up of course, as its all going greeeat!?

I apologise to the thread for my greater than normal level of sarcasm, but this plan to jab all eligible adults by the end of December looks to me like xmas nuts. In the end any extra pace WILL be genuine good news.

I can meet you halfway on most but not all of that.

Your point about eligibility is a strong one; a lot of people will soon have to wait 4 more weeks post infection.

Walk-ins for all ages have been a thing in London for a while. If you can work out how to read it (I can't figure out the incantation that turns Reddit into prose), r/getjabbed has been showing the way for a some time.

The centre I went to yesterday was definitely tooling up. When the assistant took the precaution of checking whether I was getting the right vaccine, the answer from the senior staff was very immediate and very jfdi. There were logistics guys all over the place and a sense that they all knew something we didn't. All makes sense now.

Low hanging fruit is, like it or not, where we need to be aiming when it's a numbers game. If we can break enough chains of transmission to dent infection numbers and prevent redlining healthcare it's likely to be better overall for the one vulnerable person you could jab in the same time. Not sure on the numbers you have to jab to break even but it probably doesn't need to be many before it's best for all concerned to do that.

Strongest point I'd make is to consider holding off on any naysaying and just encourage everyone you know to get jabbed for now. By all means point out the pm is a turd to anyone who hasn't noticed (we know, by the way) at the same time.

There are other ways of breaking chains of infection other than boosting you know. Boris chose this route. Currently we seem to heading to the worst of both worlds in some sectors: major hospitality is seeing economic damage with no financial  back-up as the government pretends people haven't started voting with their feet in the last few days.

I'll repeat again there is no point having logistics in places where people won't go. That's what hard to reach means... it's slower and smaller scale. Sure the vacant slots will fill in some big centres (if the shit booking system doesn't keep crashing) but they will soon empty again. Yes going fast is good for cutting transmission but the most important part of boosting was supposed to be protecting individuals and the most important in that is protecting the most vulnerable (so they don't get seriously ill and in that end up adding to NHS pressures)

I'm not going to celebrate politically motivated plans that look to me near impossible, as in the end it feeds the attitude that people shouldn't listen to Boris and jabs are cover for him. I'll take any increase in pace we get irrespective.

I'll get a better impression of what people involved think in the next few days... my 'good but could be a lot better' view of the booster phase is a real view of highly motivated people involved.

I'd dearly love to be wrong, and this new year target to all be a success, but can you seriously see nearly 20 million jabs (wintetree's plot is half-way for eligibility) in 18 days including 4 public holidays and new years eve!!!??? The Metro is gushing today about a record just over half a million , when that's what Boris promised us as an average from the start.

https://www.bbc.co.uk/news/blogs-the-papers-59632045

And what does the dog do while you are doing that? 😜

If the announcement had been "big push to vaccinate hard to reach groups" you would posting screeds about how the focus should be solely on numbers. 

My posts are about what the people doing the job want: the logistical support to do both....which although there were problems on the vulnerable side, it was much better in the first vaccination phase.

GP vaccinator on the news right now saying hot air plans are up there, the reality much lower down. They heard about plans when the public did  She is really struggling for staff support over xmas. Her message to Javid is please support us, please improve public health messaging. To people please be kinder to each other. To fellow doctors please look after each other. Don't phone GPs use the web site (and I know it keeps crashing).

One of the key things is the timing of when the Omicron infections shoot up like a hockey stick. When that happens the vaccination program is going to be disrupted just like everything else. 

If you are going to widen access to the jag program it would be reasonable to pair that with strong control measures to get a longer time before the wave hits.  If you've decided not to do serious control measures then you only have limited slots before the wave hits and you should prioritise them for the vulnerable and people who can't work from home.

OTOH if you are just playing for political popularity then you want no restrictions and high jag numbers no matter who is getting them.

I will, and I'll keep qualifying where they fall short of reality - as I did up front on this thread about the small fraction of hard-to-reach people likely being missed; once again a tricky denominator issue obscures the truth of the last few % remaining in any age bin.

The only sustainable ways of breaking them are 3rd doses or more infections granted immunity.

Control measures can slow down the jumps along those chains, they can't really break them.

What a b*rd, choosing to accelerate vaccines that bring solid, concrete protection whilst allowing the economy to function.  It's okay to accept that just occasionally they do something right...

Everyone by the end of December does seem pretty unlikely, but I'm all for setting an ambitious goal if the support is there behind it. The proof of the pudding will be in the eating, not the punditry.

Walk in to many places and ask people what they think and you're going to get a one-sided view....

Depends how we take the new timescale.  I look at it as aspirational and at every increase in pace as worthwhile - better to set a goal, aim for it and undershoot than to not try.   No, I don't think we'll meet it but if rates continue to rise that's great.

FTFY

As ever, it's going to come down to what "everyone" turns out to mean. For a start, it ain't 20m. Right now something like 1.5m of those will have been infected in the 4 weeks preceding the day they'd like to book. More than that (a lot more?) will be infected in the next 4 weeks and become ineligible. A few million won't engage. A few hundred thousand (??) will have died or emigrated.

It's almost as if someone, somewhere, (not Boris, jesus no, I mean someone who can add two numbers together) has had a think about what might be borderline achievable with a tailwind and rallied to shoot for that.
The politicians will almost certainly disingenuously move the goalposts near the end of the month to pretend they've 'offered' to everyone or whatever, and I'm sure the offwidth will have a guardian link about it to share with us when they do, but tbh it's not a completely unreasonable target.

Just been done.  About 100 people at a drop in at 8.45. 15 or so staff including 5 soldiers. Pretty impressive. 

That's a very cynical viewpoint, not like you at all 😁

However, when I'm wearing my cynic's spectacles, I tend to agree with you. I can see a post "debacle" statement something like "we did our best but unfortunately it wasn't enough".

And getting the army in (even if they don’t do much) is a genius move from that POV. If it’s a success it’s the governments brilliant plan, if it’s not they can blame the NHS and say ‘look we even sent the army in to help you, what else could we do?’

I admit I'm cynical, but barely a mention of  a lockdown Christmas party on the front pages today.  (still good they're getting a shift on with the boosters though) 

As various experts said on the news this morning: openness and transparency... let's see the SAGE advice so we know this isn't political. The move will have impacts on the NHS... it's not as cost free or simplistically good as you imply.

I'm boosted now .... efficient and quite full but no queue despite walk-ins being available. A different centre was very quiet for my second dose.

I don't recall implying that more 3rd doses is "cost free" or "simplistically" good.  

This is getting tiresome.

At this point you appear to be implying that we should not be trying to raise the 3rd dose rate, having recently criticised the government for not doing enough to meet their previous target for a 3rd dose rate.  I'm completely lost as to what you actually think here, other than being determined to take whatever is done as wrong - I can't even say "insufficient" any more.

Just to be clear, although you're replying to me, I haven't said it "isn't political".  You and TiE have called it political.  

What I actually said was "Everyone by the end of December does seem pretty unlikely, but I'm all for setting an ambitious goal if the support is there behind it. The proof of the pudding will be in the eating, not the punditry."

The problem is it won't be a pudding it will be a sh*t sandwich and we don't have a choice about eating it.

The logical thing would be to figure out how long it will actually take to 3rd jab all the willing - say mid or late January and then design restrictions which stop any 'hockey stick' moment where infections shoot up until after that point.

If you want to remove the restrictions faster then prioritise the jabs so you get to the point where everyone at serious risk is done earlier.

Or, you could be really pragmatic and have a lockdown which only applies to those who've not had three jags + 14 days and are over 40.

I don't see the jab program continuing at full pace in a situation where a high percentage of the population is infected.  The logistics and staffing will break down and people will be scared to attend.

Just back as well. Appointment after the dodgy database query problem 5 weeks ago when I was one of many turned away in the NHS Lothian patch.   Was second up, and the carpark was full when I came out.   Moderna after a couple of AZs

Perhaps one of the other home nations that isn't fully governed by Westminster will show us how to do it better, ey?

[silence]

youtube.com/watch?v=-sED4fzIV0k&

I hope you're over-egging this; the oldest and must vulnerable people were getting vaccinated at pace in January 2021 when the risk was far higher for them than it is now. Isolation requirements have been dialled back a lot, and a lot of this wave of infection is likely to be in young people with high immunity - I worry one problem is more going to be convincing them to isolate from what for them is a mild cold, rather than them being scared to come out.

Certainly a high stakes time over the next 6 weeks, and I hope there's an immediate tightening up of control measures if it looks like the current path isn't going to make it without healthcare overload; I'm looking forwards to seeing how the Omicron doubling time backs off over the last week of data and over the next week or so - the more it backs off, the better...

I'm presuming that 3rd jab availability/status, especially for care homes and vulnerable, must be a bit of a postcode lottery.

My parents in their 90's (1 in a care home) had no 3 ages ago, and me & Mrs (60-65, not vulnerable but down as carers) had ours well over a month ago.

I'm surprised that it appears that not all care homes have had no 3 yet.

Scotland is doing more 3rd doses than England per head of population.

We are also doing a better job on restrictions.

But with those arseholes in Westminster and the English controlled BBC and newspapers continuously undermining the health messages and any attempt to do anything different from England and with the c*nts in England controlling the money there is limited scope to do anything radically different.

Only independence will allow Scotland to break away completely from the Tory bullsh*t. 

The problem is it wont get rid of your own bullshit will it? It is pretty rich of you to whine about undermining health messages given your own attempts to do so with your moronic conflation of the AZ vaccine and those nasty English. Can you not give your inane bigotry a rest just for a while?

Someone, now who was it, I can't quite recall, was repeatedly telling me week after week how it was't fair to compare a small country with a big country, because of some rather dubious reasons?  Let's hope they don't see this thread and object to your comment here on the grounds that it's not fair to compare a small country with a much larger country.

I hand't looked down at the national level until now - quite deliberately sticking with top level figures -yes Scotland looks to be a bit a head and going a bit faster - great.  How nice to be in a race to the top instead of the bottom for a change, winners all around.

Trifling differences compared to the level that you are asking for however.

In reply to mondite:

Well, quite.  TiE is gunning for the 2021 award for Most Ironic Poster I think.

I don''t recall saying you did...  you seem to think a whole load of stuff I say is aimed as an attack on you (when my general position is normally exactly the opposite, certainly on your analysis) and when I am picking up something specific you say, it's usually something that bugs me (and its nearly always worth asking, especially when it becomes quickly clear where I got something wrong.... including now,  for the first time, before you even tell me, in a weird dream!).

Ignore me then. I find debate useful, be it genuine exploratory or sometimes even devil's advocate. It was how I was taught; including how to gain respect of different viewpoints, whilst disagreeing with them.

I've never known of such dangerous UK politics in modern times like the last three years. I'm openly worried about the future, so I'm sometimes a bit emotive. I retired early from a job I had loved partly as I could no longer cope with the manage-up bully-down culture and plain dishonesty that should be an anathema to academia. I live in a country where I think the government dissembles on instinct and is taking us down dangerous populist paths and has already acted on covid in a way that has led to the unnecessary deaths of tens of thousands, twice. The PM lies and lies and lies, but this time gets caught in a really serious bind with photographic evidence and lo.... he mysteriously brings in a new initiative without the scientific advisors standing by his side and without answering questions or providing evidenced back-up and where the leaked advice to him was slightly tigher restrictions ..... the booster gambit is something that will take at least a week to be clear if it will work and allows safer lies even if it doesn't. He is entitled to present on his own, but he gave up an entitlement to be trusted long ago.

Wintertree:

Offwidth:

You did.

You can tell because its in the post you are replying to.  

• Here's a link to the post - https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_56-...
• I have attached a screenshot to the post.
• Here is the text "The move will have impacts on the NHS... it's not as cost free or simplistically good as you imply"

If I have been getting increasingly snarky perhaps the reasons are becoming clear.

You've gone from arguing the government need to do more to raise the booster rate, to stating that their are drawbacks to the new plan to accelerate the booster rate whilst saying (without basis IMO) that I am implying it will be cost free and simplistically good, to saying you didn't say this when challenged on it.

 I am at an absolute, complete and utter loss about how to be more clear by this point.

From my view: This isn't about "useful debate" - it's about your position shifting from arguing for a faster dose rate then two posts later arguing against it, then suggesting I'm misinterpreting your posts whilst also flat out denying you said things which you literally just said. 

There's a difference between

• Devil's advocate - always useful on these threads from anyone and usually resulting in an improved understanding for everyone 
• Where you appear to be, which is tying yourself in knots trying to convert every discussion in to drum banging on particular points with a consistent tone that's not anchored in the data but in your expectations of the government. 

Some drums need banging, but they need banging with clarity and consistency, and that banging can be separated from trying to understand where we are and the trajectory we are currently on. 

With regards the drum on getting to the most vulnerable and hard-to-reach people,I banged that drum up front in my first post on this  Michael Hood has banged that drum.  That drum needs banging.  You're drowning out the sound of the drums with your confusion on high dose rate good / bad and arguing you didn't say things you said half an hour before.

We went through this with the early posts on what was coming in Europe where you started to interpose with the strong implication I was omitting things to bias the data ("What Wintertree isn't telling you...") and, well, we can all see what's happened in Europe since.   It never was as one sided as some people thought, and it's still not.  It's not clear cut either way.

I pretty much agree with your entire final paragraph, and the reasons you cite are part of why I left academia - and I see the pain it's causing my friends and former colleagues still there in the shitshow of the last year.  

Can I just put some 👏 out there for all the NHS IT staff who have managed to make the systems we rely on to detect, record, treat and analyse covid (and every other disease on the planet) robust to the log4shell exploit? I’ve seen NO consequences of it in any of the systems we use and I know they’ve been working 24/7 since the story broke with archaic vulnerable systems. You’re the unsung heroes right now.

/transmission 

Seeing as you've piled on the cynical bandwagon this thread, can I cynically suggest it's because those archaic systems systems aren't modern enough to be cursed with JAVA?

Seriously though, the level of openness with the data in this pandemic has been phenomenal, none of us would be arguing without it.  

The irony is that I'm sat here working to programatically extract data from .xlsx files.  

Sadly that’s not true. There’s a lot of Java about, mostly well hidden. My AI deployment engine roll out got shelved so they could find it all..

‘We’re going on a Java hunt..’ was the lead technicians description!

Son's fever pretty much gone already (barely 24 hrs) without any Calpol this morning. He seems fine playing Roblox instead of school. The odd cough but that's it. His PCR was positive, rest of family came back negative.

We'll need to reschedule the panto (boo!), but Christmas itself should be ok (if none of the rest of us develop symptoms).

But .. lots more anecdotal reports of people testing positive around here this morning. Nobody I know is particularly poorly yet though (unlike March 2020 or January 2021 when I knew people who were hospitalised or even died). I really hope that continues.

Oh no I didn't 

Of course I did ....but you're still reading too much into that. My brain, like every brain out there, works differently to yours. I sometimes joke exaggerate (with harmless intent) to stress a cheeky counterpoint, poke gentle fun at people I like, occasionally go off on tangents and, regretfully, do make more mistakes when tired and stressed.

On the obliquitous front, unlike most science based people, I have a habit of sometimes expressing existentential angst that has no necessary relation to a reply context.... I sometimes drift into vague expression... or even reply in limerick form... it's a fault/feature of my communication that goes down better with face to face context (at least for the lovely people that put up with me). I am a flawed human. I think it comes from a weird education and unusual influences;  plus volunteering to resolve too many emotive and difficult people problems; often in diametrically opposed positions (sometimes involving real anger).... art, friendship and climbing are important to me as safe havens.   As a classic excursus it also struck me it's maybe why I enjoy (and am not fussed about endings) in Philip K Dick novels as it's the journey, ideas and language that matter most to me.

On regrets... I make more mistakes recently in what I say than normal as I'm worried (and have declining eyesight, a mischievous predictive text system and I'm normally using an occasionally unstable device that is mostly OK but seems to crash at the most inopportune moments, like some haunted machine in a Pratchett novel). I do try and apologise when I'm clearly wrong. 

It's certainly a bad idea to take everything I say too literally or seriously (unless it's about Boris or other b word people).

PS I wonder if this post is some previously unlisted vaccine reaction!

“There are now 4,713 confirmed cases of Omicron in the UK. And the UK Health Security Agency estimates that the current number of daily infections are around 200,000.

While Omicron represents over 20% of cases in England, we’ve already seen it rise to over 44% in London and we expect it to become the dominant Covid 19 variant in the capital in the next 48 hours.”

Would be interested to know how they estimated that.

With those kind of numbers it seems fairly clear that Omicron must now be driving much of the rise in London.

Yup, the sound of drums.

In reply to Si dH:

I was writing this post in reply to kirsten when you posted that.  Yes indeed it must.  And it shows. 

London has been increasingly poking its head up on plot 18 and getting coloured red for the last couple of weeks.  The exponential growth signal is now really clear in raw cases data [1] and is developing in raw hospital admissions data [2].   It's really taking off in cases and hospitalisations on plot 18...

I’ve put cases rate constant plots in for London and England below by the week-on-week method.  These give a really clear and robust (non-provisional other than the last point) picture.  With the benefit of the last few days of data, we can see it looks like about 5 days since the growth rate bottomed out at a doubling time of around 21 days and is now rising towards 10 days.  This strongly suggests the new variant is taking over control of top level cases for London.

(Plot 18 shows a shorter doubling time for cases; this uses a different method that has a more twitchy and provisional leading edge.  It could be twitching up in response to the shape of the last few days of data, or to noise)

I’ve done a demographic cases and rate constant plot for London - it’s clear from the gold appearing on the right of the cases plot and from the bold orange on the far right of the rate constant plot that this growth is centred in ages 20-35; worrying signs in the rate constant that growth is returning to over 70s as well.

I expect the case hospitalisation rate and case fatality rate to both drop, because lots of young people who weren't catching Delta are catching Omicron.  Expect hospitalisations and then deaths to rise, because people who would have gone to hospital from catching Delta but who weren't being exposed to it are now being exposed to Omicron.

[1] https://coronavirus.data.gov.uk/details/cases?areaType=region&areaName=...

[2] https://coronavirus.data.gov.uk/details/healthcare?areaType=nhsRegion&a...

You are f*cking up your own threads by becoming a know-it-all who spends an inordinate amount of time trying to win every single argument even when you are obviously wrong - such as pretending that AZ vaccine is as good as Pfizer or Moderna or that an 11x higher report number for a specific symptom isn't significant, and then sticking to that ridiculous opinion even after the UK government sticks a warning on AZ for that symptom.

If Scotland hadn't been dragged in the sh*t by England we'd have far fewer deaths and we'd almost certainly be in something similar to lockdown now like many EU nations.  The top level deaths per 1,000,000 over the course of the pandemic speak for themselves: England 2,000, Scotland 1,500, Ireland 1,000.  If we were independent we'd be roughly where Ireland is.

The whole Tory, let's just let Delta rip through the schools and everyone can catch it and get immune, policy was a pile of sh*te because Delta doesn't make you immune to Omicron.

Going of what a bunch of other posters have had to say to you over the last few weeks of your increasingly deranged and denials outbursts, you might be confusing things here.

Haven't you got something better to do?   You probably do.

I have never claimed the "AZ vaccine is as good as Pfizer".  You are mistaken.

I recognise the different levels and fades in protection against infection with the mRNA vaccines holding that protection for longer.

• I recognise that both have much higher protection against serious disease, with the mRNA ones apparently having a small advantage.
• I was and remain totally disgusted by the pathetic and scientifically uninformed way you tried to mis-represent the YCS data as part of your xenophobic madness.   I wasn't the only person.  Over those two pathetic threads a couple of dozen people - almost all of whom I think are not Tory and some of whom identified as Scottish or not British - roundly and solidly disagreed with you.  

But, it was Mondite that mentioned this on this thread, not me.  Take it up with them, perhaps?

Their are other symptoms on the YCS list with massively different reporting numbers that go the other way.  You never mention those, do you?  Also, de-mo-gra-phics.

Don't know about you, but I never expected Delta to make people immune against catching future variants.  That's not how endemic disease circulation works.  At all.

I do expect it to confer some immunity against severe disease from future variants.  Have a look at figure 2 in here for an example (pre-omicron, but, you know, T-cells are a thing).

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

You accuse me of being a know-it-all - I am not, and I do things like speak with life scientists and immunologists to improve my understanding where it is weak, and I try and qualify anything I am uncertain on, and to reference things I bring to the table.  As far as I can tell, you've embraced knowing next to nothing in terms of deep understanding, and have stolidly refused any attempt to understand any of the complexities of the situation.  Explains a few things. 

The intent of letting it spread was I think not to make people immune, but to raise immunity levels across the population.  These are not the same thing.  Now I know you have developed a habit of referring to all protection levels as "against infection" rather than as "against severe disease" as it suits your transparent, xenophobic agenda driven crap over vaccines, but the real world is more complicated than that.

I actually came on here not to face another tirade from TiE but to post a couple of moments in time from the London demographic rate constants plot.

This has a second axis on the right to show the doubling times.  Adults aged 25-30 have a (provisional) doubling time of just under 4 days.  That's almost a pre-pandemic level and does suggest a strong evasion of immunity-against-infection.  

The rise in 85+ is much more worrying; perhaps suggests shielding on care home etc is not working so well?  Again the measurement is provisional and will be subject to more noise from lower numbers up at these ages. 

Looks like I circled the right part of the English D1.c at the start of the thread for the emergence of Omicron...  

Might be time to move, or stay firmly at home…

Yup; I have this week planned out carefully to minimise exposure, then once schools are shut we’re hunkering down for a couple of weeks to see what happens.  Lots of walks, home cooking, family fireside time and so on.   Thankfully things are a little bit less advanced up here in the northlands so we should get more delay from the control measures.

I  was going to jump on the private jet and head for my island mansion, but there are just two small problems with that…

You really are an obnoxious bell end.

I was going to offer you a flight on my private jet to my island mansion but I appear to have similar problems to you 😁

A couple of possibilities - the adults aged 25-30 are probably the ones caring for the 85+ at home or in residential/nursing homes. The other is that the 85+ are the most likely to be admitted and incidentally test positive due to underlying high levels of community spread.

If you go out you spend five days wondering if you got away with it, or you’re working out the absolutely-can’t-risk-catching-it-from-now-until-my-flight-in-x-days calculation if you want a hope of still seeing elderly family. (Also seem to have mislaid the private jet) 

Health is devolved... Sturgeon didn't have to mirror England's policy +or- 2 days over the last 23 months.  

They're coming to us in our case, but the risk is the same.  Don't want to jeopardise the little ones having grand parent time.   I seem to be completely unable to catch Covid despite almost everyone around me now having done so.  I'm not sure if it's just a persistent level of mindfulness and awareness over proximity and ventilation or if it's my superblood ®.  Having said that, tonight is the LFT prior to my most critical meetings of the year...  

In reply to mik82:

Thanks; the second one is interesting to think about in terms of gating for tests and what all these numbers really mean.  Nothing good in the immediate term, but beyond that...

In reply to thread:

Sunday's vaccine data was astounding, up by over 100,000 doses from the previous Sunday.  This feels like far too much to just be the un-used slack in the system being taken up by expanded bookings; and there's plenty of individual reports about new capacity coming on line.  This has pulled my projection of the current rate to all those eligible for a 3rd dose in before the old January 31st 2021 target; still a lot more acceleration to go to pull that forwards to December 31st but things are moving in the right direction.  Also - Dec 31st as I understand it is not a "jabs in arms" target but a "jabs offered" target, what-ever that meas.

The BBC continue today to do a similar kind of plot (screenshot attached) of how long it would take to "boost every adult".   Someone really needs to get on the blower and explain to them that people who haven't had a 1st or 2nd dose can't get a 3rd one...  

Whilst 3rd doses are skyrocketing, there's absolute no sign of an up-tick in the rate of first doses.  I'd hoped that the wall-to-wall coverage of Omicron might encourage some people.  

+++

I thought perhaps the media had misunderstood and the 200k infections actually refers to cumulative Omicron cases rather than daily ones. Had a look and Javid was indeed referring to daily infections.

https://www.gov.uk/government/speeches/health-and-social-care-secretary-ora...

That’s insane, even if it doesn’t keep doubling every 2-3 days. Delta is on top of that 200k but will soon be an afterthought at this rate. Where are all these cases in the official stats though? They must start coming through in the next few days. Perhaps due to existing immunity the asymptomatic % is higher than it has been historically so more cases aren’t being picked up, though the findings on immune escape would suggest that, if anything, there should be more symptomatic cases now.

Say only half are symptomatic and ignore cases picked up through asymptomatic LFD testing. And say only half go for a test. That’s still 50k and in practice would be higher. Now discount back 6-9 days (3 doubling times) - those would be the cases reported today. 6k, so could be in the noise at the moment. 

Wait for it… but not for much longer. 100k reported (in total) by next Monday?

Should have added - 200k would be 1,000 extra daily hospitalisations baked in even assuming a relatively low 0.5% hospitalisation rate. 4,000 in a week’s time. That would mean a pre-Xmas lockdown. To put it another way, by the time they get a better sense of the numbers, it will be too late. So if the 200k is credible, they need to act now. If it’s more like 20k, they might have another week. 

Sounds to me like the country has (in general) forgotten what high rate exponential growth looks like but we're about to get a rather ugly reminder.

This is not looking like it's going to be pretty, good luck everyone. I hope those of you who celebrate Xmas are able to enjoy it as you'd wish to.

Yep. Won't be visible in the daily numbers yet but when it is, the next day it'll be most of them.

Lockdown announcement sweepstake:

15th:

16th:

17th:

18th: LSRH

19th:

20th:

21st:

There did seem to be a lot of confusion after I posted here but in the end it was confirmed. 

That's a lot of people not getting tested and picked up.  I was wondering (albeit not enough to go looking) what the similar estimate for Delta is.  Also, idly wondering how many viruses we walk around aysmptomatically with, without ever knowing because we don't test for them. 

FFP2 mask mandate now for those still wanting to go into our office,  imagine that will thin out the numbers who aren't so keen on wfh for whatever reason. 

26th, even if people are getting treated in hospital car parks before that.

Much happier this am with what I can gather from govenment plans but a bit achy from the jab.

Government have dropped the dumb target of vaccinating all eligible adults by the end of the month (they will all at least  get a booking by then). Bravo! Foolish targets would be used against the program and risked damaging it.

Word on the street, from the national briefing to local areas, is this time things will be resourced (significant proposed staff moves):  NHS trusts and GP networks to clear the decks to help (much non urgent work cancelled) ; extra support for pharmacies; .a clear planning focus on the hard to reach. Lots of minor issues to resolve (especially with staff bodies) but a much more sympathetic view on that from NHS leadership.

I still have some questions: Why didn't they do this a week or two ago? When will they improve written public messaging on why getting a jab is so important? When will national leadership realise calling the national booking system excellent is a bad look when it keeps crashing at peak times?

It’s clearly in the London numbers now, although my plots are lost in a TiE rant.

We’ll see; most of the growth is happening in people who have so much immunity they weren’t catching delta on exposure.

It’s the older unvaccinated and vaccinated but very old/vulnerable cohorts that will drive any return to lockdown and the high rate exponential stuff is happening in younger adults.  England wide hospitalisations are almost certainly rising now…  

Perhaps I’m too optimistic but I’d extend your sweepstake by a week or so; at that point schools have broken up and most offices too, and another 6 million or so third doses are in the population.

I forgot to add that IndieSAGE still haven't put up their slides which had useful information on demographics in SA and the London problem identified last Friday. I think it's worth a look. Omicron data starts 6:38 in and runs for a few minutes.

youtube.com/watch?v=ntpo7FKhcEY&

I've also promised myself to try and be a lot more careful, clearer and more straightforward with you in these threads. I'll keep the 'weirder' reactions I sometimes have for things I don't properly understand elsewhere. I will specifically third person any comments on which I have things to say. It's been an anxious few days for me for several big reasons and most things I was very worried about have come good. As Sheridan wisely said "Understanding is a three edged sword: your side, their side, and the truth.” I always preferred to try for the third option.

I am holding tight to the coat-tails of your optimism. Also the weather is suddenly mild ... positively tropical at the climbing wall yesterday evening after freezing brass monkeys last week.

Like you and a couple of others on here I'm astonished I haven't had covid yet. Been commuting to London for all but three months in 2020 and Jan to March this year. I would guess I've had it asymptomatically.

I appreciate there’s a lot of stress out there.  I think my stress-fuse blew in March 2020 which helps…. 

Been getting an inside scoop on the B5 reboot; much optimism abounds.  

Crazy mild out there; it cools off towards new year but it looks like a nice kind of cold, wall to wall sun with mild winds.  Then, is that another warm spell building for New Year’s Day?

I think probably check back in on my tattered optimism in another 5 days or so.  

One way or another I don’t think it’s going to be a very drawn out process this time around.

Optimism about B5 has for me similarity with optimism for covid: I really hope something good will happen eventually.

I have seen all the TV films but not the Rangers series.

Most don't realise how many reboots almost made it to the public.

https://en.wikipedia.org/wiki/Babylon_5_(franchise)

In reply 

Just picked up Roy Lilley's morning post. He is a day out on the news (that Raab was waffling about this morning on BBC news .....as he clearly didn't want to admit the U-turn). Roys' timing is bad luck and his epidemiology is wrong but I thought it telling that an ex tory health advisor is posting something like this (and it's easier to forgive my own anger in the last few days).

"Hazardous

Don’t go to the office if you don't have to… but do buy a sparkly frock and turn up for the Christmas party. This is the sort of public health message you get when leaders don’t know what to do. When leadership lacks clarity and when leadership has run its course. When leadership is more worried about risking the support of a handful of seriously stupid backbenchers, than seriously thinking about the millions of people at risk.

Jab a million people a day… that’s the sort of leadership you get when it’s in a panic. Eighteen million jabs by the end of the month. That’s the sort of leadership you get when the leader can’t work a calculator. 

GPs tell me, they found out about the new target on Sunday night. The same time you did.

Let's get the envelope out and do some sums... Today is the 14th December, there are 17 days left to the end of the month… ignoring Xmas holidays. The NHS did manage a golden day when it vaccinated about 800,000 people in one day. Brilliant. The average seems to be around 350,000, but let’s say we can set off with half a million. Getting the capacity up and running to get above half a million will take:

 logistics, estates, locations, security, data, recruitment,checks, training...... and web-sites that work. Mmm… guess… optimistic, set it all up in 5 days? Dunno. All on top of the day job...... reducing the number of days of peak-performance, to 12 days.

If, on day one of the million-a day target, the NHS manages 500,000 jabs, that that means a short-fall of 500,000 is carried into day 2… making the target for day two; one million, plus the short-fall. On day two the target is; 500k deficit from day one, plus a million. If they crank things up and manage 600,000, the shortfall is 900,000. On day three the target becomes; 900k deficit from day two, plus a million. If they get to near-superhuman and manage 700,000, the shortfall is 1,200,000. On day four, the target grows; 1,200,000 deficit from day three, plus a million. If they manage a sweat drenching 800,000 the cumulative shortfall is 1,400,000.

… you’ve got a calculator and you can finish the sum for yourself. By the 31st December we’ve run out of days and still have a bow-wave of shortfall to ride-out.

Meanwhile the virus is doubling every couple of days. The NHS will bust-a-gut but… a million a day will not be enough and to pretend it is, is a fraud on the public. If everyone in the NHS, who can hold a syringe, is trained and pushed into the front-line, who will do the outpatients appointments, the GP appointments, the elective procedures and the community visits? 

How long will it be before, once a gain, the Daily Mail kicks-off about face-to-face consultations, missed cancer diagnoses and No19 caves-in again. The Machiavelli in me whispers;

BoJo knows a million-a-day won’t do it and failure strengthens his hand to face-down Bonkers-Steve-Baker and his bully-boys, for more restrictions in January. 

In a free country, I want to be free to get on with my life, I do not want to be a prisoner of the libertarians who want me to sit, unawares, next to the unvaccinated. I won't risk it. I'll be marooned on the sofa. Gimme a passport or at least proof of a current LF test. It is not the NHS that will fail. It is the government that has already failed. 

It is not the pressures on the NHS that will become unsustainable, it is BoJo’s premiership that is already unsustainable. It is not the NHS that will collapse. It is the Conservative Party that has caved-in.

A dangerous virus we will cope with, desperate leadership is much more hazardous."

 As long as Labour supports restrictions , Steve Baker really does not matter.There is a load of hot air from those MP's everytime and it cames to nothing. You can possibly read too much into what those group of MPs are aiming at if you are not careful.

He does and he doesn't, right - a prime minister who has to rely on opposition support to pass bills because he can't command the support of his own party isn't one with a long and rosy future ahead of him in a party as ruthless as the Tories, they're never shy about a change of leadership. And we know Boris puts his own interests first.....

https://www.reuters.com/business/healthcare-pharmaceuticals/pfizer-vaccine-...

3rd Jan.

Ballpark for what one might expect for the decrease in T-cell epitopes?

Or, put another way, 3x the hospitalisation rate of Delta.

Gulp.

But the 4th Jan would give a lot of kids a day in school. 

They represent the Telegraph scum, and a lot of people are captured by that way of thinking. The UK Destruction Group have had a huge influence on policy. The first lockdown was late because the whole government machine cocked it up, last winter the 10s of thousands of unnecessary deaths were the due in large part to the influence of the mass murderers on the backbenches. I wish we could just ignore them, but when you've got people in Parliament trying to kill large swathes of the population, it's pretty serious. I don't see how what they want is any different to poisoning the water supply.

Freedom, the one on the radio this morning told me.

They have a mighty funny idea of freedom.  

Pretty sure each member of the CRG should be required to do a 12 hour shift in a big hospital on Christmas Day.

Tattered optimism exits stage left? 

Depends heavily on what a 3rd dose dose to that protection against hospitalisation level.

I’d be a lot happier if nightclubs were closed immediately and a few other steps taken to slow things down whilst we find out.

That doesn't seem consistent with three weeks of SA hospitalisation data in the Indie SAGE presentation from last Friday.

Yeah, with the Police Crime & Sentencing Bill, we can see plainly that they've got no interest in "freedom", they just want to kill ordinary people because they hate them.

This figure stuck out at me too. However, my understanding of the early South African hospital experience with Omicron is that a very high proportion (90% in one hospital in Gauteng) of people with covid in hospital were incidental - ie they were there for something else and found out they were positive through testing in hospital. I don't know how reliable some of these reports are but it does suggest there may be a lot of asymptomatic infected people around. It makes intuitive sense to me as a layman, with a more transmissible variant, that people who previously were exposed but resisted picking it up might now have it for a few days but be asymptomatic.

I'm looking out for the next ONS survey with interest to see whether it suggests a much bigger gap between infections and cases than previously.

Definitely. 

It's worth looking back to figure 2 in the link below - it's reinfections detected by random sampling by the ONS from the delta era. For most people - excluding a few with low Ct infections the first time around - upon reinfection there is:

• Much lower viral load inferred from the Ct value
• About half the prevalence of symptomatic infection

Won't translate directly to omicron reinfections or breakthrough infections, but it's pointing in the same direction.

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

Sweepstake news:

https://www.theguardian.com/world/2021/dec/14/more-covid-curbs-possible-but...

Does that make it more or less likely to be after Christmas, now that Raab has said after...?

The estimated 200k infections a day is the first bit of slightly good news I’ve heard on Covid for the last couple of weeks. Terrifying growth, but if prior infection and double vaccination didn’t prevent bad outcomes in the vast majority of the population we’d already be seeing a massive uptick in hospital admissions I think.

The Omicron juggernaut is in motion, and given what looks like a very high level of asymptomatic infection, can’t be stopped at this point. I’m not sure a lockdown would work if 90% of the population are asymptomatic…

Fingers crossed for boosters to go in arms quickly and for boosters delivered 3 months ago to still be holding up (probably the more pertinent question in my mind).

Re LSRH’s sweepstake

As Rob says above, I’m sure all teachers will be planning on it happening the day after schools go back. Again.

Is it just that re-infections which presumably make up quite a chunk of the early omicron wave are not being reported as new cases? If delta is falling slightly too (seems unlikely given town is heaving still) that'd further mask the fraction of new omicron cases presumably growing in the headline figures for a a week or so maybe.

26th

jk

The day after we have to confirm our Christmas dinner order from Ocado.

(Yes, I know, first world problems.)

I wonder if they do PCR tests?

https://www.bbc.co.uk/news/uk-59651166

That's pretty shit. Getting a home test kit always adds at least a day to the time to get a result back because of the posting timescales. I wonder if it's just high demand, or if a lot of the usual resources have been moved to the booster programme. (Edit, it does look like PCR testing numbers have just hit an all-time high)

Wintertree might have to exclude an extra 2 or 3 day's worth of data by this Saturday...

Openshaw on the BBC news right now in agreement on my point on SA hospitalisation (including new data)  being better than that research study kirsten linked might suggest for omicron. 

The hint on the BBC news for the lack of PCR tests was a distribution problem.

It's more a case of slipping the update by a day or two; to try and unpick the weekend sampling low on the leading edge - and for general consistency with the day-of-week effects - I really need good data for a Monday, so pairing back points fails that.

Not I think much point in. dealing, it doesn't seem likely to me that testing is going to be able to keep up for the next couple of weeks..

A funny thing happened, I read that article and found myself having some respect for Raab, when he called out one of the cognitively deficient MPs from his party:

Defending the government’s plan to introduce passes to show vaccine or test status, Raab said it was “crass” to compare the measure to Nazi Germany, as rebel MP Marcus Fysh had done. “I don’t like that kind of language and I don’t think it’s appropriate,” he told BBC Radio 4’s Today programme.

Perhaps Fysh is a UKC poster, it would explain a few things from another thread yesterday.

In reply to VSisjustascramble:

In terms of sending cases in to decay, perhaps not.  In terms of stretching the peak demand on healthcare, unarguably yes.

The doubling times for London continue to get shorter (worse), and looking at a similar rate constant plot for Scotland, Omicron would appear to be dominating top level cases there too.  

Top level cases in England aren't taking off yet, but it can't be long.

Demographic plots for England and London.  

• Another day off the doubling time for 25-30, now down to just under 3 days.  
• The surge in the growth rate for ages 85-90 has grown, but there are very low absolute numbers under this so it is going to be more twitchy to noise.  For now.

Vaccines

• The results of opening up the booking system and adding capacity have - I assume - led to another outstanding growth in terms of doses given on a specific weekday
• Yesterday's total is up by 186,000 over that from the Monday before, an increase of 56%.  Usually, Mondays are the second lowest day of doses in the weekly cycle, this is higher than all but one day of the week from the previous 7 days.  It's setting high expectations for today's total...

A bit weird how 85-90 is going up a lot in London but not the other older age groups. I wonder if it could be one or two big care home outbreaks? Even then I'd have thought it would affect others over 70 to some extent.

I've put an actuals plot in.  It's low enough with significant day-of-week effects that I'd treat the leading edge measurements for older ages as very twitchy for now, but it's clearly rising significantly.

I suspect it's quite stochastic - as you say, an outbreak or two at this point - and different bins will see that break-through their relatively stable baselines at different points in time.

Island mansions aren't all they're cracked up to be you know, I've got to work from mine as from tomorrow now!

We have 3 confirmed Omi cases here as of yesterday. The first was a recently travelled person who identified as a contact of someone in the UK with it and got tested ASAP, one other was a contact of them and I'm not sure about the third.  Our current 7 day infection rate is 822/100k pop., down from a peak of 1235 on the 7th but still way higher than the UK.  Theoretically virtually pure Delta cases.  We're seeing  124 new cases a day, which would equate to ~124,000 in the UK which has ~1000 times our population. 3 people in hospital, equating to 3,000. The decline is pretty much due to a mask mandate in public buildings, non-classroom areas for secondary schools, shops and wfh encouraged. Obviously people are being more careful in general as well - town was only about half as busy as it would normally be at this time of year on Saturday night.  Notice came out today saying schools will shut on Friday instead of next Wednesday (but kids can still go in if their parents want them to - school is essentially childcare for many), and we have a government briefing at 6 tonight which will discuss current case levels Omicron and strengthen the wfh message apparently.

I suspect it'll be a re-run of the previous waves where workers & students took it home with them as they fled the capital.

Sajid Javid in the commons - doubling time 2 days, estimated 200,000 cases yesterday - 42 times the confirmed Omicron cases.

Gulp. 

Is that an SGTF percentage doubling time?  I think delta is probably heading in to decay which means the omicron doubling time is hopefully longer than the SGTF percentage doubling time.

Its not the omicron confirmed vs estimated total gap that’s interesting so much as total cases vs estimated total.  Edit: All-though that distinction is fading rapidly with time…!

Could be worse. The demographic plots show its mostly in young adults.  How that sloughs out to other ages is where the worry really sets in.  

Currently it’s spreading mostly in ages with almost no 3rd doses (let alone 3rd doses + 1 week where the effect really kicks in), and so we’re seeing transmission unmoderated by a third doses.

Control measures tightening up.

Lots of reasons to expect more moderate growth in older ages.  

End of university term however as Toerag notes…. Big movement events happening right now.

"Omi" = "Granny" in German. I had to read your second sentence twice, having automatically read it as "3 confirmed Grandmother cases"...

On a lighter note, Ch4 news - guy in Scotland says "I would love it if it was limited to 3 households, yes, the thought of spending times with my in-laws, is er, I'm not looking forward to it".

That will go down well with his wife and in-laws.

Some more views on the press release from discovery health SA data:

https://www.sciencemediacentre.org/expert-reaction-to-press-release-from-di...

For the record, I am not Dr Peter English despite these comments from him:

It is hard to understand why, when you could look up the number of HEPA filter units in every classroom in New York State before the 2021 summer holidays; and when we have known for over a year how to control spread in schools, hardly any of the mitigations we should have put in place before schools returned after the summer break are widely in use; 

I'm flabbergasted at how much confusion there is over HEPA filtration. There's an HSE example that recognises it clears viral load from recirculated air, and CIBSE guidance touches on it in terms of where to put a portable HEPA filter, but there's no clear, categorical, criterion based advice for where HEPA filtration (or biocidal UV treatment) can be used as an alternative to forced external air ventilation.  There appears to be a lot of inertia and a lack of clarity on this at the local authority level as a result of this.

“(I prefer to refer to “third dose” than “booster” because it has become clear that, at least with current vaccines, the primary course must comprise at least three doses.  I would apply the term “booster” to doses given at least 12 months after the previous dose.)

I've been trying to exclusively use the term "third dose" in posts given that it results in way more gain of immunity than is lost by waning.

I missed your last reply on the Babylon 5 front; I had plans for a coffee meet in a few weeks with someone from the show, but I think Omicron is going to torpedo that six ways to Sunday; still - how cool would it be to land a small part in the reboot?  I'm also hoping they bring Neil Gaiman in a bit more across the writing, and definitely need to bring Ian McShane back.

My wife's German, I have lots of fun with this :-D

My first thought was "Allez Opi Omi!"

Forgot to mention the live case count currently 677, was 912 at one point - equivalent to just under a million in UK terms.  Briefing says we now have 6 Omicron cases from multiple sources i.e. it's in the community. New additional rules - masks compulsory in places like cinemas, churches and theatre situations (unless performing).  Omicron cases now treated as Delta cases (they did have to s.i. regardless of vax status, now have to do 10 days LFTs if vaxxed or s.i. for 10 days if not). WFH where possible. It's all about flattening the curve whilst boosting.  I had mine today (age 45, scheduled appointment working down through ages i.e. anyone older getting jabbed when they were supposed to should have been boosted).  They're increasing the number of drop-ins available and probably opening them up more - currently only >45s second jabbed before 14th September can access booster drop-ins (and it was >50s until today).

Indeed, though increasingly unlikely perhaps. I do find this focus on Xmas somewhat amusing as I don’t celebrate it either. My family and I celebrate NY instead, which I imagine will be subject to more restrictions, partly due to the passage of time and partly because cancelling NY isn’t a big deal for most people. Didn’t visit my parents last December. Might go over early this year to get ahead of any restrictions… 4 people from 3 households, limited social contacts, all double jabbed and 3 of us already boosted, LFDs beforehand - seems reasonable. 

26th for proper lockdown. 18th for some kind of additional inadequate measures which the CRG loons can rebel against at the next available opportunity.

Fairly predictable that changing the rules to let contacts do daily LFDs to avoid isolating would lead to a shortage of LFDs…

Question... covid obviously is here to stay, it doesn't appear that omicron is more severe, is this the point that any lockdown measure only apply to those not boosted? It's no good having vulnerable and single dosed mixing in restaurants with the boosted as they could still catch it etc, but perhaps society needs to operate with covid for those who gave taken maximum steps? It could mean some businesses survive and with almost zero additional impact on health services, it would of course require a pass scheme and whole households will need to be boosted for it to function well. 

Turns out royal mail was the rate limiting step there. Which would explain how it was fixed relatively quickly.

There are still shortages in pharmacies. Our local Boots said their last delivery only lasted an hour! I currently have a collect code but will need to travel more local pharmacies to see if there is actually anything available to collect.

Sure but the main new bit in the BBC article was about PCRs.

There has been a stall in the middle of our town's shopping centre for several days handing out as many boxes as you want. There appears to be absolutely no shortage here. I grabbed a couple of boxes and was told I could have more if I wanted. I first saw them there on Saturday, they were still doing it yesterday. Weird that there seems to be so much of a disparity in availability

Somebody using their brain and engaging it.  Pop up LFT shop.   Excellent.

Yes, I was delighted to see it. And it's just an open counter, so literally take them and keep going, absolutely as easy as can be! And loads of people taking boxes

People keep trotting this out, but it's more meme than evidence based science at this point.

Lots of people who wouldn't even catch delta are catching omicron.  For them, exposure to omicron is more severe than exposure to delta.

Thats not a good start when it comes to evaluating its severity on people who would have become gravely ill on exposure to delta.

It's far too seen to get an informed picture from the data.

There's a lot of noise being made but it all needs heavy caveats to interpret and translate between nations.

In terms of exclusion from venues, that's what we're moving towards.

In terms of actual lockdown measures, I think the degenerating situation in Europe and brief-but-failed flirtations with that concept showed (a) it doesn't work (b) riots.

Sure, this is the "learn to live with the virus" line that the Tory rebels keep trotting out.  It's beyond question that we have to move to a society that operates with Covid in circulation.

A critical part of learning to live with the virus is learning that we need good social welfare so people don't feel compelled to go to work when sick (or else), and we need well funded healthcare.  What we have, almost 24 months after the start, is...

• People on low paid jobs feeling compelled to go to work when sick - making it very hard to shield those most vulnerable from illness even amongst the vaccinated.
  • The vaccine seems to reduce someones effective age by a decade in terms of risk, but we have people two decades older than the point where Covid becomes a major problem.
• Healthcare that's almost out of capacity and has an ever growing backlog in many areas, and that has demoralised staff, decreasing staffing levels and ITUs that have been running at high occupancy for months with predominantly unvaccinated individuals with Covid.

Instead of learning to live with the virus, the government have singularly failed to prepare healthcare for the first post-vaccination winter.  

It starts to feel increasingly like what "learning to live with the virus" means is "f*ck healthcare and learn to ignore all the people dying of the virus or being pushed further in to poverty by consequences of it".

Ahem, sorry, got a bit political there.  I try and avoid it on these threads but, this is a clown shown.  93 of the muppets voting against basic control measures far short of what you suggest, and insane lies coming out about Covid currently killing as many as "the carnage on our roads" and comparisons of vaccine passports to Nazi Germany.  I think the first step of learning to live with the virus might be recognising that we need a very different government.

Edit:  New UKC feature - it asked me not to use inappropriate swear words.  I consider this an appropriate swearword...

Learning to live...I'm not suggesting total unlocking, but there could be mutations for the next 3,4,5 years and we won't know how severe each will be until several months into their spread. Boosted is considered pretty good protection if you're until say 60 with no existing conditions, these shouldn't be treated the same as a anti vaxer asthmatic. IMHO. 

Yeah it's harsh, two tier society and all. It's effectively what's introduced in sweden already, if you're fully vaxed you have more freedom to attend events than anti vaxers. Note: self testing doesn't count, it's fully vaxed or you're not coming in. Folk will still be ill, but a very very high percentage won't need any medical treatment. 

I think the uk is obsessed with home lft as being the answer, when vaccination is.

Note. The above does require a pass and credible id system.

Disagree.

Vaccination is not "the answer" - it's a step on the journey.  One that critically makes moving to endemic circulation without totally overwhelming hospital a realisable possibility.  The UK is close to the end of achieving that I hope.

The answer to me looks like endemic circulation with periodic vaccination applied to those more at risk and ever improving clinical care and therapeutics - much like we do with flu.  To begin with, periodic vaccination may be leaned on more heavily due to the number of people who've only had their first immunogenic events at a great age rather than as a child or young adult - a cohort only ever decreasing with time once endemic circulation is in place.. 

I'll outline my view of our journey to this point.  It's important to understand that we're not at the steady-state endgame but have been progressing constantly towards it.  What we've been doing has been part of that journey.  Times will change; I had hoped when the time was right for that change; omicron will likely speed the process up. 

We're basically at the limits for who will engage with vaccination in the UK.  

• There's been a massive rush of demand for 3rd doses, but the 1st dose rate has shown no change at all in response to the media outpouring over Omicron.
• We'll see if the vaccine pass makes a difference to the first dose rate.
• We either mandate it for everyone else, or we deal with the consequences of their vaccine refuel.  I've seen no enthusiasm for a mandate in the UK at all.

It's seems like the rate at which unvaccinated people are being admitted to hospital and ITU is decreasing.

• It helps to think of them as "immunologically naive" rather than unvaccinated at this point.
  • The question that predicts outcome is not "have you been vaccinated" but "how much immunity do you have?".  
  • Vaccines take the risk out of the first rounds of acquiring immunity.
• Their immune naivety is being ripped away by live infection, has been for months, and soon there will be an insignificant number of people left who are both (a) alive and (b) have never had an immunogenic event with regards Covid.
  • Right now, unvaccinated people loosing this immune naivety represent a threat to healthcare if their rate of infection rises much.  

Restricting unvaccinated people when times were good to control that threat to healthcare would simply have kept that pool of pandemic potential charged and delayed the problem.

• This is precisely why we saw case rates surging in much of Europe starting 7 weeks ago despite them having generally more stringent measures than the UK.  This was promptly followed by wide-ranging lockdowns.  
• The UK vaccinated a large enough fraction of the more vulnerable that it could then allow spread, and the LFT you say we're "obsessed" with was one of many mechanisms that were preventing case rates rising to much higher levels, which kept the rate at which the unluckier unvaccinated people were processed through hospitals to a sustainable rate.

> but there could be mutations for the next 3,4,5 years and we won't know how severe each will be until several months into their spread.

But in 3, 4, 5 years time there will be basically nobody left alive who is immunologically naive against Covid, and so long as it remains in endemic circulation in the mean time, people's immune protection against severe illness is going to get refreshed and track the virus, as it does for other circulating viruses that now cause mild respiratory diseases.  In 3 years time there won't be a large pool of working age adults who have no prior immunity against Covid and who are at risk of going to hospital if they catch it.  They'll either have died or recovered with some immunity and - hopefully - a new-found enthusiasm for vaccination.    

As an additional member of the viral respiratory pantheon it's likely to raise hospitalisation death rates for the most elderly and vulnerable, vaccinated or not.  That suggest's we need more capacity in healthcare going forwards.  I repeat my point that to live with the virus we need to improve healthcare, not bring it to its knees. 

I'll bow to your wisdom. It's possible that here they think there is increased immunity because schools have never closed and so on. 

Longer term, are the uk public prepared to pay more to better fund healthcare, they'll clap, but will they pay!? 

Time will tell.  We're two pretty different places with two similar trajectories through the pandemic compared to much of the rest of Europe to date, generally it seems with more voluntary measures on your side and more mandatory on ours delivering those similar pandemics; not unreasonable to expect that to continue.

They've been happy to fund a £120m RT-qPCR testing lab that apparently ran with no quality control when the funds could have gone to established NHS labs with established QA and GLP levels...

• https://www.bmj.com/content/375/bmj.n2535

It seems they've been happy to continue funding a second lab from the firm that, shock horror, may have major issues too...

• https://www.leicestermercury.co.uk/news/local-news/loughborough-lab-facing-...

They've been happy to fund £3,700m of contracts that raise red flags over corruption...

• https://www.transparency.org.uk/track-and-trace-uk-PPE-procurement-corrupti...

I start to think the willingness of the public to hand vast gobs of money over to the government isn't the problem here.  It's where it goes....

Omicron isn't the only thing growing at a bonkers rate.

The number of superlative words from experts in quotes on the BBC Live page is growing faster than monoliths on Europa. 

It's beyond question that a freight train of what looks like Omicron with mild symptoms is coming to the younger vaccinated, the big uncertainty is over how much that's going to convert to hospitalisations in the more vulnerable. 

With doubling times now of less than 2 days (!) being discussed, pretty soon we'll need a time machine to preserve healthcare capacity if it does show significant bleed through.

If ever their was a time to make some obvious closures for a week and to put out some fear-of-god messaging over isolation for the unvaccinated and more vulnerable, now was the time. 

https://www.bbc.co.uk/news/live/uk-59664383

I agree with pretty much all of that.  'Naive' already has a specific immunological meaning but I think what you mean is pretty close to it.  There are other, genetically determined, variables in both innate antiviral immunity (non-T cell, non-B cell mediated) and in antigen presentation (HLA, T-cell repertoire) as well as general health factors (age, BMI, comorbidity) that determine how well an 'immunologically naive' person copes with their first encounter - vaccination very largely de-risks the process.

I would say that your summary almost makes it seem as though there was a sophisticated and coherent strategy throughout.  Whilst I don't doubt that many of the scientific advisors understood it, I have a feeling that, given the political dithering, there was quite a lot of luck involved too. 

I agree with pretty much all all that.

Where I'm still not totally convinced is a big majority of people in ICU are unvaccinated (although most English reports say this is the case). The latest UKHSA report still shows roughly a third of hospitalisations are unvaccinated and a fifth of deaths. Both are easily explainable as the majority of the population are vaccinated and the vast majority of the most vulnerable are vaccinated. Most of the very oldest patients are nearly always assessed as gaining no benefit from ICU.

ICU admissions are low compared to hospitalisations so almost any scenario from a small minority to a large majority of the unvaccinated looks possible. We really need proper data across England on this. Scotland had a report of a small majority of unvaccinated in ICU in the summer.

https://www.thetimes.co.uk/article/covid-in-scotland-half-in-intensive-care...

Everything will shift a bit with omicron and the new medications of course.

What is certain is risks per age (and heath condition) of hospitalisation, ICU and death ARE all much higher for the unvaccinated.

Gulp! Batten down the hatches. Despite all sorts of advantages such as vaccines and everything we have experienced & learned, this looks very like the unconstrained growth of early March 2020. We know from late March 2020 what we can reasonably expect for a small fraction of a large number of cases.

Omicron is still Covid19 so the best we can reasonably hope for is a smaller fraction (mainly due to vaccinations).

> Where I'm still not totally convinced is a big majority of people in ICU are unvaccinated (although most English reports say this is the case).

Statements from individual NHS trusts and the Northern Irish government categorically stated this was the case to levels of 80% or 90% between July and September this year - https://www.ukhillwalking.com/forums/off_belay/the_unvaccinated-742037?v=1#x95...

I take this more credibly than individuals being quoted in media reports who had similar things to say.

Two factors that bias ITU occupancy this way over admissions are the length of stay in intensive care with regards vaccination status, and the age ranges likely to be admitted or not admitted to ITU.

• With vaccine uptake increasing with age, I think there's a bias where:
• Vaccine busting hospitalisations are in the oldest and most vulnerable who are less likely to be judged to benefit from procedures such as sedation and intubation
• There are more severely ill unvaccinated people in ages who benefit from intensive care.

So a reasonably interconnected bunch of factors over the demographics of illness severity, the demographics of vaccine refusal and the demographics of who is likely to go in to intensive care when severely ill all seem to reinforce here to mean the unvaccinated are highly represented in intensive care. 

Hard data on occupancy vs vaccination status seems to be lacking.

Regardless, we'd expect the fraction admissions and occupancy that unvaccinated to decrease over time as the pool of people with that level of susceptibility is ever-shrinking...  It's a shame the data doesn't copy/past in-order out of the weekly vaccine surveillance reports; that would have put a plot of the changing rates within easy reach...

So, hopefully there is an absolute lower number of unvaccinated people in ITU than a few months ago.

Agreed, although intensive care admissions also has an age component that needs to be considered.  

Agreed, but why not provide the data to prove it? It's an incredibly useful piece of information to help convince people to get vaccinated.

Just spotted a report on some worrying information on sequencing in London, especially so given it's the centre of omicron growth. 

https://www.londonworld.com/health/coronavirus/covid-tests-swathes-of-londo...

Might be worth asking at school, most of the ones I've been in have had dozens of boxes lying around.

Does it matter at this stage for Omicron?  If it isn't already dominant, it clearly will be within days so sequencing want tell us much.  It might, detect future variants, I suppose.

Of course it is, it might indicate areas in London which need some specific extra help.

Not if ~100% of cases are Omicron.  All you need is case numbers.

Given the difference in growth between Delta (circa flat) and Omicron (through the roof), I had two thoughts:

1. You can probably tell where is worst affected by which is growing fastest

2. Given how fast it's growing, by the time you've worked it out and put anything on the ground to help, it's probably too late. I don't in reality think most of our response cycles can deal with 2-3 day doubling - you look at up to 5 day gaps between announcing restrictions and them coming in, couple of day lags on case reporting, even the week or so lag after injection whilst boosters do their thing, and I'm inclined to think that anything that's meaningfully going to help needs to already be in train - boosters done already or about now, isolation of positive cases and potentially the end of school and a lot of workplaces winding down for Christmas and so on. Or it needs to be another Sunday night "nothings open on Monday, Christmas is cancelled" special in terms of immediacy.

Edit: I'm thinking particularly in the case of London or other hotspots in the above, areas where there's more time remaining will see more benefit from the booster surge and so on.

You might think that.  I couldn't possibly comment.

Ive just been told by a very reliable source, That R is 5.5!

It's worth noting that the rapid doubling looks to be solidly planted in younger adults, so actions yet to be taken - such as 3rd doses in older people - are still going to make a material difference.

We're on a pretty thin tight-rope between that one one side, and some real unpleasantness on the other.

Still time to grab the 15th...

"We've just had confirmation that Prime Minister Boris Johnson will lead a Downing Street press conference at 17:00 GMT."

Well, that would be interesting, because it nudges above many R0 estimates for Delta...  

I've come to the conclusion that the only thing that's really important is the race between 3rd jab vaccination uptake and Omicron growth. Either Omicron will win and we'll need a proper lockdown sometime soon, or vaccination will win and we'll all go "phew that were close".

All the other factors, vaccine passes, masks, distancing, etc. might affect personal risk but I don't think they'll make a significant difference to the main race.

Having come to that conclusion I can see that all the "new" restrictions that have come in (or are about to) are political in nature and are merely to soften us up for a probable lockdown.

I appear to be having a rather cynical lunch-break 😁

Kuenssberg said SAGE would be meeting with the leaders of the four nations this afternoon...

Can't be that reliable with no credible interval.

The unreliable bit will be me, Ive just asked for some clarification.

Cobra wasn't it? Same people, but they bring the red button.

Sorry yes I did mean Cobra.  I was too busy fitting the red light bulbs to get the details right.

Oh, following precedent I thought you'd merely got your papers in a muddle. 

A good contender, I'll give you that.

That was Roy Lilley's take.... softening up a broadly supportive big majority of the  population for a possibility of lockdown by exposing how mad his back benchers really are.

In rely to AJM

By response I mostly meant putting local trusts, ambulance services etc on high alert.... We don't know if that 9% is even random...it could be just Pillar 1 and missing nearly all omicron cases. From the S gene drop-out data a few days before, it was clear confirmed tests were well below 10% of the level out there. In any case it's a terrible idea to be in this phase of growth with substandard information.

I'll take it

jk

Apologies, I'm just being facetious. Would like to know any source you can point to to support that figure though. I think delta has an R0 of about 7-8, so R0 of 5-ish for omicron sounds low.  Likely the effective reproduction number (R) of omicron is at least 3 I would have thought. 

Sturgeon said between 2 and 3. 

I think similar, but I doubt they will go for a lockdown. I think those in charge are aware that many folk will be going ‘we get 3 variants a year - at this rate we will be locking down every Christmas.’ 40% boosted and I heard that you get the benefit of the third jab quite quickly (days, not the 3 weeks like the first jab).  

Might make more sense to shift Christmas to summer - I can see this happening every year for a good while yet. 

My reading must be out of date, I had estimates in my head of around 6 for Delta R0.  Well, doesn’t matter know, the whole topic of Delta’s R0 is about to be out of date…. 

I though “3 names” was referring to the effective reproduction number of the variant rather than R0… 

Fair point, assuming there's still a material amount of older age boosters yet to go. I've lost track of whether it's in the available data - is there a saturation (boosters/second doses) ratio available by age bucket? I had assumed most of the boosters yet to come will be to sub 50, say, but you know what they say about assumptions...

Id assumed the message I received was referring to the current UK R.

but  may be wrong which is why I asked for some more details ( which as yet have not been forthcoming)

I haven’t seen an official “saturation level” for third dose eligibility; there’s a pot on the tail end of #55 with one made by shifting the second dose curve right by 3 months, this doesn’t account for deaths amongst the eligible however.  This was also used to look at % completion and libretto projected time to completion by age bin.  Things have spend up since then…

Whats your view on the position in Europe. I am assuming that they are going to be catching up on us very quickly and are probably only a week or so behind us.

Age buckets with 1st, 2nd, 3rd jag uptake 

"Category","Received First Dose","Received Second Dose","Received Third  Dose"
"12 - 15",61.7,2.8,0.4
"16 - 17",79.1,30.7,2.9
"18 - 29",79.4,70.7,9.8
"30 - 39",85.2,78.8,17
"40 - 49",92.3,88.4,38.1
"50 - 59",98.2,96,63
"60 - 69",100,100,90
"70 - 79",100,100,94.7
"80+",100,100,89.1

Age buckets with jags administered in last 7 days. Age 60+ only 30,000 jags so largely saturated at about 90% 3rd jag uptake (or if you prefer as complete as it ever will be on the ultra-rapid omicron timescale).

"Category","Combined","First Doses","Second Doses","Third Doses"
"12 - 15",0,3645,2042,217
"16 -17",0,805,6284,981
"18 - 29",0,935,3331,15908
"30 - 39",0,461,2059,31203
"40 - 49",0,197,1026,92460
"50 - 59",0,111,539,119068
"60 - 69",0,64,253,23083
"70 - 79",0,33,114,5906
"80+",0,11,51,3955

Data taken from https://www.travellingtabby.com/scotland-coronavirus-tracker/ where it's well presented.

Omicron is definitely showing up in the case numbers now

78,610 - highest ever reported today - up over 30% in a single day

Looking overseas, I'm less worried about Europe than Asia:

https://12ft.io/proxy?q=https://www.ft.com/content/afc1eecc-8b3d-4b98-8b65-...

Or the USA, hospitals full and plenty not vaxed. 

Not sure you're picking up what the ft is putting down there... Sure the USA has crappy vaccination rates, but a lot of Asian countries could be effectively back to zero. So the ones that managed the zero covid strategy have zero immunity. So if (when?) omicron gets loose in China ........?

Edit to add: also seems counterintuitive that an inactivated virus vaccine would turn out to be less useful against a variant. Was kinda thinking it would be one of the more robust technologies.

The article about sinovac is referring to antibody levels after two doses. Those are also inadequate if better after Pfizer et al. What's probably more important is T cells now and antibodies after a booster. Will be interesting to see how hard China try to stop Omicron spreading though, if cases turn up there in the hundreds or thousands - I suspect they will probably do city wide strict lockdowns again.

Worth noting that of today's big scary number of cases, more than usual are LFT. Compared to Monday in the last couple of weeks the PCR number looks by eye to be continuing the same trend (there will be a few more cases to add yet, which will make it look a bit worse) whereas the LFT number has taken off massively. 

Graph for England from the dashboard just now.

Good spot. Nice to know the people who snapped up all the LFDs are using them at least.

My instinctive guess is that the infection to test result lag is 2-3 days shorter for LFT as you don’t have to book it or wait for a result. so we’re only seeing part of the picture.. PCR will follow on ?friday

Complex situation.

They've got much less immunity across the population than us as a result of less vaccination in ages where it counts, and less spread of the virus.  So, they've already been forced in to much more stringent control measures, which should limit the spread of Omicron pretty effectively.

So, immediate term, I don't think we'll see it storm to prominence anything like as rapidly as it is here.  But the problem they face of how to move beyond lockdowns and hard control measures just got a lot worse....

Their set-back is however less than that faced by parts of Asia, as LSRH notes.  With vaccine escape and at least the possibility of a higher R0 again, their job of holding elimination just got even harder.

That, I think, depends strongly on the adjuvant.  As I understand it, it's de-novo synthesis of proteins that normally activates the T-cell training responses, and an inactivated virus doesn't do this.  The Chinese inactivated virus vaccines are I think adjuvanted with alum which as I understand it works buy pissing the body of in a non-specific way.  The novovax whole-protein virus and the Valneva inactivated one both have novel adjuvants which seem to be behind their magic.

They find out how well a poorly adjuvanted, inactivated whole virus vaccine protects health from a variant that escapes immunity-against-transmission?

That's correct which is why I said it will go up further - but it won't be proportionally as much as the LFT data. You can get a good idea of how much is left to add using one of the other graphs on the dashboard.

Good to see Peston at no10 doing his bit to prevent that ever-threatening chin to chin transmission vector.

Edit: and he begins with a nice hearty thespian throat clearing before mounting his high horse. Legend.

From the "clutching at straws" department - the number of LFTs being taken has rocketed in the last few days of data on testing.  You have to look at the actual numbers as the graph stacks them on PCRs and the PCR numbers aren't in.

So, some of that growth is increased engagement with testing.

In reply to thread:

Doubling time for PCR only cases at the top level in England remains pretty stagnant at around 35 days; Plot 18 (next post) suggests cases may even be falling in other regions - presumably as restrictions and changed attitudes bite in to delta before omicron takes off.

Doubling times for all cases in London are still shortening, 7 days measured by the week-on-week method.  The demographic plots shows them at around 3.5 days for the fastest growth age bands - much less change than over the day before.  Over time the top-level rate constant tends towards that of the fastest growing band.

Some disconnect between these doubling times (even for the fastest demographic band in the hardest hit area to date) and the ~2 days being quoted in the press.  I'm wondering if that's 2 days as applied to SGTF data, where falling delta (even mild restrictions were likely to send delta in to decay) could be causing the % of tests flagged as SGTF to rise faster than the absolute number...  Someone on here might even know the answer to that....

Whilst very sensitive to noise, some of the oldest age bands (low numbers from breaking the data down by region and age band) are still showing short and worsening doubling times.  That's the immediate worry in the situation to me.  

Plot 18...

• Shows hospitalisations unarguably rising in London now - the start of the rise is well out of the provisional zone.
• Suggests cases may be falling in many regions; take with some skepticism - I normally only update this plot on a Saturday, as the method of exponential fitting to the data is pretty sensitive to the weekend low when updated around Wednesday-to-Friday which may cause a false decay signal.  I should update it to the week-on-week method.  Still, no great omicron surges elsewhere yet.  Delta has been teetering on the brink of decay for moths, all it takes is a warm spell to send cases in to reverse - so it wouldn't surprise me if the new control measures and increased mass individual precaution aren't sending delta in to significant decay in some regions before omicron really emerges.    I do also wonder about comments from Toerag about the London Underground as a key difference in London.  

Plot 22 shows national level hospital occupancy rising.  

• It's been a bit weird recently where occupancy (x-axis) continued to fall but ITU occupancy (y-axis) didn't.  Probably related to the worsening demographic shift at the top level over recent weeks, but the hospital data isn't available with a good demographic breakdown to test this - at least not from the dashboard
• That fall is reversing, now we watch to see how much that translates in to ITU occupancy.

The vaccine plot shows another stand-out day for 3rd doses

• Tuesday (yesterday) is up by 265,000 doses over the previous Tuesday - 69% rise.

The vaccines demographic plot shows 3rd doses compared against 2nd doses given 90 or more days before - i.e. those eligible for a 3rd dose.  This does not take in to account that some of those people people will have died which could be a big biassing factor in the oldest ages, meaning the target is on the order of 5% to large and uptake is better than it looks.

Real race-against-time stuff this.

A rate constant plot for all cases (including LFD) in England - rising more than the PCR only one was. More of that to come.

Also an updated vaccine plot showing all age bins now the 3rd dose is available for 18+.  Take the project times to completion for younger ages with a massive pinch of salt as things are still spooling up there I expect. 

I know someone who works around China/Vietnam/Thailand and they say it's as though there are pockets of population who have resistance because of what they think could be less serious viruses doing the rounds there over the decades, not necessarily sars, but other stuff that's made the leap. And other cities or regions which are forced to lock down as numbers just escalate. They say these peaks and troughs don't necessarily correlate with vaccination rates, which aren't high. All rhetorical and void of evidence, if there is local resistance, they doubt they have any personally.

"People who have cold-like symptoms in London are more likely to have Covid than a cold, according to the scientist behind the Zoe coronavirus symptom tracker app. Prof Tim Spector told BBC Radio 4’s Today programme that most of the symptoms of Omicron were the same as those of a common cold, including headaches, sore throat, runny nose, fatigue and sneezing. Spector urged people with cold symptoms – and not just the classic Covid symptoms – to take a test. “Things like fever, cough and loss of smell are now in the minority of symptoms we are seeing,” he said. “Most people don’t have classic symptoms.”

How fast does the common cold spread, out of curiosity? 

It's hard to take the responses to Peston seriously. Boris lied again about parties and got the epidemiology wrong. The CMO and the lead doctor effectively covered for him.

Let's say omicron cases are up by a factor of 8 in the next week and it becomes totally obvious hospitalisation rates are serious enough to increase NHS pressure a lot (the SA data shows it's likely, unless growth self limits, given our older demographic, significant unvaccinated percentages and it's our winter)... what then? What does waiting gain us?? It just looks like finger crossing from our PM and public health leadership. Luckily I'm pretty sure most people will continue to act on restrictions on their own.

Hospitality looks to me to be out on a limb... not restricted so no state support but numbers will be right down with any remaining customers likely to be the most risky. How many more great restaurants, cafes, pubs etc will go to the wall?

Indie SAGE calling for immediate 'circuit breaker' returning to pre-April mitigations:

https://www.independentsage.org/emergency-statement-on-omicron-15-december-...

Common disease R0 values here:

https://en.m.wikipedia.org/wiki/Basic_reproduction_number

common cold 2-3, about the same as wuhan covid. Delta is 5, omicron.. more.

attack rate also depends on generation time but I think that’s similar at around 4 days.

Indie SAGE call for tighter restrictions. That’s a new one that I haven’t heard before.

It’s clear that Omicron is going nuclear. In my mind we have two options:

1. Lockdown now with similar restrictions to last winter until May. Spend another 200bn and then hope we get enough immunity over the summer to avoid a repeat next winter.

or

2. Focus on booster, keep limits of social contact minimal and accept the consequences. If cases are running at 1m a day everyone will be either dead,  immune or vaccinated by the end of February/ March and the “pandemic” phase truly ends in the UK.

I’ve got a feeling the government is leading towards number 2 at the moment, but who knows. We must have locked in 1m of cases a day right now, if we wanted to go for 1 it might be too late.

Why would cases hold at a million a day? What happens when a big fraction of the country is all sick at once with a disease that makes a small but significant fraction of them critically ill? How is that the better option?

At the moment someone dies for roughly every 300 detected cases, thatvs with hospital care available. Assuming omicron is as bad then that's ~3000 per day for your million infections a day. If 2/3rds of us get it this winter that's maybe another 120K dead by spring. You can probably double that at least if you tank healthcare. Are you really sure that's the price you want others to needlessly pay for your freedom? 

Jk

Do you have ANY idea what that would actually entail? No healthcare (no beds and no staff), massive food shortages, schools closed (no teachers) and the elderly dying in huge numbers (through lack of care as much as covid). I’d go as far as saying breakdown of society and riots in the streets we’re on the menu. Yes, I’ll get a thousand dislikes but I don’t care. I think this is probably not far off.

I think you're being a bit unfair. He didn't actually say that's what he wants. He said that's (option 2) what he thinks the Government is doing. I'm inclined to agree with him after this afternoon's press conference. It seems we are in for the ride.

Yes, good point. I misread the post, apologies. Still, I think the concerns are valid even if VS wasn’t saying that.

update on R for delta.. seems to be around 7 in the uk, while delta is about 1. So it’s 7 times more transmissible in the current scenario. Some of that will be immunity evasion and some with be intrinsic (R0). Hard to say how much of which, but either way it’s not pretty. R0 being double that of delta (so 10) isn’t unreasonable based on alaistair grants analysis (Twitter). Measles is the record holder at 15 (ci. 12-18)..

But it's totally impossible anyway. Once the hospitals are full, society goes into lockdown. Either the government mandates it, or some chaotic situation ensues which ends with troops on the streets. I don't get how anyone can believe that once the capacity to deal with people dying is exceeded, that there won't be a change in policy - it doesn't make sense. People in the UK aren't prepared to bury their own dead in mass graves, they won't just shrug it off and say "well at least the boozer's still open". 

This was nonsense in March 2020, and it's nonsense now.

We know exactly what's going to happen. The hospitals will fill up, then there'll be a lockdown. Probably minimal support (I wouldn't be surprised if pubs can stay open but no one's allowed to go!), lots of business go to the wall, NHS totally flattened, worst of all possible worlds.

Remember who's in charge. 

Really? Show me posts of his that admits a lockdown might significantly likely be required? Actually he can tell us that himself as if he does admit that, I might change my mind.

When we were facing delta he was in my view fairly harmless. However,  unless we get really good news soon on omicron, he does seem to be coming across as pushing a plain extremist line. He may well share that position with tory backbenchers but that just shows how extreme our politics have become. Extremism has no place on UKC imho.

A standard tool of extremism is simplifying multiple possible responses into two ...one the extremist doesn't like (so they make it sound as unpleasant as possible) and the other they want. In reality there are many grey scales between his 1) and 2).

If healthcare was totally shot and lots of people were dying unnecessarily I'm tempted to agree. I don't think it would be troops on the streets though, I just think most people would stay off them anyway.

This isn't definitely going to happen though. The strategy can still work if we have some luck with booster efficacy and omicron doesn't turn out too bad in terms of severity. We just don't know yet and it's obviously a big gamble...but then a full-on lockdown would leave big problems to be addressed down the road. It's also worth pointing out that healthcare being shot isn't black and white; it's a continuum and the Government will do a good job of presenting it as white for as long as possible. They did that last winter.

So when do you call lockdown on the growth we have when the already if it doesn't slow and the already broadly know hospitalisation rates (from SA) firm up? No one I'm aware is saying we definitely need harsher measures, let alone a full lockdown, but increasing numbers are saying extra precautionary measures right now are wise (partly as it may well be too late to reverse when an overwhelmed NHS becomes certain). Scotland has done this. Whitty and Harris are effectively saying ignore what we mandate, act anyway.

VS gave an indication of his views on further restrictions upthread with the snarky response to Offwidth over indi-SAGE's calls.

Jk

I think the uncertainty is a lot greater this time around.  There's something to be said for certainty because it encourages decisive action when the certainty is really, really bad.  Lots of uncertainty encourage hope and gambling...

There've been big changes since March 2020

Big changes in our favour for now:

• Most susceptible adults have 2-3 doses of vaccine in them, and most of the rest have gained some immunity the hard way in the last 4 months.  
• Two vaccine doses likely means only between 10% to 25% of the people going to hospital that would have gone this time last year if they caught Covid, and these people are going to spend less time in hospital as well.
  • Hopefully the rapidly progressing third dose program improves this further.
• Clinical care and therapeutics are moved on a lot from March 2020.  
• The rapid spread of Omicron is mostly in young adults (under 40) where hospitalisation was very low risk last year, even before immunity had built in the population
  • But.... are cases starting to bleed through their parent's ages?  Perhaps...
• So far, London is looking like a special case for this rapid rise - Scotland (Glasgow?) is following up but their crap demographic data makes it harder to grasp the key details.
  • Perhaps London is genuinely different (the tube?) or perhaps it's just ahead of the pack - either way, rules are tightening and that means the other regions should see their exponential rates more moderated than London.

Big changes against our favour:

• The number of MPs who are apparently disconnected from reality is growing, making responsive measures harder if we do get in to a bind.  
• Healthcare is not in a good way, not at all.

For now I'm holding off giving in to the view we're totally up poop creek without a paddle - a view that is rapidly spreading.   If we see cases exploding in ages 50-65 in London over the next few days that's a much more worrying sign, and likewise if the doubling time in young adults doesn't back off or the other regions start to show rapid doubling times....

In reply to Si dH:

If we put troops in to the care homes, we could free up 30% of hospital beds.  I don't understand why there hasn't been a really obvious, high priority effort to unblock the logjam running throughout healthcare.  

You'd only end up with troops on the streets if there were bodies piling up and the govt refused to act, and just said "suck it up". 

Yes. That's why some plan that involves flattening the peak starting now is required to avoid it in January.

True. But even if the hospitals can't treat everyone turning up, there is a point at which they can't process the people dying. That's a fairly hard limit.

Indeed. Some of those grey scales are outlined in the post he responded to.

A pity he didn't read it before replying.

VS reminds me in some ways of LordAsh who posted similarly when delta took off. 

Jk

The other big point is mandation forces government support for hospitality etc. We are crashing parts of our economy for no good reason as the cautious majority are voting en masse with their feet and will only get more scared from now on with the numbers.

I’m really brave coming on this thread to do sums, but these look so obvious I’ll have a go.

19% of over-12s haven’t had a first vaccine, and as Wintertree noted that figure hasn’t budged despite the coverage of Omicron. That’s 10million people, but of course some of them will have some infection-acquired immunity. I don’t know how many.

Today’s cases - 78 000, doubling every 2 days, gets us past 10million  before the end of the month. Nearly a third of the entire workforce. How many of those will be off sick at once is anyone’s guess. But it’s hard to see any business/ service/ school/ hospital functioning normally.

I can’t see how it’s a choice between “public health “ or “the economy”.

LordAsh2000 (silent of late) was interesting - I utterly disagreed with them on Covid (and pretty much everything else...), but they always recognised the consequences of how they wanted this handled, rather than lying or deceiving as the endless rain of pop-up posters have.  

I was horrified at how they wanted to proceed, but I could respect them for being honest about it.  Kudos to them for not trying to deceive others in to what they wanted.  Literally nobody else agreed with them, which was reassuring.

Of course. Obvious from the start, but it'll still be trotted out by the hard of thinking.

And we've got "public health vs. freedom" too. As if all your freedoms don't go instantly down the pan when society goes tits up due to healthcare overload. 

My back of the fag packet maths is:

- Omicron cases are doubling every 2 days

- Therefore an average person infects another every second day

- Someone who’s got Omicron is infectious for 10 days

- I.e. average person with Omicron infects 5 others

At the level of spread a bit more mask wearing or advising people to limit socialising won’t make a jot of difference in the grand scheme of things. 

I find it hard to see what effective measures you could put in to reduce the R rate to below 1 short of a lockdown. How else could you reduce social contacts to a 1/5th of current levels?

If only..... Don't let it put you off though. Nobody should be afraid to scratch the surface.

NIMS or ONS?

Is it though?

Plot here estimates it. Look for the one about "immunity wall"

https://12ft.io/proxy?q=https://www.ft.com/content/2b309e14-046e-4dbd-976f-...

It will self limit before it gets to 10 million, for reasons already mentioned. Not pretty.

It's not looking great for either.

I'm taking it as a tenant of faith that the purported 2-day doubling times won't hold.

(I say purported as I'm still a bit skeptical of them, given the demographic cases plots and a suspicion that it's all referenced back to SGTF % doubling times, which will be biassed if recent measures have sent delta in to decay.  Perhaps I'm just wanting to grasp at straws for security; it's very hard to tell from top level data when other cases are high)

Short doubling times have long been a feature of local outbreaks, and they rapidly lengthen I think because people respond to the outbreak by changing their precaution settings.  Somewhere about 30 threads ago I made a plot of rate constant vs cases/100k for all English UTLAs they really nicely illustrated this.  I also suspect it's a function of the non-uniform network of people; there will be those most socially connected and Covid will energise that network like a lightning bolt with a quick doubling time, then more gradually soak out in to everyone around the lightning.  

Then chuck in the sudden increase in LFTs feeding presumably extra asymptomatic cases in to the top level number (in part due to the new isolation or LFT rules?) and again I'm staving off the sense of rising doom.

Agreed, the economy is literally built out of people, and so it's built on top of public health.  

This whole situation could turn on a knife-edge, and I'd like to see significant more measures taken last week - or failing a time machine, immediately - to slow things down and give more time to evaluation.  Nightclubs and vertical drinking suspended for now would I think go a long way...

Cautious majority? Or responsible majority? I’m not concerned about covid personally having had it twice already and had 3 jabs. But I could still catch omicron and give it to 7 or 8 other people at random. I’ll try not to.

You and your wayward clubbing ways...

If I have my own way, I'm not going to meet 8 people in the next 3 weeks, let alone random ones...  Hopefully the closure of schools and many workplaces goes on to further limit things...

In reply to Longsufferingropeholder:

That is a happy plot.

I think indie-SAGE agree with you!

It’s complicated. Assuming there aren’t already antibodies capable of binding to the viral proteins then probably the ‘other’ bit of the cell-mediated response gets activated by macrophages and subsequently dendritic cells presenting munched up protein to CD4+ T cells (rather then the cytotoxic CD8+ we normally hear about in the context of killing virally-infected cells). Among their jobs is stimulating antigen-specific B cells to produce antibodies.

Thanks!  I hadn't yet managed to penetrate the literature to understand how a fully folded protein gets converted to fragments that T-cells can train against - something that must be happening with Novovax and Valneva given the data and press releases over their T-cell response.  That seems to be where their new adjuvants are making a big difference over the alum adjuvanted inactive-virus vaccines?

The protien-fragmentation approach presumably means that post-translational modifications could go on to obfuscate the information carried in fully assembled proteins vs the bits presented during de novo synthesis?  Now there's a rabbit hole I hadn't even thought of reading in to over Covid.  Especially around species-hopping and the different PTM machinery in different species.  

Long ago I spent some time helping someone analyse macrophages in data from florescence microscopy.   Watching them down a microscope creeped me the hell out.

Here is the data for you. Whitty referenced this source in his slides today, I didn't know about it before.

I think the 2 day doubling time thing is probably someone misinterpreting the confirmed Omicron case data for the 15th (and change Vs the day before) due to some data delays on the 14th. It's still frighteningly fast though, obvs.

https://www.gov.uk/government/publications/covid-19-omicron-daily-overview

Thanks, I'm glad there is some reason to retain a glimmer of hope. I felt pretty bleak listening to the press conference, and watching my profession completely ignoring it (we could easily stay open while putting in place social distancing just as we did before, it just reduces capacity; and for that reason it won't happen).