UKH

Post 1 - International Comparator Plots

I'll write this post on the assumption Omicron isn't going to change anything - not because I think that's the case (I certainly hope it is...) but because it's the only sane position to start from.  For now.

The phase-space plot looks very swirly this week as nations turn towards decay as a result of nations moving towards lockdown level control measures.

• Of the Western European nations, Belgium and Switzerland remain in growth whilst also having high daily case rates.  Probably time to do something about that. France is not so far behind.  
• Austria is in decay and is days away from the end of their 20-day lockdown.  The results of that probably come to a head around Christmas time.  
• Nordics - Norway and Finland continue to grow cases at a more moderate doubling time than other nations were experiencing before their lockdowns.  Sweden is experiencing rapid doubling as with France and Spain.
• Portugal has growth in cases levelling off, despite having continued to reduce control measures lately going off the OWiD “Stringency Index”.  Curious and interesting.
• Look carefully at the upper-left corner of the plot.  That’s a bit of South Africa’s trail.  There’s a separate zoomed-out plot to show it in full, and the next post looks at this a bit more…. If you're wearing peril sensitive sunglasses, this plot will appear black.

Looking at the actual and the extrapolated, "locked-in” death rates on the international comparison plot, almost all of Europe is now locking in extrapolated death rates in excess or far in excess of the UK,  with the only ones remaining lower being Spain and Sweden - for now.  Take the South Africa extrapolation on here with a pinch of salt as the change their is so rapid I have little trust in the extrapolation method (applying recent reasonably bounds of the CFR to cases), and as it’s likely the first surge of the new variant, bringing more intrinsic unknowns.

Link to previous thread: https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_54-...

Post 2 - Here Come The Drums?

So, we’re waiting for all sorts of data to come in on the Omicron variant, first identified in South Africa.  Lots of concerned noises out of lots of credible scientists, and some concerning data shared at the end of the last thread.

Speculation alert: The general feeling seems to be coming out  a a bit like this…

• maybe a bit more fundamentally transmissive
• most likely evading immunity - including naturally acquired - when it comes to being caught and tramsitted.
• probably: prior immunity likely to provide good protection from severe health consequences.
• changes to fundamental lethality as yet unknown.

Otherwise may disagree with my take there!   It’s all very speculative right now.  For nations able to remain out of healthcare overload with relatively weak restrictions through sufficient immunity (a rapidly shrinking list), a small change to the protection from hospitalisation represents a large threat to healthcare; as a drop of 5% could take us from 95% protection to 90% protection, doubling the number of people about to go to hospital.

To me, something like the above bullelt points - if they come to pass - reads like a recipe for speeding up the problems being experienced in much of Europe, and for tipping the UK over in to a level of growth that there’s not a rats chance in hell healthcare can sustain for very long at all.  Lets hope the 3rd vaccine dose staves this off…

To get an idea for the growth currently happening, I’ve done a plot  of OWiD cases/million/day data for South Africa, the United States and the United Kingdom.  I thought the USA would be an interesting canary to watch, given their lax approach to control measures, balkanised vaccine uptake and enthusiasm for super-spreader events [1].  This is plot SUU.cases.  

Looking at rolling case fatalist rate (CFR) estimates is critical context for these case rates - the plot cfr below shows what I consider reasonable bounds for the recent CFR in these nations; compared to the UK it’s about 4.5x higher in the USA and 18x higher in South Africa.  So, whilst the UK has more cases / million than the comparators, it has  less death per-person and likely therefore less severe illness 

Case rates are taking off in South African and the USA with gusto - the doubling time in SA is a kind unseen except in the early days of Covid when people were behaving in pre-covid ways, and in individual UK university outbreaks (much could be inferred from that).  The 7-day doubling time in the USA is pretty exceptional for western nations in recent times as well.  It doesn’t appear to be a result of enhanced testing inspired by Omicron as this plot [2] suggests they’ve seen a recent, significant decrease in their testing rates…   These testing rates certainly hint at obvious explanations for the differing CFRs.

To understand if SA’s rate is exceptional for its own pandemic history I’ve made a different version of the phase space plots - "SU.phase space (cases)" shows orbits for all the nations from post 1 above over the last year and a half; greyed out.  South African and the UK are drawn boldly in colours.  It looks a bit like a toddler’s been at a piece of paper with gusto, but you can see the general cyclical nature of waves of growth and decay.  The plot "SU.phase space (deaths)" shows the same for deaths; it’s much less dispersed along the x-axis, strongly suggesting that the dispersion of cases plots is in large part down to different testing efficiencies.  The cases version of this plot makes it clear that the situation is SA is exceptional both for its own history and in the context fo the whole of Europe.  

One interpretation is that they South Africa been relying on very high levels of immunity from basically population wide spread of their last waves, as well as partial vaccine uptake, to control the spread of infection. If it was, it doesn’t appear to be doing so any more.

The up-tick in the USA could be related to seasonality but it feels more extreme than that.  Give it another week or so - although the data from their can be quite deceptive given how much of a political football testing is in their culture war without end.

The UK is showing growth in cases as well, but in exponential terms (not absolute) and so far - for England at least - this isn’t outside the usual bounds for the short term weather effects.  Be nice if it stays that way.

So, we wait and see what the week ahead brings.

[1] https://arstechnica.com/science/2021/12/2nd-us-omicron-case-just-traveled-t...

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

Post 3 - Four Nations

Much the same as the last few weeks - little change in the top level numbers with the leading edge of the trendline being quite twitchy to the noise.    As the demographics for England show it’s not a steady-state however with the pandemic being squeezed in to an ever higher rate in an ever shrinking demographic pool, as immunity builds by various means.  Data for Scotland in past weeks has shown similar there.  A process that I thin was close to winding up pre-omicron; we wait and see what happens with that addition to the mix...

Post 4 - England 1

The fall in all measures except cases has been sustained for over three weeks now, hard to allocation how much is down to the new therapeutics and how much is down to the ongoing demographic shift to younger ages - driven I think by seasonality rising the exponential rate of spread, and rising immunity taking lumps out of that in older ages in particular.  

I don’t think the demographic shift can keep giving for much longer, at least until the 3rd dose is going in to arms less than 50 years old.  Without omicron, the next shift would be towards the steady state defined by an endemic situation withal dependant boosters.

Post 5 - England 2

The week-on-week method rate constant plot shows that we’re clearly back to slowly rising cases in England, excepting a blip presumably caused by disruption from Storm Arwen.   The demographic splits plots shows that cases are still falling in over 65s, and are rising faster in younger adult ages than in the school ages.

It’s great that cases are still falling in 65 plus, but rising cases in the band 15-59 isn’t great - whilst individually, very old people are much more at risk of going to hospital from Covid, there aren’t so many very old people; this bar chart [1] shows how ages 18-64 have contributed a very similar total number of hospitalisations as 65-84, making up about 40% of all admissions.  Much to my frustration the hospital data continues to be reported on very coarse age boundaries that differ to the cases and deaths data.

I think we’re about at the tipping point where the ratio of cases in older adults to younger adults has shifted enough (with the dramatic effect of the 3rd dose) that hospital admissions will be rising again, as we very nearly run out of older people needing to go to hospital, the fall in which had been masking the rising number of younger adults going to hospitals.  This is supposition on my behalf from the cases data, I haven’t looked at demographic hospitalisation data.

The descending blue diagonal of decaying cases continues to march down to younger ages on the upper right corner of plot D1.c

Plot 18 suggests that London is leading the return to rising cases in England, and potentially leading a return to rise on other measures too.  So far, this rise looks in the groove for the link to the weather and the current cold spell; I'll post an updated weather plot in a few more days when it'll be clearer.  This is where I might expect omicron to show through in the dashboard data first if it's bad news.

[1] https://coronavirus.data.gov.uk/details/healthcare?areaType=nation&area...

Post 6 - Scotland

Everything is falling.

In what was news to me, the band Steps are still a thing, and may have precipitated an early super-spreader event for omicron [1].

[1] https://www.bbc.co.uk/news/uk-scotland-glasgow-west-59521556

That’s started, had ours today, and that was with the 6-mth gap. 

Good, good.  I should go look at the demographic data before posting...  

Imagine having to admit that you caught the omicron variant at a Steps concert. No... uh... It’s not what you think... I was... uh... at a brothel or something.

Got mine booked for the 18th (44).

managed to pick up Covid this week so expecting to be super-duper boosted before Christmas 

They won’t give it you within 28 days of an infection… 

Curses!

Wow. The chart comparing cfr for UK, USA and South Africa is really stark.

Kudos for the reference to Peril Sensitive Sunglasses.

I read somewhere today - probs in the Guardian - that no-one is known to have died with the omicron virus. Do we know anything about hospitalisation rates or are the numbers too small for that to be useful?

Low numbers mean the demographics and vaccine statuses aren't well explored, so a selective picture can emerge in those early weeks. Beyond that, there's the newness of the situation to consider; it's only 10 days since the first case was reported, and recently it's been taking around 10 to 15 days from the onset of symptoms to death.   So until right about now, we'd not expect anyone to have died from omicron.   

So reporting that nobody has died of it is likely both accurate and irrelevant.

With both low numbers and the lags not fully played out on the earliest low numbers, it's a week or two too soon to draw any conclusions from top level numbers.

I've not seen any of this aggregated, bit early days yet; I imagine it will appear in submissions to SAGE soon enough.  A google for "Omicron hospitalisations" returns a couple of different stories about South Africa, neither of them at all reassuring; but with the rate infections are skyrocketing (perhaps worse than the cases plot suggests given the rising CFR over recent months) hospitalisation would be going up dramatically even if the new variant wasn't worse.

There's also the low vaccination rate to consider. If we assume that the vaccines have some effect on severity still, even if reduced from the other variants, the we can assume that our hospitalisation rates *should* (all fingers and toes crossed!) be lower as we have significantly higher vaccination rates than SA

Maybe, maybe.  

SA has had a lot of Covid infection, and what they lack for in vaccine induced immunity they perhaps have in infection induced immunity.  It's not clear to me which is going to provide better protection from hospitalisation against this new variant.  (Edit - for 2 doses of vaccine at least; the 3rd dose looks transformative against delta at least...)

One take could be that SA have had so much Covid and so much excess death (not well accounted to Covid) that they have already lost the most susceptible 0.4% of their population.  Which, if the new variant is not any more lethal, would mean we expect a lower fatality rate as the vulnerable are already gone.

There are so many different ways to interpret the situation right now that its a bit of a fool's errand perhaps.  Give it a few weeks and we'll know...  (In terms of immediate policy, I'm all for assuming it's bad news when making decisions - decisions that can be rolled back if it turns out not to be bad such news.)

Thanks as ever wintertree.  Really appreciate your work.

Thanks once again. A question on the numbers - the SUU.cases graph shows SA at c. 2.5 days doubling but the space plot shows c. 3.5 days. Are the cut off dates different?

A bit of musing. If Omicron is as bad as it seems in terms of spread in a population with a significant level of immunity, as you say our healthcare capacity won’t stand the pressure for long and my money would be on a lockdown by February. The straw I’m clutching is that SA’s immunity is mostly from infection and a lot of that will have been a while back, so may have faded, whereas we’ve done a fair few boosters for those who really needed them (I don’t know booster uptake levels by age). On the other hand, I don’t buy the ‘it’s only mild symptoms’ theory some seem to be promoting. 

Sorry; I meant to explain that.  The phase space plots suffer massively from noise turning them in to a jagged mess as it presents on both axes; so I do a lot more filtering for them.  That means a peak value or the current value of a rising or falling trend is lowered by the stronger filtering.

I think it’s one of those things people say when they don’t know what’s going on; no idea why.  I’ve tried to trace it down to hard evidence and have come up wanting.  If the virus isn’t more intrinsically lethal then this wave in SA should be milder, simply because of loss of vulnerable people and more immunity in the rest from previous waves. 

I’m probably being super thick here, but if SA cases are ballooning and deaths have not caught up yet, why is the CFR shooting up? 

 

Once again thanks.

So for various countries (especially SA) the message appears to be "we're pretty sure that something's about to hit the fan, we're not yet sure if it's shit or not"

And for the UK "whatever's heading towards the fan, if we're lucky might just miss us"

Thanks for again for everything (and tidying up NZ!)

IndieSAGE had some good data on Omicron on Friday. Slides and presentation linked below. In the YouTube link the Omicron bit starts from 10 minutes in. For once I'd say you should watch it, as it does give some hospitalisation information and quite a bit more where you might miss key emphasis from the slides alone.

https://www.independentsage.org/wp-content/uploads/2021/12/WeeklySlides_3De...

youtube.com/watch?v=fg0tnIl6CTM&

That, detective, is the right question.

There’s so much goes on behind the scenes, and I’ve not sunk the time into a detailed analysis of the SA situation to get to the bottom of it.  Nowhere else that I’ve found does this level of contextualisation internationally.  

The rising trend in CFR set in a couple of months before omicron was a concern.  This could be a “long tail” artefact of their previous wave if their deaths metric used by OWiD doesn’t have a 28 days cut-off, or it could be an effect where engagement with testing falls off when absolute cases and deaths are very low, leading people to not fret about the odd symptom of two.

Whatever the cause, it means I don’t think it’s fair to carry the current CFR forwards in the way the extrapolated part of the plot does.

I don’t understand why almost every single nation doesn’t report a rolling longitudinal CFR from medical records; the data is there.

In reply to Michael Hood:

Yup.  

> And for the UK "whatever's heading towards the fan, if we're lucky might just miss us"

We make our own luck, and of late the UK has I think been a standout in that sense.  A couple of key decisions that got a lot of flak are, in the fullness of time, not seeming quite so one sided.

Fate, protects fools, little children and ships names Enterprise.  Will it protect us?

Thanks. My thinking is that here’s little evolutionary pressure for a COVID to become less lethal. Firstly, the IFR is less than 1%, so doesn’t significantly impact spread. Secondly, most spread happens prior to severe disease anyway (people struggling to breathe don’t go to Steps concerts).

Thanks; the hospitalisation figure in the FT plot from John Burn-Murdoch sets the pucker factor to maximum.

https://mobile.twitter.com/jburnmurdoch/status/1466480113487392769?s=20

JBM has long been a stand out in the media when it comes to know what to plot and how to plot it; a point really driven home in the last month.

Yep... IndieSAGE Omicron presentation section had that and more. Worrying growth in hospitalisations in SA of primary school kids in particular was a big surprise.

Sorry; yes I was referring to the plot as from the presentation you linked, but I gave the Twitter link as JBM has more relevant plots.

The hospitalisation trend is half of what I alluded to with current Google search results above.  With cases rising this fast, everything is going to rise fast; there’s also a demographic trend to where immunity reaches high levels first, so there’s some chance this isn’t awful news but it’s not what any parent wants to read .  No sign of JCVI moving on micro-dose vaccinations for younger children.

The cynic in me says that if Omicron does hit children harder, there’s going to be a ‘think of the children’ media storm and we’ll see measures brought in sooner than would otherwise be the case - there’s always a silver lining...

TBH the data is a relief in a sense (the stuff on kids aside). To me, unless I'm missing something (especially in that curve of immunity escape vs infectiousness where omicron must lie somewhere) it's looking like somewhere around 'Plan B plus a bit' might even be enough. I do worry about our government's skill in foot shooting our way out of any potential success. Messaging is still a mess as we approach more xmas mixing, mask mandates were much softer than expected, working from home seems to be drifting away, ventilation improvement seems to have been partly vented out of the building, vaccine targets look 'ambitious', the most deprived and vulnerable seem to be getting left behind again (and external world help looks too poor).

I got the usual attacks on breaking the news of the SA tweet on UKB, first being accused of exaggerating risks of omicron and then effectively generating smoke whilst supporting the current government position (whilst doing neither). In particular I find it incredibly odd that after all we have learnt from covid some intelligent people are still saying lockdowns won't be accepted again (just as if covid cares about what we think..... if our already struggling NHS starts being overwhelmed, there is simply no choice).

A bigger question is (as posed by Farrar in the Observer today) is when will world leaders stop messing about and coordinate proper global action on vaccines. When will we stop 'rolling the dice' with a risk of a more dangerous variant still. I'd add what damage will omicrom do elsewhere where combined vaccination and infection based immunity is lower.

https://www.theguardian.com/world/commentisfree/2021/dec/04/omicron-proves-...

Thanks as usual. Have you seen the results from the Covboost study? Quite interesting. I could speculate that foreknowledge of this might have been the reason Javid spouted off on Valneva...

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02717-3/...

"Safety and immunogenicity of seven COVID-19 vaccines as a third dose (booster) following two doses of ChAdOx1 nCov-19 or BNT162b2 in the UK (COV-BOOST): a blinded, multicentre, randomised, controlled, phase 2 trial"

On SA - I'm disappointed there is very little data on provinces other than Gauteng that seems to be available.  I've seen little information also on how the testing strategy has evolved and how that might be expected to influence current figures.

I thought they were all making very valid points on the other channel. You were doing your standard “la, la, la, I’m not listening - look what the guardian says” and they were rightly calling you out for it.

In terms of your other points about lockdown compliance & the article you referenced. Personally I wouldn’t change my behaviour if we had a lockdown again. If we are really “closer to the start of the pandemic than the end” after two years then we need a rethink about how we manage it. Life is for living, not for enduring in order protect the NHS.

Besides, omicron might be too infectious to control with lockdowns (who would have thought measures to reduce the spread of a virus might have put evolutionary  pressure on it to spread faster?). That could make things exciting.

Covboost; I don't think the timelines of data submission and Javid's spouting match up.  I think production delays linked a week or two back seem more plausible, but who knows...

The Covboost results are very reassuring - and tally with what we're seeing in demographic case rates.  But, they are limited to serology assays for antibody responses; I'd expect Valneva to stand out more through T-cell responses and to perhaps have more robustness against the ongoing variation process, and none of these are covered by the endpoints in the Covboost study.  All very academic right now as the options on hand in volume are working fantastically against delta...  It will be very interesting to see what happens if they follow the study cohorts through the omicron wave...

OWiD have test numbers; tests-per-case have plummeted in recent days from ~100:1 to ~7.5:1.   Seems way too big and rapid a change to be mostly down to testing strategy.  The problem rapidly becomes lack of testing capacity in another week or so....  They'll more or less be flying blind.

In reply to Offwidth:

I am getting far too much insight in to institutional inertia and confusion over ventilation at the moment.  We could do worse than getting one of the people behind the design, commissioning and testing of state CL-4 facilities (because they will understand all this stuff) and making them a "Covid air handling czar"  with a remit of producing harmonised guidance across the HSE and CIBSE that gives rational, scientific and evidence driven criterion over air exchange rates, HEPA filtration and biocidal UV systems, and to build a field team to go and support organisations - large and small - in translating guidance to their facilities.  

Good point! 

All those new variants have come out of places that have been effective in controlling the virus, like Australia, and the Far East...and none at all from places like Brazil and South Africa, and indeed the UK. You've cracked it!

His comment was about breach of contract which was total bullsh*t.  Valneva were having difficulties building their factory as fast as expected due to Brexit related delays with supplies of equipment and construction materials. The UK government were kept informed about this and were positive until that f*cker Rishi decided they needed to save money, then suddenly Javid cancelled a 100 million dose order because when Tories need to save money they'd rather f*ck up a constituency in Scotland than one in England.

Probably Valneva were not going to be ready in time for the 3rd dose campaign. So to some extent the Tories had a reason for pushing out or even cancelling the order.  But they chose to lie about it and try and wiggle out of paying rather than be honest and fork out some money as compensation.

Valneva had strung out its cash flow as a small company trying to get their facility up and running in the face of Brexit related bullsh*t and the Tories hung them out to dry by pulling their largest order and telling the world they were in breach of contract and their vaccine was sh*t. Very likely the end result will be the facility in Livingston getting shut down and the production moving to the EU who have actually given them a 30 million dose order. They don't just have a Covid vaccine they've got vaccine candidates for other diseases including Lyme disease.  Total kick in the balls for Scotland's economy, as f*cking usual from these Tory scum. 

I think Si dH was referring to Javid’s comment in Parliament which was not about breach of contract.  

That is awful of the tories and I cant think of anyone else who would do such a thing. Still at least they only said they were in breach of contract and didnt take them to court as well eh.

Wouldnt claim the "intelligent" bit but I am really not sure that it will work as well next time round. Problem is the government took all that good will and willingness to sacrifice for the greater good and pissed it up the wall by repeatedly deciding the rules dont apply to them.

With that and the loons getting more and more organised I think there could be serious splits between those willing to lockdown and those deciding its too much hassle.

Genuine question as I haven't looked at the details, why can't the Scottish government fund it if it's such a promising investment? 

I agree; the latest round of lockdowns have had a much poorer reception in continental Europe and the same right-wing forces have been pushing on wedges here as well.  

We've seen most major supermarkets announce that they are not going to enforce mask rules this time around - too many customers not doing it and giving staff abuse over enforcement.

Total coincidence that the number 10 Christmas party story just broke...

Oh god! What have you done?!!

Did you catch the Andrew Marr show (might not be your cup of tea)?

The South African take on reinfection from Omicron seems to be that risk is very low if you’ve been previously infected.

“The second thing we have data on is re-infections, so as you know, after you’ve had Covid you have about a 1% chance, or perhaps even less than a 1% chance, of getting re-infected and even getting disease again, of course, by this virus [Omicron].”

Early days still, but some positive news.

In that interview they said it would be a month before they could comment on vaccine evasion - I missed this bit you quote but seems an odd disparity?

Understatement of the year.  

When I have listened to him for brief periods I don't find him the most enlightened of sorts.

Early days.  We'll just have to see.

Edit: 

I looked.  I normally avoid it.  It's been a while since anyone criticised UKC for the single-page, un-threaded layout but it's perfect.  Please, never change it.

Is that Dan back over there?

My two main critics on UKB are no fools. However as an ex academic union rep I've plenty of experience of dealing with the outcomes of incredibly intelligent people doing stupid things. This 'compliance won't work' line seems to be a clear political tory line rather than based on any evidence.  On compliance expectations I prefer to trust the ONS data and the general expert view. Even after Barnard Castle most people behaved well.

We always had gammon style bluster on UKC from posters saying there was no way they would follow lockdown rules, or not follow them anymore. In public there was always a minority of aggressive protest, I really don't see that has grown much. 

My counter anecdote is in my big Sainsbury on Wednesday  and in my local shops yesterday there was a step change from below half to significant majority mask compliance.

Hmm… how do I put this politely. Some people might think that you don’t have the most well rounded view of the world given your background. Presumably you lived/ worked in a bubble for most of your life and are now retired with an income not linked to the performance of the wider economy?

It’s not all or nothing. People aren’t either protesting or fully accepting restrictions. Towards the end of the last lockdown most people I know were “flexing” I.e. breaking the rules to suit them. Going round to the neighbours for drinks ect. I think the trend will continue if we were to lockdown again. 

Wasn't recent ONS data showing that compliance with control measures had been fading?

I don't see how an observation that the latest round of lockdowns across the water has elicited the strongest civil disorder yet is in any way a "political tory line".  

Compliance obviously isn't binary, and there's lots of different hints out there about how it might be received next time.  

If we did need a lockdown, I think compliance would vary depending on the reasons - being very different if it was due to a global threat from a new variant or if it was due to the choice of a minority to remain unvaccinated.  

Here's to hoping we never find out...

I really do have to comment on this. Basically you are saying we need to re-think how we manage the pandemic because they way we have been doing it isn't working because no one takes a blind bit of notice of it. Maybe more like China would help? Life is for living I agree but I don't want to live my life at the expense of those around me. Not just for COVID but for all the cancer patients and others who are struggling to get treatment at present. The NHS is what makes you able to go out and live life without too much worry about the consequences.

I admire your optimism. If it’s as bad as it looks, we’ll be in lockdown by February. Just imagine doubling or trebling current admissions of around 700 a day - you know what capacity is like…

The way I see it is that there’s a wide gulf between locking down due to an uncontrollable, novel pandemic and locking down due to a failure to maintain healthcare provision to a level needed to make it through something less than a stand-out bad flu season.  One is completely, undeniably justifiable and the other feels dangerously close to shafting people to enable the rundown of the NHS.

It is, but the pandemic can’t shoulder all the blame for the difficulties the NHS is in.  

Just think how much smaller it could be if we always used lockdown instead of healthcare to make it through the winter respiratory season.  A lot of lives extended as well.  I can see why some are wary of a creeping shift in the purpose of control measures and I think it’s a conversation that should happen without each side jumping to conclusions about the other’s stance. 

It depends on your existing behaviour. If you go climbing outdoors with one or two others, especially somewhere ‘local’, it’s hardly going to be an issue. If you go to an underground race with 100 other people, that would be a pretty irresponsible thing to do in a lockdown type situation. The reality is that in a lockdown most social interactions are cut as a result of certain business being closed or told to WFH and education switching to online learning. That’s what has the biggest impact.

Life is for living until you or someone close to you needs the NHS. Which is especially relevant for people who engage in high risk activities.

The current theory is it emerged in someone who had chronic Covid infection due to a weak immune system. Lots of HIV+ people in Southern Africa unfortunately. Farrar’s point about supporting less well off countries is well made.

As for lockdowns, of course they would work - if most of someone’s social interactions are cut, they can’t spread the virus as much (or at all, depending on how far their interactions are cut, depending on their family situation and job etc).

At the end of the day, regardless of politics, here comes a point when any responsible government doesn’t have a choice any more. We’re seeing this on the Continent already (again…). If we get through the Omicron winter without a lockdown, I would consider that a significant achievement.

So the main thing for me is I have a girlfriend who I don’t live with. Would I stop seeing her because of lockdown rules - not a chance.

Apart from that I do a bit of cycling (usually by myself), a bit of bouldering and I work from home. I consider my behaviour to be very low risk, although unlikely to be compliant with lockdown rules.

Off topic rant. It’s very easy for people like Offwidth et al to demand ever tighter restrictions, but lockdowns have a significant economic and social cost. I suspect why some people are so pro lockdown/ restrictions is that they’re largely insulated from the impacts of them (or are oblivious to them in the case of an ex academic union rep).

The Valneva thing is very odd. Even if they were late to deliver, we could always use those doses later or donate them. As you say, Rishi is keen to save money but doesn’t seem to see the bigger picture.

I don’t know if you fall within the bubble rules but you wouldn’t be alone in bending the rules a bit when it comes to personal relationships (edit - personally, I ended a 4 year long relationship last December due to Covid restrictions but that was inevitable really as it was cross border and I could see what was coming). As for cycling and bouldering, as you say it’s not a big deal, though I’d be avoiding highballs.

Experience has shown that introducing softer restrictions earlier on (such as WFH), underpinned by clear messaging, pays off in the medium term. We need to slow down Omicron as much as we can while people figure out how bad it is. This is pretty much what the latest SAGE minutes suggested.

Yes, and compliance has been weakening each time some far but it’s still pretty easy to achieve in some key areas - WFH which in turn reduces commuting and other interactions, shutting certain businesses (or making them takeaway only) which then reduces general crowding of city centres and associated public transport use, moving education online. We can’t stop Jo going to see his/her friends at home but even there with strong messaging a lot of people would avoid / minimise that or opt for a walk in the park (to that end, I actually wonder if it would be better to permit outdoor gatherings in small groups).

We seem to have digresses from the data discussion…

Totally agree.

It has been chipped away at for years (whilst politicians say empty words about how much they are doing for the NHS) the pandemic was bound to make things worse but has really brought home how far down we have slid.

It reminds me very much of the tactic used by some owners of listed properties, who let buildings fall into wrack and ruin before pulling it down when it becomes dangerous.

Yes, sure but I was talking about compliance being consistently higher than the tory back bench predictions throughout the pandemic.

The low point for mask use must have been around this ONS report when 70% reported wearing a mask shopping  but only 19% saw nearly everyone wearing a mask.

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

The Leicestershire tory councillor on East Midland today said almost word for word the same as someone here.

I will say it again that it really doesn't matter that the pandemic can't be entirely to blame if hospitals get overwhelmed if it's at least half of it. What else can you change to cut NHS pressure once all the non-essential work is delayed again?

In reply to Misha

My 'optimism' (if you can call it that) comes from the R~ 2 in SA with close to all the population having some immunity, what looks like a younger shifted hospitalisation demographic and their much worse vaccination/booster rates (plus an assumption of a lot of vulnerable UK shielding). I fully acknowledge it's a middling guesstimate of a wide range (and I don't have a clear idea how much to offset for the UK winter). I also mean a real Plan B +, not some joke version with the same shit messaging we have now and with less top down NHS interference.... that bit, of expecting the government to behave, is optimistic.

Absolutely not. Those who voted Tory can shoulder that blame in its entirety.

If we end up in lockdown this winter, it's because there isn't sufficient NHS capacity, which will be due not only to chronic underfunding but staff shortages thanks to Brexit. Then, while the vaccination programme has been good, it hasn't been good enough: 2/3 of covid cases and hospitalisations are in the unvaxed. Should've made being "vaccine hesitant" or an out-and-out anti-vax wanker a much less attractive option from the start. And also, we needn't have got the hospitals as full as they are now at the point where we're facing, quel suprise, a new and even more transmissible variant. 

Everything the government has done has either been stomach-churningly shit (all of 2020) or nowhere near good enough.

And those that voted for it will all be crying "boo-hoo, another lockdown" as if it isn't a direct consequence of their own choices.

As if by magic, as shopkeeper appeared.

Updated week-on-week rate constant plots.  The rate constant might be levelling off - the last data point is almost certainly suffering a lot of provisionality.  

The demographic splits show cases growing in younger ages and on the cusp of growing in 60+; this could be a sign that the effect of 3rd doses is now embedded, and that the weather link is returning but to a much lower number of cases.  We'll see.

The weather passband plot shows the medium frequency passband - this is a difference from a local long-period moving average (colder or warmer than normal) with noise on the timescale of days smoothed out by a short period moving average.  

• The last weather wobble has closed out - this was the warm spell between Guy Fawkes and Storm Arwen.  
• As well as the rate constant remaining in growth for the start of the warm spell (red shading on the plot) in disagreement with the usual relationship, the decay during the warm spell was tiny - normally the more extreme the deviation in temperature, the more extreme the deviation in rate constant 
• I think this is just a consequence of the lag playing out in an unusually complicated demographic setup involving school ages and then household transmission to older adults, rather than anything more ominously omicromnic.  
• The crossover to growth (in the passband - which tells us if the actual rate constant is higher or lower than the long term trend, not if it's actually growing or falling) has come right on time for Storm Aria, and so far isn't looking dramatic.
• So, it's a week to soon to really understand the impact of this cold spell, but at least the early alarm bells aren't going off.  

There's also a plot 22 update; the rise in ITU occupancy vs general occupancy seems to be reversing, and the trendline - which is very twitchy to nose - isn't falling so much as I'd like.  Perhaps next week's open-optioned poll can be "Plot 22 looks like...."

You'd have enjoyed earwigging the last conversation I had with my old next-door neighbour.  This general topic came up after they stopped me to tell me "what a marvellous job Boris was doing".  I didn't engage my brain before talking (Neighbourhood survival rule #2 is never discuss politics with any neighbours).  My view unloaded itself.  Pretty quickly they moved past your observations  to calling me a "bloody-leftist marxist academic" and noting that if I'd been in charge during the war "we'd all be speaking German by now".  I'm not one to back down on that sort of thing so I was quite relieved when a "For Sale" sign went up a few days later...

How history shape-shifts.... in real historical documentation you can read the Fail supporting the blackshirts.

R of 2 in a highly immune population with 40k+ cases and 700 admissions a day is pretty bad though - that would escalate pretty quickly. Unless vaccine immunity especially post booster is better than what they have in SA. It could also be that their overall level of immunity is considerably lower - I saw the estimate of cases based on deaths but would be interesting to see an antibody study.

When you say  a younger demographic being hospitalised - do you mean now compared to previous waves? I’ve not seen the SA hospitalisations data. They could of course be because it hasn’t yet spread to older age groups yet. 

Unfortunately most people don’t seem to appreciate two fundamental principles. You must pay for what you desire. And you must lie in the bed that you have made. 

You should have replied in German

It's pretty obvious surely that the members of our wondrous Government generally do neither of those things...

Why would the UK government go to court?  They claimed breach of contract so they could justify cancelling the 100 million dose order and not paying.  They didn't need a court order.  If anybody was going to court it would be Valneva to get a judgement the contract was not breached and forcing the UK government to make the purchase.

The company is pretty f*cked up by this because they were investing to build a facility to make 100 million doses of vaccine and stretching out their cash flow to do that with the encouragement of the UK government and were in regular contact with the UK government about their progress.

The factor that changed was Sunak deciding the UK government needed to start saving money.  It is interesting that the people who were formerly in charge of the UK vaccine purchasing program have both made fairly angry comments about the Valneva decision.

As you say it was interesting what Kate Bingham ( who also happens to be married to a Tory MP)  said about the Valneva cancellation saying it was short sighted as part of developing vaccine security for the UK.She pointed the finger at lack of scientific and manufacturing  knowledge in the Civil Service rather than penny pinching.

Considering her stellar reputation from the vaccine programme ( even though she is heaven forbid a  venture capitalist )I reckon that most people in this forum would buy into that view.

Jesus wept, these people really are f*cking idiots. You'd need to be off the scale stupid to close a vaccine research program after the last couple of years.

https://www.independent.co.uk/news/science/covid-vmic-variant-omicron-vacci...

Another day of data for the week-on-week method rate constant plots.

Cases themselves are at a high level in England, but the top level rate constant is remaining very low - showing the virus is only just managing to grow rather than decay. 

The splits plots show that cases in those aged 60+ are still just clinging to decay.  The reversal from the last cold spell is that cases are now rising more rapidly (exponentially speaking) in ages 15-59 than in younger ages.

One take would be that the last cold period raised immunity enough in the school ages to damp down growth this time despite the yet colder weather in this cold spell, but that there remains more potential for growth in 15-59.   There are many other possible stories behind all this.  It'll be interesting to see what the next ONS immunity survey shows.  I think we're defiantly at the point where hospitalisation from rising cases in 15-59 are going to take over driving top level change against a diminishing fall in numbers from over 60s.  Hopefully the growth in occupancy will be less from this age band.

So, a couple of weeks ago I said I found the future very uncertain over the cold spell - it was perhaps the litmus test that would show if the England had achieved sufficient immunity across its population to resist the seasonality driven growth storming across Europe.  Certainly the LSHTM paper shared in that thread was highly encouraging, and it's starting to look like that is indeed It.  A milestone on the way out of the pandemic phase.

It would have been nice to enjoy that moment without the threat of omicron coming.  

There's still a lot of talk in the news about how it seems less lethal and to have less symptoms; this could however be a big conflation - if it's producing symptomatic infections in people who were sufficiently immune to not develop symptomatic delta, we're hopeful seeing an infection that escapes sterilising immunity but that is still blunted in terms of health effects by the rest of the immunity.   This means the different outcomes could be due to the immunological history of the people being infected as much as anything - outcomes that couldn't have happened in such numbers without a variant arising that escape immunity-from-infection.   This doesn't mean the variant is "better", and indeed it could be worse for a person with no prior immunity, but if this is the case it would mean we move on to the first round of the endemic phase already.

 Another litmus test...?

Boundless optimism brought to you by the sponsors of Omicron https://www.cityam.com/from-covid-curse-to-blessing-coronavirus-experts-rel...

Mild in South Africa’s very young population where Delta and Beta has already polished off the vulnerable…

Having said that Fauci is sounding rather optimistic about it - might not all be bad news.

The wait continues.

Has this variant hired Saatchi & Saatchi to handle its PR?

I'll be over the moon if the variant turns out to be intrinsically less lethal, and that the apparent lower lethality isn't arising from some mix of...

• the demographic bias (or under-sampling if you like) of early outbreaks
• an effect of not letting all the lags play out
• the younger demographic in the SA population vs here
• an effect of the virus mostly spreading in a population with high levels of immunity from recent infection and vaccination
• an effect of the virus mostly spreading in a population that (given its demographic and the excess deaths figures) has had an exceptional loss of vulnerable people in the last year

In the mean time, we might just keep an open mind for another couple of weeks and not throw the doors open just yet...

Potentially South Africa will be the first country to truly exit the pandemic phase assuming your second point doesn’t hold true.

When you think about it, one country exiting the pandemic phase and so no longer having little reason to control infection (outside of care homes and healthcare etc as per other infections) would be a big step forwards for them, but in terms of variant generation and immune evasion having this step desynchronised between different nations probably raises the threat level for those other nations - especially for ones with big gaps in their immunity. 

I'd not thought that far ahead before.  

everybody loves a false summit

I don’t know how healthcare works in SA but they have a lot of poor people - do those people get a chance of hospital treatment or are they just left to die at home? Answers on a postcard. 

What, like COP26?

Ferguson apparently thinks Omicron cases doubling every three days in the UK, according to The Times front page. Can’t find more details outside their paywall. That would be consistent with SA but there’s a question in my mind to what extent the doubling time is due to imported cases, given numbers are still relatively low here. Probably clutching at straws.

also buried in here, although numbers may not be so low: 

https://www.theguardian.com/world/2021/dec/06/patchy-monitoring-means-uk-om...

Too much speculation about and not enough relevant data focus. Lethality of hospitalised patients isn't the issue, hospitalisation rates are the key factor and things look much the same to me as they did on Friday.

https://www.cidrap.umn.edu/news-perspective/2021/12/report-south-africas-om...

The Guardian had a focussed look at the harsh reality of id in the UK for the immunocompromised

https://www.theguardian.com/society/2021/dec/07/michele-brown-was-vaccinate...

Of course lethality in hospital is important. (a) we want fewer people to die, (b);if the severity of disease in hospitalised patients is lower then you can discharge them quicker, and/or change your thresholds for people coming in to start with.

The two things that actually matter and why we worry about covid are (1) death rates and (2) hospital occupancy when it is very high. Hospitalisation rate is one half of the equation that contributes to (2).

Well COP27 on the horizon, so in some ways - yes.

Suggestions of a 3-day doubling time for Omicron in the UK in that article.   I'll have that red light bulb when Met Éireann are finished with it...

I've been trying to find the right words for how I see this.

A doubling time of 3-days in the UK would mean a lot of people who are catching omicron upon exposure would not have caught delta upon exposure given our current doubling times of around 40 days.

Assuming this is driven by immune escape from protection against catching it then exposure to omicron may well be giving mild illness to people who would have developed no illness upon exposure to delta.   This means the average severity of detected illness goes down because we are adding lots of mild illness to the pool but critically it does not mean we are removing cases of severe illness from the pool. With this extra transmission, R starts to go through the roof once this reaches the top level numbers (i.e. more omicron cases than delta).  These people getting mild illness  have effectively exited the pandemic phase.  Call them Group 1.

Now consider Group 2 - people who would have been going to hospital after exposure to delta.  What happens to them after exposure to omicron?  If the answer to that is "hospital", the acceleration to R from Group 1 accelerates and compresses in time the process by which people from Group 2 are going to go to hospital.  

Nobody is in good place to take an acceleration of that process right now.  

I hope to be proved wrong, I really do.  (Edit: Preferably starting with that 3-day doubling time turning out to be an artefact of enthusiastic and enhanced testing around omicron...)

South Africa /Africa may have less obesity and western lifestyle related health problems, which covid seems to exploit. 

Raab on radio 4 this morning said that plan B wasn’t required for Omicron.

Not that I trust Raab, but does it imply that the government have got preliminary data back from Porton Down and have chucked it into their models? 

Seems bold to say no to plan B if a lockdown is potentially on the cards.

Also, demographics.

Hospitalisation probability increased roughly exponentially with age.  That's a staggering effect, and means small numbers of older people can completely transform the load on healthcare.

About 40% of UK hospitalisations are aged 65+.  

About 18% of the UK population is aged 65+.   For SA, it's less than 5% of their population.  A bit of basic maths and if all else was equal, they'd see 30% less hospitalisation than the UK just from demographics - but the differences are even more extreme towards the upper end of that band.

Well quite.  I'd take that to mean plan B at least will be in place sooner rather than later.  It really has got to the point that nothing ministers say  can be trusted or taken as a considered statement.

Added to which, Raab is a bit dim.

I  mostly agree with you  (given my tablet is a bit unstable I type quickly then edit ....I was caught out being sloppy with my words on my drafting there as for some reason my edit button seemed not be be working). Also the "Id" in the second part of my post should read "life".

What matters is total hospitalisation levels, certainly not, as my post could be read, new admissions. However, you can't discharge patients who are still very ill just because significant fewer die.

We simply don't have the full data yet from SA, let alone adjusted for our very different demographics. Having half the admissions rate per capita is not good news if this variant infects double or more per capita as delta as hospitalisation levels might be the same or more than now. 

So many of our NHS trusts are on their knees and any winter factors might push some of them over the edge. We can't expect to get through winter running hot on covid throughout.

Given this government will say one thing then completely change the message the next day I wouldn't read too much into this. 

Remember the plans for Christmas last year? All it will need is something "unprecedented" (i.e. known about for weeks) and Boris will be on TV at 5pm telling everyone they need to stay at home.

But only in a few days time to let everyone speed up their plans and hence render the christmas lockdown ineffectual.

At least he has cancelled his Christmas office party ( a sarcastic comment)

I think measuring a doubling time at the moment with Omicron is a waste of time unless you can do it with and without cases linked to travel. We had that data for Delta in the variant technical reports so I hope it will be replicated for Omicron as soon as the next report comes out.

Sort of agree, sort of disagree; there's a lot of space between an anecdotally reported 3-day doubling time and our current doubling time of ~40 days.  For sure in the early days travel importation provides some of the growth but there's also plenty of evidence of community transmission, so I expect R for community transmission is going to fall somewhere in between the two.  You never know, it might even be a two-digit number, which would be nice.  

Indeed. 

Omicron superspreading events in Norway & Denmark where 50+ people and >50% of attendees get infected sound very scary for attack rate or ease of getting infected.

I'd forgotten the choir superspreading events of last year so it turns out the high attack rate is not unprecedented.

https://www.cdc.gov/mmwr/volumes/69/wr/mm6919e6.htm

Perhaps the Norwegian & Danish events involved singing or shouting into each other's ears over background noise.

I'd say its unlikely to be double digital day doubling. If it's milder for most, as it seems, loads more people wont realise they have it to test and we are only testing about a third of positives for S gene dropout, with a 5 day delay (including some estimates of a thousand cases)

https://www.theguardian.com/world/2021/dec/06/patchy-monitoring-means-uk-om...

Just realised the first report with Omicron data was issued on Friday. Lots in there but obviously very preliminary. They have the travel graph so hopefully that will be useful over the next few weeks.

https://www.gov.uk/government/publications/investigation-of-sars-cov-2-vari...

Table 6 looks really odd.

Not sure what to make of it - if I’m interpreting correcting (I acknowledge due to the small sample size it has to be taken with a pinch of salt) then vaccines are still providing strong protection against catching it?

The next edition of that report is the one to watch - good to see how they're setting it out.  A few quick comments:

• Table 2 - throw everything but the kitchen sink at understanding it.  Good.

• Figure 8 - TaqPath coverage (the test with the primer sets that allow SGTF detection) isn’t great - one third or so - worse in the South West, better elsewhere.  Perhaps time for hardware/consumables supplies to collaborate on primer design?  IP issues abound.

• Figure 11 - eek

• Figure 15 - error bars?  This particularly figure would benefit from them.  Clearly travel biassed at this point, give it time...

Very roughly.

If vaccination did nothing you'd expect nine times more vaccinated cases as unvaccinated as 90% of over 12's fully/partially vaccinated.

There's only about three times as many vaccinated as unvaccinated so maybe 70% protective.

Am I right to say not very different to protection against Delta & other Covid?

See "Figure 21: Vaccine effectiveness against symptomatic disease by period after vaccination for AY.4.2 and Delta not AY.4.2: AstraZeneca (AZ), Pfizer-BioNTech (PF) and Moderna (MD)" on page 41 of previous technical briefing.

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/...

Delta is enough to put pressure on NHS at the moment so if Omicron is no worse for the individual that catches it but causes the number of cases to rocket that's not good.

As you say, to be taken with a pinch of salt.

Pinch of salt I think but it'll be interesting to see next week if it still looks similar.

Also, there are interesting vaccine tidbits in here if you can stomach the source:

https://www.theguardian.com/society/2021/dec/06/moderna-or-novavax-after-as...

mRNA clearly give the strongest antibody responses.

AZ and mRNA give similar T-cell responses.

But AZ followed by Novavax seems to give a stronger T-cell response than anything else, including double mRNA or mRNA followed by Novavax?

It's a good strategy, tell everyone Xmas is on. Folk will shop and spend, then on 23rd December you cancel it. The economy still had the spending, but you've reduced transmission, win win!!  

From a lot of such conversations I've reached the conclusion that

Leftist Marxist = Having empathy and using your brain

Neo-liberal freedom = f**k everyone and let me do what i want

Not necessarily, no.  Although the early modelling on ACE2 affinity isn't a great start when looking for silver linings.

Is it not possible that Omicron infection could result in less severe illness?

Sure, anything is possible.

But I've not seen anything that suggests this yet.  

• The point is that many of the "mild" infections reported in SA are couple well be group 1, and if exposed to delta instead they'd have had no infection instead of a mild one.  
• I'm giving an example of how lots of mild illness could be reported in a way that does not mean our situation with respect to hospitalisations or the vulnerable has improved at all.

Really we need to wait patiently for another couple of weeks at least to hope to understand this. 

Yup... 

Latest on the NHS:

https://www.theguardian.com/society/2021/dec/07/doctors-report-13000-cancel...

Remember in the early stages (like a few days ago, when that report was compiled) a big proportion of the cases would have been travel-related. And it's very hard to do any travelling unless double-jabbed. It'll be a bit skewed.

stealthy omnicron: 

https://www.theguardian.com/world/2021/dec/07/scientists-find-stealth-versi...

The rate constant for English PCR cases is doing a convincing impression of having maxed out  at a pretty low value; and there's signs of that in the demographic data - which has more reporting lag - as well.  The most recent point on the PCR plot might go up a bit more tomorrow with provisional data, but we also expect it to be higher than "reality" as it falls 7 days after the Storm Arwen reporting low, which will bias a 7-day method value up.

Stepping back from rate constants: I put in a plot showing absolute daily case numbers for each of the 3 age bands I've been using on the splits plots.  With no further decay in ages 65+ and with about a 20% increase in the daily numbers for the band 15-59 over the last week or so; we can see why the decay in hospital admissions has stalled and is reversing.

With the cold spell closing out in a few days, the ensemble forecasts converging on a couple of milder weeks ahead, very limited potential for the virus to spread in cold spells, and 3rd dose vaccination and live infection both going on at scale and being rolled out to all aged 18+, it feels like we're basically really nearly growth proof in England now.

Unless a vaccine escape variant comes along...  

Of interest to the thread.  I've just worked out the 7 and 14 day infection rates for Guernsey, Jersey and the UK.  Guernsey has the highest vaccination rate (77% of population, 93% of adults) but the least total infections (7% of population); Jersey is less vaccinated at 70% total, but more infected (13.8% of pop); and the UK even more so (68% vaxxed, 15.3% infected). No Omicron in the C.I. yet as far as is known, Guernsey and Jersey are both sequencing positive PCRs. Both islands are pretty much 100% Delta infections in this wave as you'd expect.

7 day infection rates

Guernsey- 1,235 per 100k and has been above 1,000 since the 26th and above 500 since the 16th

Jersey - 794 down from a peak of 889 around the 27th, above 600 since 16th

UK - 478 and rising, October peak was 488.

14 day WHO-style rates:-

Guernsey 2,035 having peaked at 2,233 around the 19th

Jersey 1,612 having peaked at 2,091 on the 29th

UK 913 and rising.

Hospitalisations - Guernsey's had 2-3 in at any one time for a few weeks now from a live case load between 400-900 cases (0.3-0.8%). Jersey has 12 in hospital from a live case load of ~1250 (0.9%), UK has 7317 for a live case load of ~550k (1.3%). UK has much more poverty than the C.I., fewer pensioners and about the same number of fatties.  I am surprised the UK hospitalisation rate is currently higher given the amount of previous infection, especially in the earlier waves when treatments weren't so good.

Guernsey was unrestricted until about a week or so ago when mask use in shops and public buildings was mandated, encouraged elsewhere, and WFH gently encouraged. Masks recommended in pubs, restaurants, and clubs, but not mandated in any way. This, along with people generally taking more care, has caused the infection rate to slacken off. Jersey has had similar restrictions to the UK. Positive cases in both islands have to self-isolate, contacts can go about their business if non-symptomatic, fully-vaxxed and do LFTs daily for 10 days or so.

  So, the data can give some idea of how things can go in terms of infection rates, vax levels, and non-pharmaceutical interventions. Obviously there is some overlap of infections and vaccinations (about 3-4% of infections in Guernsey in the current wave are amongst the vaccinated - 2158 people (nearly half the total number of cases)) so we can't infer the level of herd immunity accurately. Neither island has A&E pressure like the UK from what I can gather, although there is the backlog of elective surgery being caused by healthcare staff off work for the various covid reasons. Neither island is considering more restrictions this side of Christmas. Government advice is that you can go to your office xmas party as long as you've not got symptoms and you do a lateral flow test the same day. Many people are cancelling social events or indoor activities of course because either they don't have enough people to run them or they're being societally responsible.

Wow, if I follow that right you’re running infection really hot, enabled by good vaccination and a well curated health service?  

No local papers screaming about high case numbers in isolation?

The FT guy has done some interesting and optimistic-looking analysis of the Omicron data from SA just now:

Edit wrong link:

https://mobile.twitter.com/jburnmurdoch/status/1468310548609744904

To re-emphasise a later tweet:

So a couple of very promising pieces of evidence for Omicron causing less severe outcomes, but once again, this does not mean "Omicron is milder". As the endlessly helpful @rjlessells put it to us, this is what we would expect regardless given levels of immunity in South Africa.

I can't repeat this enough, and I'm getting concerned at how carried away people are getting with other interpretations in the absence of hard data.  It will be nice if they turn out to be right, but I'd rather we wait for data on how it unfolds in our country against our population in our climate first...

I agree - however, if we are hypothesising that previous infection with Delta or another variant significantly reduces the probability of severe outcomes with Omicron, then that in itself is also a good thing and was not a dead cert.

Edit: totally agree re: a good thing

I think this is where the immunology isn’t coming through in a lot of commentary, and where the focus on sterilising immunity assays and antibody fade is not so informative with regards to protection from severe illness.

The epitopes presented for T-cells are on the order of 10 amino acids long; there’s something like 1200 amino acids on the synthesised precursor to the spike protein.  So it would take about 120 uniformly spaced mutations to invalidate all the epitopes; but the mutations concentrate in certain subdomains that’re still optimising themselves for humans so most epitopes don’t change.  There’s also a bunch more proteins getting synthesised that have less variation going on and that present equivalently to the T-cells.  As well as effects on both types of immunity there are changes to intrinsic lethality to consider; RBD changes tend to be driven by increased ACE2 binding affinity which isn’t a good start.

Putting my amateur virologist/immunologist hat on (there’s some real ones here I’m always happy to hear from especially if I get it wrong!), in terms of sterilising antibodies this variant is like throwing a very big knife switch whilst cackling Hammer Horror style.  From a T-cell perspective it’s a bit like a few bugs on the windshield.

Another reason I think it was pretty close to a dead cert; if immunity from severe outcomes broke as easily as immunity against catching a virus we’d mostly all be dead already.  There’s a natural order to things - there has to be, otherwise there couldn’t survive as hosts with multi-decade lifespans.  There’s been nothing I’ve seen to suggest this virus is different to endemic comparators, the only obvious differences lie in population immunity.

I say “another reason” -it’s clearly not an orthogonal reason; the more I think on it, the more it starts to feel like two different immune components (B- and T- cell) have been honed by evolution to allow this order of thing so that we can track variation over multi-year timescales whilst also avoiding constant, endless, immediate re-infection, so that life doesn’t suck too much to hunt for food, and so that the inter-generational time and mutation rate of viruses is strung out as much as possible.

Edit; I could definitely be wrong here, this is my best take on it but there’s only one way we’re going to find out…. Preferably led by precaution at all times.

Indeed but they have previous on this. 

All the MPs will be getting it then…

So, Omicron without S69-70del.. what were we saying before WT?

Booster bookings allegedly now open for 40+ at 3 months. So if that's you, ignore the yellow box and give it a try.

https://www.nhs.uk/conditions/coronavirus-covid-19/coronavirus-vaccination/...

I wonder if it’s an insertion or an early branch from before the deletion?  Previous ones without the deletion were branches from before it happens I think; a bit less obvious here?  Insertion feels less likely than deletion?  I wonder if it’s the same codon?

The scientific version of the wheels on the bus…

In reply to Longsufferingropeholder:

Thanks for the heads up.  I’ve got a new plan for tomorrow now!

All well and good but currently those jabs are going into arms way too slowly and it's still not obvious where the extra capacity we need will come from. The original rate required was highly ambitious looking and it's growing all the time.

When I re-booked my 3rd dose this morning, looking around there were lots of vaccination centres nearby with many open slots tomorrow and this Friday; locally at least it seems we're strongly demand limited. Hopefully that will change today.

There must be a reasonable amount of spare capacity for their to be so many empty slots with a rate of ~385,000 third doses/day.

That's the spirit

They’re slow at jabbing where you are!

My booster is this Saturday and I’m in my early 30s.

There are bound to be big differences around the country. There were last time. I suspect this is the real reason for saying 'the NHS will contact you' rather than publishing an ambitious schedule to start with. They want to be able to hide the fact that some people are better off than others. No word where I am yet (late 30s) but didn't really expect my age group to be offered until late December going off the overall schedule.

Noticed some clarification in the news that the end-January deadline committed to is now only to 'offer' the jab and that the available dates to book for some over 18s may be after January. Feels like a backtrack since you could then meet the target just by opening up booking to everyone tomorrow.

Oh ... you will start me off again.

There is a big difference between empty slots and a lack of demand. The more complicated logistics of this vaccination phase are well known by those working on the vaccination programme but the government were not listening to them. After bashing on that square peg in that hexagonal hole for a while, they are being forced into paying attention. Notice how there are sudden adverts for volunteers now (a month too late). It takes time to get them jabbing: I know a vaccinator who just took three weeks to pass the training. Plus locations need booking, setting up and must be convenient in location and time for where demand will actually be.

Pick whatever words suit you, it seems around here there was a lot ability to give doses that was going unused.  That represents immediate, additional capacity now the booking system has changed.

I have no idea how much capacity was being unused nationally, but it’s clearly a lot more than 0 doses/day.

Good for you... if only those way more vulnerable in care homes were all jabbed already.

https://www.alzheimers.org.uk/news/2021-12-03/alzheimers-society-urges-revi...

I used the words: delivery logistics are key. The right places at the right times and with the right staff. My city has one of the lowest vaccination rates in the UK but we have staff shortages and queues at the most convenient places at the most convenient times! We have a real problem with the antivax community trying to disrupt things as well

This is definitely true.  We are well past the stage where quantity of vaccine available is the limiting factor in the UK.

All I’m saying is that there was apparently a lot of capacity going unused, and that now the booking system has changed it seems people are booking it.   That is some of the extra doses/day you are looking for.

I’m not arguing that there isn’t enough capacity at some sites etc if that the slack in the system was enough for any specific goal.

I’m not sure what I’m not explaining clearly here.

Ferguson on PlanB+

https://www.theguardian.com/world/2021/dec/08/omicron-covid-cases-doubling-...

I think it's more a case of 'feeling our way into the unknown' - we know we have good vax rates, and indeed there had been much call on social media in recent months to eliminate the travel testing and isolation requirements we still had in the summer.  It got to the point where pretty much everyone who wanted to be jabbed could be and the island couldn't stay travel-restricted forever, so government has been allowing the case numbers to rise steadily until the autumn move indoors caused the rate to increase. Healthcare-wise we're a bit better off than the NHS  - waiting lists for operations are normally lower and A&E doesn't get swamped, but then we have to pay for primary care (GP visits, ambulances and A&E) which keeps people out of A&E unless they actually need it. We are isolated with low levels of redundancy though - if the one orthopaedic surgeon is off no-one gets orthopaedic surgery unless we ship them to the UK, and of course the UK hospitals are stacked out anyway. We can't just bus doctors in or ship patients to the other side of the country like the UK did last Christmas.

Not really, but then the 7&14 day rates aren't published so many people don't know how things compare. Some people are screaming of course, but there's not really an alternative - although we could lockdown and go for elimination again it's harder to do with Delta and people don't like travel restrictions. It will be interesting to see how people feel after the Christmas party season is over - because we've had a lot of unrestricted society over the past couple of years people are thinking that the current glut of self-isolations, cases and restrictions isn't as much fun to 'live with'. Conversely, people are also saying 'there's only 3 people in hospital, why do we need restrictions?' 'Why do we need to wear masks in shops when people can go to nightclubs without them?'. I just tell them it's all about reducing the rate of infection whilst allowing the economy to function, and ask what they'd rather do - not wear a mask in a shop and pay more tax to support furloughing the hospitality industry, or wear a mask in a shop and have their favourite restaurant not close down.

I'm not sure why you feel I need you to explain. Our government promised all adults would get a jab by the end of January. They just moved the goalposts as that target now looks highly unlikely.

We will always have spare capacity in any realistic logistical plans. We here can drive up the road to a town where there are loads of earlier free slots. An hour and a half round trip outside rush hour is hardly convenient or cheap though, let alone the practicality of dealing with any immediate negative reactions.

Buried in the BBC news feed this morning:

“Away from the Downing Street party row, Prof Neil Ferguson, a key government adviser, has been talking about the spread of the Omicron variant across the UK. He says there is a rationale to telling people to work from home again.

He said case numbers of the variant are doubling "at least every three days, maybe every two days at the moment" and it was likely to overtake the Delta variant to become the dominant type of coronavirus in the UK before Christmas.

At the moment, it represents only about 2% to 3% of cases, but he said the overall case numbers would accelerate within a week or two due to its rapid growth.

Prof Ferguson said that with no action the Omicron wave was likely to peak in January but the question of what measures the UK would take was likely to depend on how severe an infection it turns out to be.

"At the moment, we don't really have a good handle on the severity of this virus, there's a little hint in the UK data that infections are a little bit more likely to be asymptomatic, but we really need to firm up that evidence at the current time," he said.

He said there was "a rationale, just epidemiologically, to try and slow this down" by telling people to work from home so there is more time to administer booster jabs, but it might be possible that a lockdown is required again.”

Perhaps that my pointing out there is more capacity in the system than we were using, which was literally a demand problem, which is available and being booked immediately now the booking system has changed, doesn’t need to be a jumping off point for endless negativity about everything.

Yes, but opening up the booking system makes use of much of that spare capacity by supplying more demand.  I’m not sure what’s so difficult to grok here.  I’m not claiming it’s *the* solution, but it’s a part of it.  

> Ferguson on PlanB+

When reading a doom and gloom Guardian-quoting-Ferguson headline I like to check back in on his earlier comments…

https://amp.theguardian.com/world/2021/jul/18/uk-covid-cases-could-hit-2000...

… out by a factor of 4 that time…

As Si dH has noted up thread, current data has a lot of travel importations and so doesn’t exactly tell us about local transmission.  I’m still hoping for a double digit doubling time; if not it seems likely we’re going to need a lot more then plan B+ pretty soon.  

Tell you what though, I’m glad that despite the politicised negativity from some quarters we didn’t spend the post vaccination late summer and autumn bottling up the remaining pandemic potential and pretending we could carry it through winter and future variants whilst taking pot shots at countries trying a different approach.  Because then I’d be bricking it in the face of winter and a variant with escape from neutralising immunity vs large pools of people with a high pandemic potential.

There is a bit more from Ferguson in the Guardian link I provided just above.

Another local problem we had was turning people away having queued in the cold for over an hour because they didn't know this.

"If you or your child are under 18 years old and not at higher risk from COVID-19, you need to wait 12 weeks before getting a 1st dose after a positive COVID-19 test."

Or, to look at it a different way, a whole bunch of people who weren’t catching covid on delta exposure and now catching asymptomatic covid on omicron exposure. 

I’m going to have to give up banging this drum soon before it breaks.

Understanding the true doubling time of omicron is pretty critical, that’s going to need to be strung out; WFH is an obvious step to start doing that…

Good news for the German health minister though, his timeline of spring 2022 for vaccinated/recovered/dead is looking more certain. 

I got my message from my GP and when I went to book there was loads of spare slots. Loads of them.

I’m not at risk, but I’m just doing my Civic duty to get boosted. 

Of course, if you prefer, you can keep going “la, la, la, I’m not listening - look what the guardian says”, or you could acknowledge the points people are making.

My 22 year daughter got hers booked for the 4th Jan.............

Website still updating as it won't let me yet.

Ferguson always used his modifiers correctly on his predictions.

I still think there is a significant chance Plan B+ might be enough with below dddt but we just don''t know yet. Hardly negativity. I've repeatedly praised the English early vaccination efforts (care homes and vulnerable people stuck at home aside...where I thought Scotland were better). I see this vaccination phase as broadly OK but not going anything like as well as it could, based on the opinions of people who work in it that I know: the biggest problem is not listening to local needs in a much more complicated process.

Some of those same 'negative' people urged JVCI to agree the vaccination of kids earlier and improve ventilation in schools and use masks in schools so there would have been less covid about and less disruption to schooling. Also to run a bit less hot to help the NHS and save lives (as improved treatments and boosters were due). We can't escape politics in a pandemic. Still we are where we are and need to focus more on what to do next.

Let's wait and see what happens with Omi in the EU... we will have a good idea by xmas but I'm mostly very disappointed with their leaders as well. My concerns are about avoiding practical failures (the political parties in power across the EU are varied).

I  am not sure where all the volunteers will come from this time. Those people I know who helped out last time were all at home furloughed and basically helped out as they had nothing better to do....

I am still surprised that there appears not to have been in place a contingency plan set up for a rapid booster programme. It surely must have been a scenario worth considering in the summer.

There again its easy to throw bricks at these things as it always takes time to set these programmes  up even with planning.

There was a good bit of wasted capacity in late summer as they were too optimistic on the numbers who would turn up but the planning problems were bigger since the booster programme started, but changing for the better at last.

On what our government might do with omicron, checkout Paul Mainwood today:

https://mobile.twitter.com/paulmainwood

"I despise politics. But...."

Ministers who saw no need for Plan B, apparently about to sign off on... Plan B: 

"Ministers are expected to sign off new rules to impose home working and vaccine certification across England in the face of rising Covid cases, the Guardian understands.

Downing Street said no final decisions had been made but ministers and officials convened on Wednesday to move to plan B and to begin imposing some restrictions as early as Wednesday night."

Yes, just leaked all over the shop.

It's almost like someone was trying to make Raab look stupid...or maybe he's just stupid.

(Of course, as I've seen pointed out elsewhere, the real reason for the plan B U-turn being announced today may be to cut short the airtime given to the Christmas party debacle, which apparently Johnson has just apologised* for in the Comms.)

*Yes, really!

Or to try and distract from the current screwup which wont help people buy into it.

Sorry, edited my post...yes.

So cynical..... 

Aren't we about at the point where there's a circular conga-line of farces all distracting from each other?

That's very good to hear.

It's sitting on record for me and I've just been watching the end of this (which was superb in covid content terms):

https://www.bbc.co.uk/iplayer/episode/m0012b15/the-richard-dimbleby-lecture...

The January goal doesn't look far fetched in terms of delivery capacity; projecting 3rd doses at the rate of the last couple of weeks and comparing it to a 2nd dose curve shifted right by 3 month (representing those actually eligible for a 3rd dose) they just about meet, and we might expect an increase in the rate now more people can sign up given the slack capacity in the system up to now.

Both 1st and 2nd doses started to tail off about half way up the plot however.  Thinking back, the first tail off was shunting capacity from first to second doses (not an issue this time around), and we had interminable arguments about the second tail off that didn't really illuminate things.

I don't think the vaccine program can fairly be accused of not having the needed capacity looking at this plot. 

Lots of potential for an impedance mismatch between supply and demand.  One thing I've not seen considered before is for the government to pick up the taxi fares to take people (with a friend/relative/carer if wanted) to less conveniently located vaccination centres where that works.

He's apologised for the video of people making light of the restrictions - he's still denying that a party took place or that rules were broken though.

Apparently, he just has a bunch of insensitive aides who like a good joke about parties they didn't have, for which he is very sorry.

Also he says the Cabinet Secretary will investigate and if any rules were broken those involved will be disciplined. It's a shit-show even by current low PMQ standards.

Yes, I assumed too much from a headline and the first few lines of an article, you are right.

Errata to that post. 

I shifted the black curve by 4 months not 3 in the post above.  Corrected image below.  It doesn't make much difference as the relevant part of the second dose curve is almost horizontal at this point.

The problem you are missing in that plot, is, this time they are moving faster through the age brackets (picking more low hanging fruit). No bad thing for population immunity at first sight. Once the low hanging fruit have gone the booster rates will drop a lot. It also leaves a lot of people 'stuck' who are cared for at home and still too many in care homes; people who are frightened, vulnerable and desperately want protection. If this variant is more infectious, history shows us many of those will catch it irrespective of PPE measures. There is a disincentive for GPs as they get paid per jab but they have to wait after each home jab in case of side effects. Those in care are the group we most need to protect as they are the most likely to be hospitalised and add pressure to the NHS.

The urban poor with inflexible time and travel opportunity will get a second class service. They also tend to have higher proportions of the vulnerable who are more likely to be hospitalised than average. As such paying for taxis would be a great idea.

This is not a disaster like some previous government actions (especially the Sept and Dec 2020 delays) but it could have been done better.

There are words as well as plots. I thought those words acknowledged or pre-empted your points, and that I qualified what I was inferring from the plot, but there we go.  I'm guess I'm not being very clear today.

I'm not denying any of the issues you raise.  We're still plodding on with first doses at 20k a day, the existence of a long tail to the vaccination is clear as day.  Right now though it's a numbers game and the numbers add up to be close to the on of January goal; given the first tail-off in the 1st and 2nd dose curves as to do with limited capacity to handle overlapping first and second doses, I hope we don't see that again.

Yeah but what's important here is that he's totally lost authority to introduce restrictions and everyone's going to kick off. He'd need a big unrelated announcement to kill that story, this one's just going to make it worse. Hilarious! The anti-restriction bell-ends could be quite useful in bringing the government down here. Support drained from every side.

There might be some impact on compliance with any new restrictions, but I'm agnostic about whether that would really be any make-or-break for how the winter goes. They're not harsh restrictions and there'll likely still be a decent degree of compliance because people understand that wearing a mask etc. is a matter of pro-social behaviour rather than acceptance of government authority.

I think vaccine passports - while I'm broadly in favour-ish - are an uncomfortably policy which it would be nice to avoid. On this I expect a huge anti-government backlash given the partygate hoo-ha. I'm hoping there can be maximal impact on the government with minimal impact on public health through the incredible cock-up that the government have created for themselves. It's a great twist.

Pfizer preliminary vaccine efficiency data against Omicron is out:

https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-b...
 

It’s looking rather promising.

Very much what happening here. NHS Highland only just started to open clinics for boosters this week.

We got ours on Monday and whilst that's brilliant for us (other half is in a priority group and I'm a contact of someone that's immunosuppressed) it's not looking so good for the elderly in our town who are patiently waiting for the GP to call them for the jab.

The roll out of the booster up here has been glacial with them only now getting to the 65+ group!!! Many of these folks that are waiting don't have access to transport to get to a clinic or don't even know that's an option (the GP website tells them to wait until contacted) and thus just have to wait. 

Unless my GP is anomalous (chatting to others in NHS Highland suggests not) I fear there's going to be a lot of people in the elderly groups that are still waiting for boosters well into January ☹️. 

There is no need to wait for GPs. They have opened several new centres in Highland in the last week or so, and there are slots available within  a few days.  

Yes and no. 

It’s news towards the best possible end of the spectrum but it’s a spectrum labelled “bad news”.

Seeing that 80% of T-cell epitopes are unaffected is great.  I'd quietly been hoping for 90%, but I’m not complaining.

Reading that 3 doses restores protection against infection to a similar level to 2 doses against delta is reassuring, but it does suggest we're going to loose the "3rd dose advantage" that has been showing so clearly of late in the D1.c plots as hammering down cases in older adults; that hammering down has been a critical part of being able to allow top level cause numbers to run so high for so long.  

Suggests to me that the biggest difference the 3rd dose is going to make in the immediate term is limiting how high omicron can push the R number.

Take that advantage away we're going to need to compensate somewhere else, which is feeling like restrictions and precautions over the Christmas break at least.  Perhaps wind back those festive parties - even ones that didn’t happen…

I can't speak for other care homes, but ours had a visit from the vaccination team in the second week of booster jags being approved and all staff and residents got them on site. Quick, easy and efficient. We all got our flu jags at the same time. 

Have you caught a taxi lately ? Most have packed it in and gone off to work for Amazon or retrained as HGV driver. Better jobs elsewhere.  

I know that and that's how we booked, the issue is that many elderly don't know this and thus are patiently waiting for their call up ☹️. 

We've made sure anyone we know is aware but there's going to be a bunch of folks that won't have friends or family looking out for them and thus have to rely on the GP to get around to them. 

Here's a plot from the government dashboard data for England.

Left plot:

• Blue bars - cumulative 3rd doses by Dec 12th
• Black bars - cumulative 2nd doses 90 days before as an inidicaiton of the size of the eligible cohort 

Middle plot:

• The same 3rd doses data as a percentage of the 2nd doses eligible under a 90 day gap

Right plot

• The number of days it would take to reach 100% of the current eligible level (changing very slowly for older people) as a function of the average rate over the last 14 days of data.  Take this with a pinch of salt in terms of predictive value, particularly the left side.

It looks like around 90% of the eligible at 70 years of age and over have had their 3rd dose.

Interesting denominator question (and this time it's not about NIMS): what % of each 5-year age group isn't in it 6 months later? 

Good question.  It's a can of worms but I don't think that it's a big effect as it's only 5% of each bar that is moving right a bar or dropping out of the plot over 3 months (3-month shift, not 6), and with similar % uptake in adjacent bars it becomes a second order effect where the values change by only 5% of the small difference in adjacent bars.

The main worry would be if Covid had killed a significant fraction of any of the bars in the last 6 months which thankfully it hasn't, as this would have a different flow of vaccinated and unvaccinated people between the bars and the exit.

 Lots of other effects, but I think it's more sane than issues over other denominators!

Is it time to mention my idea of a face-mask with a straw hole for Christmas Parties?

Ah, I think this effect drops out on the first plot I did using the data given as % of population of mortality doesn’t depend on vaccination status for most (partially valid…) but it doesn’t drop out with actuals as in the demographic plot.

Still, a fractional change of 5% (3 months / 5 years) applied to a change in bar size of 50% max (most extreme case) is a small effect, perhaps 2.5%.  So; things are marginally better on the far right of my plot than it suggests.

Yes! It will go well with my assless chaps for the photocopier.

The Tories always want to use the army to help the vaccination program.  That's the sort of thing a couple of squaddies could help with.  Just grab anyone trying to f*ck up a vaccination centre hold them down and jag them on the spot.  

If it is really doubling every two to three days, the German politician had it right.  In a few months almost everyone is going to be vaccinated, recovered or dead.  It's really about whether you manage to get your third dose before you catch it.

I find this attitude extremely frustrating. It's perfectly possible to self isolate through a high covid period if not vaccinated, be that through hesitancy or the few who have genuine medical reasons. That German minister is an idiot. The ones who will be almost certainly be dead or recovered are the likes of anti-vax covid deniers who mix indoors ignoring the risk.

A few observations.

Had my booster today, in the end got it at the GP as they started doing them. Steady flow of people while I was there, although when I noted that it looked busy I was told it wasn’t that busy - all relative I suppose.

Picking up on the volunteers point - they had two people in the corridor directing people, they had high vis ‘volunteer’ jackets.

A friend wasn’t eligible / able to book until the 12th. They went to a walk in centre and got jabbed today.

Tomorrow’s office Xmas party cancelled due to firm wide mandate to cancel them from tomorrow. Of course I wasn’t going anyway. The Torygraph front page nails it: Don’t go to work but do go to parties.

Still, the silver lining of Partygate is it may have prompted Plan B to be introduced earlier than it would have been otherwise (but still later than it should have been).

I reckon we’ll be lucky to avoid lockdown this winter but it should largely be ‘over’ here by Easter. Unless Pi turns up…

Clearly that was hyperbole but he was broadly right. The numbers able and willing to shield effectively aren’t material. Of course not all unvaccinated people with no previous infection will catch it, even if they aren’t shielding, but I suspect most will. So at a high level (say 99% of the population) I think it really will be vaccinated, recovered or dead. Unfortunately some of the recovered and dead will be from reinfection.

Tuesday’s SAGE minutes. Sobering reading. Some fairly strongly worded findings.

https://www.gov.uk/government/publications/sage-98-minutes-coronavirus-covi...

It certainly was for original flavour and alpha, it got more difficult for Delta, it looks like Omicron is significantly more infectious than Delta.   We should obviously try and slow it down  to spread out the consequences in time, give more change for vaccinations and quantify what level of precaution is necessary to be effective.

I don't think he was an idiot.  His basic point was if you don't get jagged you are going to catch it.  That seems fair, especially with Omicron, unless you take extreme precautions.  The main problem I would have with his statement is that jagged and catching it anyway is also a pretty likely outcome, although with reduced chance of serious illness.

Hmm, my 1-line summary of SAGE would be...

"do something NOW or we are going to be in heap-loads of shit"

Well the government has now done something, but is it enough?

It is at least encouraging to see the government responding quickly this time. It appears that they only learn at the fourth attempt.

If there’s enough people in the population who can’t mount a sufficient immune response who haven’t been infected then we never leave the pandemic phase.

They HAVE to catch it for the pandemic to be over.

How many people do you know who have had small pox? Do we have a small pox pandemic? 

Ah yes - a virus we’ve managed to eliminate.

Do you support elimination?

This isn’t small pox though is if?  Elimination is off the cards, and it seems every single nation is aiming for endemic circulation 

The pandemic phase only ends once people have sufficient immune response and/or medication (the line blurs with MABs) that this virus goes on to cause common cold like symptoms instead of covid like symptoms.

It is, if you can work entirely from home, or are retired. You can buy everything online and receive it whilst distancing 4-5m. You don't get ill, need dental work etc..  nothing breaks in your home where you need a trades person. 

So it's possible short term, near impossible long term and a fair proportion of the population couldn't cope mentally living like that. 

Might have slipped your mind as it was such a short, almost unnoticeable, miniscule debate, in fact I bet barely anyone even remembers since it didn't drag on for months nor overrun these threads or anything like that, but it wasn't that long ago you were pretty insistent that it would be impossible for a considerable section of society to avoid crowded, stuffy indoor places...

I agree, I'm not sure if I have or haven't had it (ill before testing), but I expect in the next decade I will catch it a few more times. Hopefully I will barely notice as my immune system will be progressively more responsive to it, even if the virus doesn't weaken. Booster jabbed 2 days ago and had no reaction so far. 

The only challenge is protecting those who are permanently or temporarily vulnerable (cancer treatments etc.). Anti vaxers, cannon fodder, most are lost causes in terms of convincing them anyway. 

The pandemic phase is already over, it's here, it's going nowhere, everywhere has it. Deaths are fairly constant and cases are seasonally effected. What possible next stage is there?

Eliminate if even possible, or vaccinate and protect those who genuinely can't. Half restrictions are just mild inconvenience and don't actually stop you doing what you're planning. Indoor events in sweden now have vaccine / just recovered passport on entry. It's pushing vaccinated rates up, 80% population of over12s double jabbed, 85% single jabbed (lots of school kids waiting for 2nd dose). 

Eliminated or irrelevant, end result is total freedom. 

No, it isn’t.  Not all the way.

Only because cases are fairly constant.

What I think is actually happening is that the pool of no-immunity people is shrinking, lowering the rate constant whilst seasonality is biting and raising the rate constant.  This has been keeping the rate constant around 0 meaning little growth, whilst the pool of people with pandemic potential shrinks.

One where the pool of zero immunity people aged under 65 is as empty as possible.  I don’t think we are there yet.  That pool + omicron could equal a rapid burst of cases driving unmanageably high hospital admissions in older people in a way that won’t happen by the truely endemic phase. 

This is the million dollar question. 

We dismissed the great barrington declaration as the consensus was that it was impossible to isolate a vulnerable population. Unless people take extreme measures and are sufficiently independent so that they don’t have to rely on others, it being impossible still appears to be the case.

Eventually they will be exposed. If vaccine conferred immunity doesn’t work, you have two alternatives. Catching Covid and recovering or catching Covid and dying. I.e. what the German chap said.

If we have enough people in the group who would get infected by Covid because the vaccine hasn’t worked effectively (i.e. the immunosuppressed) then, unless they’ve caught it and recovered, every winter will be a shit show of trying to avoid lockdowns.

Agree. That's the clearest I can remember them ever being that something must be done. It leaves absolutely no room for manoeuvre unless someone accepts that the objective is no longer to avoid "unsustainable pressure on the NHS."

Their doubling time assessment is pretty stark : seemingly between 2 and 3 days, recognising the uncertainty but saying that it is no more than 5 days and assigning the statement 'high confidence'.

Every sensible person supports elimination. It is the absolute best case scenario. The question is whether it is still possible in the short term future.

Before all the 'we all have to catch it so the pandemic is over' gets out of hand let's also remember that a virus disease wiped out 30% of the population of seals in the north sea only about 10 years ago.  There are extremely bad possibilities with mutating viruses, it doesn't have to be the happy case of more infectious but less deadly.  You could roll the dice and come up with really infectious and really deadly.

No Tom, only the terminally thick support elimination.

We’d need a global lockdown of terrifying proportions and theoretically even if we eliminated it in humans (after considerable chunks of the world population had starved to death and the economy had died ect) then we still have an unidentified animal reservoir to deal with.

Or catching Covid, getting really ill, surviving with reduced quality of life and life expectancy.

Or catching it, recovering, catching it again and not being as lucky.

There is a big difference between the vulnerable population in 2020 and the vulnerable population after three jabs and with antivirals available. That's hopefully obvious.

There's nothing thick about thinking we'd be better off in the status quo ante without Covid.

The question is whether there are practical methods to reach that desirable situation. 

This statement is bollocks because you are making an assumption about how it would be achieved and assuming the method was a global lockdown a completely unreasonable prediction about how long it would need to be.   

We have eliminated diseases in the past and we have never had the level of technical capability we have now. What we have is an unsolved but potentially solvable technical problem.  In that situation smart people will innovate and perhaps find a solution. 

Very few.  Have any highly transmissible, rapidly mutating viruses been eliminated?  Of course it may be possible at some point if vaccines etc develop sufficiently but within the next few years it won't be, so need to plan accordingly.

I take your point but I disagree: as I see it hyperbole leads to the same in the other direction: it heats the discussion and feeds the conspiracy of the anti-vax movement. Public Health messaging needs to be calm and honest.  Plus it could be a terrifying message if you are one of the unlucky small minority for whom vaccines are not recommended for health conditions or after bad reactions for a first jab. I think public vaccine compulsion has an even stronger negative effect (and is stupid in that, as passports can inconvenience those who make the non vaccination choice, whilst protecting public health).

We have the similar ministerial idiocy on the news this am. Don''t go to work but its OK to go to xmas parties. Poor Javid said he didn't come on the BBC news yesterday because he was so upset with the No10 ten video (I was almost moved to send him a card). Then when asked why he was so upset, he waffled and came across as honest as a dodgy used car salesman (so I put the card away). When asked "so you were so upset you couldn't come on to deliver an important public health message?" he said wouldn't put it like that. Then he dodged questions on what happened, who spoke to him a out it, and what should happen to those involved. This is all from the Secretary of State responsible for public health in the pandemic response.

With the doubling rates of between 2 and 3 days (seems too high for R~2) and the likely affect on public compliance of ministers who obviously lie on national news I'm thinking Plan B+ might well look too optimistic now.

Smallpox was pretty transmissable AFAIK.

Obviously we can't plan to eliminate it until we have a credible method of doing so.  But equally we shouldn't decide in advance that elimination is impossible.  If we decided in advance that getting to Mars was impossible we'd never get to Mars.

It's a fantasy for the foreseeable future Tom, and none that has no place in policy decisions now or within the next few years.

Not a good analogy, for many reasons.

You are right. If people have to go to such areas (or couldn't cope mentally with isolation) maybe they should choose to get vaccinated rather than risk the consequence of infection.  You pointed out to me in a debate on masks, on a previous thread, that in extremis it's possible to choose to not use public transport and maybe even choose to leave a job that requires indoor work (I'd agree in theory). I just think vaccination is a  practical choice and leaving work to avoid it isn't.

Doesn't leave much room for hope, does it?

If much of this rapid doubling is due to immune evasion (hard to imaging otherwise given the evidence stacking up from serology assays) then this is a really gnarly situation - most of the people it is spreading in will hopefully go on to have mild, cold-like symptoms.  They're going to get isolation orders in something that rapidly makes the last "pingdemic" look like a Sunday picnic.  Right over the Christmas period.  Chances are it means more symptom-free infectious people as well.

The reason we have to use isolation orders? It seems there's still enough adults who have declined vaccination to fill up ITUs at current case rates; these people are going to be exposed to much higher case rates from Omicron I expect.  Not much slack in the system there for faster admission rates.

If we end up facing lockdown-level control measures to allow intensive care units to accommodate those who have refused vaccination this needs to be made precisely clear.  

Edit:  BBC article this morning had an updated SGTF plot... https://www.bbc.co.uk/news/explainers-52530518

Edit 2: 

The next set of data on the MSD antiviral isn't so promising (no effect)

https://arstechnica.com/science/2021/11/womp-womp-efficacy-of-mercks-thor-i...

Some argy-bargy going on:

https://www.ft.com/content/7ded2361-e797-465e-ac25-a42c1d899881

Haven't seen real world, post-approval data on either yet.  Important to see how the Pfizer one holds up post-release given the cloudier picture now in the data over the MSD one.

But the virus wasn't mutating rapidly.

It also didn't have extensive animal reservoirs.

It also wasn't transmissive before symptoms.

It's symptoms weren't the sort of thing that people have all the time and that it was culturally acceptable to ride the bus or go to work with.

It's symptoms were the sort of thing that had other people staying as far away as possible.

But other than that, great analogy.  

And if you like something more modern, someone else is doing some Friday night plotting.

It isn't - the wave that will affect the UK in the next couple of weeks is another pandemic wave rather than usual endemic seasonal variation. It's starting mid-summer in South Africa. 

I noted in the sage minutes they discussed the decreased effectiveness of isolation if the turnaround from infection to infectious shortens. 

I tend to agree though - on a personal risk level the need for isolation for the whole family at once is by far the most off-putting consequence, and at a societal level it doesn't feel possible to run a million infections per day whilst also requiring them and their close contacts all to isolate. The system can't cope with that level of staff shortage in jobs that can't be done from home, one suspects...

That's also hyperbole (though not as daft as 'the everyone has to catch it on behalf of the country' madness). This is a seriously nasty virus but lets not pretend it has super powers.... you catch it by mixing indoors in poorly ventilated areas with an infected person. 

Vaccination will help a lot but again there are no super powers. Luckily the vast majority of the vulnerable vaccinated are either retired or will have legal H&S protection to work from home.  Hence, I personally worry most about vulnerable people in hospitals and care homes. It's a public health disaster that 1 in 4 in care were reported last week as not yet  booster jabbed.

No, that isn't updated, it's the same as the report that you linked that came out yesterday.  Sorry...

Yes, everything feels set to accelerate things.

Indeed

It can't, and it can't cope with 10x the number of unvaccinated individuals in intensive care wards either if the current exit-wave gets massively accelerated.

There really can't be many immunity free susceptible people left in the UK...?  Certainly a lot less than elsewhere going off the divergence we've seen from Europe in the last 6 weeks and the LSHTM paper link a couple of threads back.

Lockdown everyone or allow the demand for intensive medical care from people who have declined vaccination to exceed the supply.  Rock and a hard place.  I've an ugly suspicion it's a much harder place in many other countries.  Looks like the organisations pushing against vaccination are going to see the wedge driven in just as they wanted.  Terrorist organisations IMO.

I agree such anti-vax and anti-any-restriction organisations meet many of the criteria of enemies of the state in the public health situation we face. Go for them, not the ordinary hesitant people who are nearly always deluded victims rather than super villains. We have excellent support for vaccination in the UK and very good population compliance for legally backed restrictions, despite threats and exaggeration of the opposite.

Did you miss that yesterday he said contacts of a case would no longer have to isolate? It seemed to me this would soon apply to unvaccinated people, as well as to double vaccinated and kids (as it already does, so none of you have to isolate your own families anyway unless you are unvaccinated, which I don't think.) You are just advised to take a PCR. The only people who are told to isolate will be those who have actually tested positive.

Obviously a huge wave of infection would still have an effect on businesses but it's not going to be through being pinged as a contact (or being a household contact.)

(Edit, as of last week, I forgot, you do need to isolate if you are a contact of a confirmed Omicron case.)

Edit 2 - I'm not sure about the unvaccinated bit actually, I just looked and couldn't find anything in writing, so this might have been some carrot-dangling to the backbenchers.

Re bold text - the Omicron rule change (ignoring subsequent changes yesterday) meant even the double vacced had to self isolate if they were a close contact of an Omicron case, no?

Do you have a link in terms of the change? I did see it on a BBC infographic panel but not in the text of any of the articles I saw and not in any detail, so I was vaguely aware the concept might exist but hadn't seen it solidly enough to confirm it wasn't a mistake/misinterpretation

Edit: found reference to it in the text - "no date has been given for this change" 

Sorry, I edited my post - my understanding is basically the same as yours.

However being a confirmed Omicron case takes sequencing which comes late and will often not arrive until your 10 day isolation period is up or almost up anyway. I doubt that particular clause will affect many people.

I did miss it yesterday but read it whilst going through the guidance this morning.  The details don't appear to be announced yet, nor the data for the change, just that it would involve testing daily instead of isolation.

The BBC page [1] says this:

Ministers also intend to change rules so contacts of confirmed Omicron cases can do daily Covid tests instead of the recently-introduced mandatory 10-day self-isolation period. No date has been given for this change.

Not sure how much testing capacity could be impacted in the next month limiting this....

[1] https://www.bbc.co.uk/news/explainers-52530518

Yeah I think our posts crossed!

Had not realised the delay. That's something of a relief, selfishly...

Yes, I picked up on that as well. Seems it’s not just Ferguson saying that. Clearly it’s an estimate but it’s the ‘not more than 5 days’ but which is crucial.

We should but to save the economy self isolation for vaccinated contacts is being replaced with daily LFDs. Not clear how this will be enforced. To be fair, that’s also the case with isolation.

Yes. Shame no one in government is brave or honest enough to say this.

I expect lockdown in January. The government are just in denial about it. 

This is what we have here, and similar I think in Jersey. If you are double-jabbed and a contact you have to do 10 days of LFTs but can go about your daily business unhindered (unless you develop symptoms, in which case you need to do a drop in PCR if you test +ve by LFT, or call up and book a PCR.  You must SI whilst awaiting test results.) You are not allowed into healthcare places (doctors surgery, hospital, care homes) unannounced unless you go to hospital in an emergency.  There is no enforcement as such of the LFT taking.

No, because their effects haven't warranted the effort to eliminate them. Same reason there's no vaccine for the common cold, it's not worth the effort to create and maintain it.  However, it's entirely possible to eliminate covid within a jurisdiction with a decent lockdown, it's been done multiple times by different places. I should know, I live in one!  What you cannot do is keep it out forever if you have a porous border with somewhere that has it.  If all the world's leaders decided to actually try to eliminate it I think it would certainly be possible to eliminate it within the human population, and possibly elsewhere - it doesn't seem to do very well in animal populations. It would certainly be possible to eliminate it within Europe for example.

But it's all or nothing (or really closed borders forever).  And since it simply isn't possible (practically or politically) to eliminate it everywhere at the same time, overall elimination is also impossible.

Absolutely no chance.

https://www.theguardian.com/world/2021/dec/09/south-african-covid-cases-up-...

the link misses out the % sign... 

Another article that doesn't dig in to why it is likely that Omicron is less lethal in SA - i.e. almost everyone there has had a round or two of infection (at least), which has removed those most susceptible to severe illness from life, and has left the rest with a lot of good immune protection against severe illness.

Which means the pandemic phase is probably truly over for SA.

For countries with a small (UK) or large (Germany, France, etc) reservoir of susceptible people with no immunity, it probably means the remaining part of the exit-wave from the pandemic phase gets compressed in time or needs a lot more control measures.

I've still seen no data on intrinsic lethality (if that's the right term for lethality when it comes to people with no prior immunity).  Both alpha and delta have raised that rate over what came before; omicron... ?

Given their much younger demographic than western Europe and estimates the pre-vaccination IFR in the western Europe, and excess deaths in SA, it seems likely the culling effect of Covid on their population has been a lot more severe than in western nations, removing people far less vulnerable than are surviving here.

We'll see.  

The supply of unvaccinated people to fill ICUs can't last indefinitely.  

Also unclear how much hospitalisation is going to come from the oldest folks with 2- and 3-doses if we get a proper rip in the younger as seems to be getting started now.

Only one way we're going to find out.

Which is ok pre Omicron. That said, it may be the only way if cases really take off. 

Agree, the issue is the weight of case numbers in a short period of time. Whatever the ‘supply’, we can just about manage it at 1k a day but 2-3-4k is a different matter. 

S gene dropout reported to be in excess of 5% already, so that's suggesting in the two to three thousand cases a day range, according to the beeb..

https://www.bbc.co.uk/news/health-59580290

At this rate of growth it seems already too late to stop daily omicron cases exceeding current daily case levels, so fingers crossed hospitalisation rates are a lot lower than for delta.

'I can't think of how to do it today, with technology I, as a layman, am aware of therefore it is impossible'.

It would look very different if the world spent say 500 billion a year for ten years researching and developing technologies with a view to being able to eliminate infectious diseases.  If you had ten years to develop and build out infrastructure the problem would look a lot more soluble.  And maybe we could get a few more diseases crossed off at the same time.

We went through this higher up. Yes, just possibly, it can be eliminated in decades but that's not the timescale we are discussing. 

However it is very unlikely because however much you might see every problem like an electronics problem, in the real world there is cost, politics, trust, conspiracy theories and many other factors standing in the way.

Not decades. Maybe a decade if the world was determined. Maybe less if one of the tens of thousands of people who would be thinking about the problem if it was funded on the scale I suggested made a breakthrough.

My point is not about whether it can be done next year or the year after but that elimination of Covid (and other serious infectious diseases) should be recognised as a medium to long term goal.  It is exactly like putting humans on Mars - we don't have all the technologies available today but we are close enough to sketch out how it might be done, it is definitely going to be very expensive but we will learn a lot by trying and if we are determined we will probably succeed.

See my edit.

No it isn’t.  

Not the first time I’ve asked; have you ever worked on a life sciences project down at the cellular biology level?

Edit: a much more interesting question distilled from the nonsense analogy - we could if we chose eliminate infectious diseases when sending people to a Martian colony.  

Should we?  

You just need a few billionaire tech bros and the job will be done in no time

(Actually it won't but they will come up with a shit version of something that exists, market it to Believers and make more  billions.  E.g. Musk with tunnels, submarines,  electric cars)

Elimination isn't even necessarily that desirable. Think of it like flu or rabies or tuberculosis. Even if you eliminate it completely from humans you still don't get to relax. You need immunity in the human population ready for the day when a badger sneezes on a cow or a migrating goose craps on a chicken farm. And since the immunity is there it makes sense to lean on it to keep itself up to date if that's an option.

If we went a few generations with it eliminated and nobody exposed to it, and then one day someone gets a little too friendly with a bat and a pangolin, we're going round again.

Are there risks of similar with e.g. smallpox?

If androids dream of electric sheep - can we catch diseases off them?

It’s a shame Philip k. Dick never answered the big questions.

Of course not. Doesn't mean I am wrong.

I bet there were a lot of monks that would explain why printing presses were a bad idea or internal combustion engine experts who would tell you why electric cars wouldn't catch on.

Yes.  And we should get rid of every infectious disease we can on earth too.  Science and engineering are about understanding how things work and then taking control of them. I'm not interested in getting some horrible disease just for the sake of nostalgia, if we can eliminate them we should eliminate them.

10 out of 10 for ambition. Just out of curiosity is that just in humans or in all species in which case what counts as infectious? Parasites?

Did he ever answer any questions, or did he just frame every single story in terms of “is this real or is this in my head?”?

Perhaps I should read more of his stories but the ones I have read all finished for me with an underwhelming sense of being cheated out of an ending.

Except Mr Spaceship.  That had an ending, and it was naff.

I don’t think it’s a great leap to consider the way the immune system adapts and responds to low lethality viruses as effectively harnessing them as self-replicating, transmissible vaccines.  If you can’t beat them, put them to work.  A philosophy seen across the scales in living matter.  But as processes go, bootstrapping a new virus in to an existing population is a shock.

Now, a cool future step in evolution could have been lateral information transfer about epitopes between memory B- and T-cells in different humans, mediated through exosome exchange using some immune exchange body parts.  Downsides include auto-immune disorders becoming transmissible and upsetting Dr Raymond Cocteau. Or epigenetic transfer of the information from immune memory cells to progeny; or progeny that can reverse engineer epitopes from antibodies transferred via breast milk.  Sometimes I think it would be great to have a large budget and a mad science lab.

Edit: sorry; rambling nonsense.  Feverish times after my 3rd dose today…

Potentially domestic animals will have diseases eliminated before humans because there are fewer rules and less issues with civil liberties so progress may be faster.

Sure, let's get rid of midges and ticks and tropical disease parasites too.  Human progress has always been about gradually replacing randomly evolved ecosystems with an engineered environment which is better optimised for us.

In a few generations (i.e. about 50 years) at the present rate of scientific progress we won't care, it will be a trivial problem. 

Also at the present rate of 'civilising' wilderness areas in a few generations you won't find pangolins except in zoos and any populations of bats with dangerous diseases for humans will have been eradicated.  I'm surprised the Chinese haven't killed all the bats in the caves near Wuhan already.

I view it more like human progress has been about over consumption devestating ecosystems, which have led to industrial processes filling the gap. That 'optimisation' has led to an obesity crisis due to appalling western diets and great swathes of the planet turned to monoculture.

I would be a little more cautious about wanting to engineer solutions to everything you don't like in an ecosystem. The outcomes won't always be what you expect.

Really? And wasps and other species we don't like? Then as Tacitus put it, we shall have made a wilderness and called it peace.

Could we though? Even if nothing but humans went there, sterilised air, etc etc, we have populations of microbes in our guts. We are never alone, and things can mutate.

That may be an ignorant comment on my part. If we could, I have an equally gut-based feeling that we shouldn't, but I'd have trouble explaining why.

Careful - Tacitus (or his proxy mouthpiece) was talking about Scotland IIRC, you don't want to set TiE off!

The martians did that in the war of the worlds. Worked out well for them, right up until the point that it didn't. I would suspect we would be in for a similar kind of experience.

Oh gosh yes it was wossname on Mons Graupius wasn't it...

IIRC Scotland sent the Romans homewards to think again. 

Those are wild and fairly dangerous statements.  Removing (or adding) elements to ecosystems tends to have far-reaching and unpredictable results.  Not to be done  without care and very good reason is the historical lesson.  Since ticks and midges are near the bottom of the food chain, removing them would have effects all the way up.  The Engineering Council code of ethics requires engineers "protect, and where possible improve, the quality ....natural environments", which I don't think your suggestion fulfils.

The outcomes are never what you expect.  When that happens you go back and fix your system until they are close enough to get paid.

My prediction is population will keep growing. Less developed countries will keep developing. Wild spaces will be civilised.  The rate of technical progress will increase because more people than ever before are getting a good enough education to contribute to it and we are just entering the age where AI will significantly augment human intelligence.  If we get production level quantum computing, as looks likely, there will be a step change in what we can compute. Very likely we will solve the problems which currently make it difficult for electronics to operate within a human body and we will start augmenting ourselves with bio-electronic systems.  In itself a chip within your body continually monitoring what is going on and reporting to a server could detect disease fast enough that people could be instructed to isolate before spreading it and the isolation could be enforced.

If you are betting problems we can't solve now just because they are complex - such as eliminating a viral disease - will still be insoluble in 50 years you are probably wrong.

You are still viewing it as a technical challenge.  That isn't the hard part.  It's the human side - political, economic, trust - that is the hard bit.  

That's true. But 'how would you like to not die or get really ill' is not that hard to sell.

Have you been paying attention for the last 18 months? It is a very hard sell in some quarters.

You seem to be getting a lot of flack for suggesting what you think is likely to happen in the future. I think this may be because many are reading it as what you want to happen.

However I don't think you've expressed it (edit since seeing your latest posts: any of the negative "progress") as a desire, more as a fatalistic resignation based on humanity's behaviour to date.

I think many of your downvotes are therefore unjustified, but I'm sure you're used to it and have developed a sufficiently thick skin.

Iain (M) Banks's culture novels give an idea of some of the possibilities if we gain complete control at the atomic level. None of what you've expressed would be difficult in his worlds.

I've been working in engineering for 35 years and this is the first time I have heard of the Engineering Council code of Ethics.  I don't have any idea who the Engineering Council is - I guess its some English Government quango?  Nobody cares.  Engineering is global and the UK has p*ssed away whatever position it once had. It is the EU, China and the US that make the calls and it only takes one of them to decide to pursue something and it will happen.

I've been paying attention and what I have seen over the last two or three years is the emergence of China and an approaching tipping point where China rather than the US is the most advanced and fast moving technical economy, particularly in electronics and computing.

If the west gets held back by the luddites the Chinese will just pull further ahead.  It won't stop the transformations happening.

Which suggests you aren't a professional engineer

Pretty much confirms you aren't an engineer.

OK.  The US equivalent body, NSPE has

"Engineers are encouraged to adhere to the principles of sustainable development1 in order to protect the environment for future generations"

https://www.nspe.org/resources/ethics/code-ethics

The EU bodies has similar

https://www.ecec.net/fileadmin/pdf/ECEC-Code-of-Conduct.pdf

I can't read Chinese but assume they will have a similar requirement.