UKH

Post 1 - European Comparator Plots

So that it doesn’t become an elephant in the room, I’ll start with the new variant, Omicron.  People are discussing it elsewhere [1,2].  Nothing else to say about it here, other than my usual take that it’s better to be over-cautious for a week or two in advance than to pay the price for being under-caution in light of what we may know by then.   Others disagree - some for more caution, some for less.  One way or another we won't have to wait for long to find out.  I'll write the rest of this thread on the assumption nothing is going to change because that's the only sane starting point.  I hope not to have this thread voided in the next few days by another branch towards the worst timeline...

The dramatic change this week is with the “actual and extrapolated” plot where the UK has dropped down almost to the lowest point, when ranked by an extrapolated, “locked in” death rate.  A reminder that this is estimated based on the most recent week of case rates and reasonably bounded CFRs and is not a prediction.  It's an extrapolation based on nothing changing.  Lots of things change. But it gives us a starting point for a comparison and for seeking understanding when case rates themselves are so incredibly deceptive due to differences in testing and demographics etc. 

I’ve put linear and logarithmic x-axis plots in for the extrapolations.  They’re not happy plots.   Not much to say that the plots don’t make abundantly clear themselves

Germany  down to 2.5 weeks to veer off a course of locking in a death rate higher than ever seen in the UK, and Belgium is about 2 weeks away from that point.  

So, same situation as last week - UK avoiding exponential growth through very high levels of immunity, most of Europe facing a choice between exponential growth to catastrophic levels or lockdown level control measures - which postpones their problem of vaccine refusal.

Who knows if the new variant is going to change all that - whilst it’s becoming clear that the approach taken in the UK over the last few months did have a rational basis in terms of pulling the more-or-less inevitable forwards from winter, in terms of control measures and readiness for an escape variant, our lower use of control measures puts us in a a worse position if an escape variant gets loose...

This phase-space continues to look like a bit of a dogs dinner, but you can squint to track a particular country.

• France, Sweden and Spain are all now clearly members of the “main sequence” - with France in particular having a short doubling time. 
  • Perhaps Macron jumped the gun a bit with his comments about a vaccine passport meaning they’re going to be okay…
• Norway and Finland look to have joined the main sequence as well, but with much more moderate doubling times. 
  • Finland may well be positioned to far up and right because of some sampling noise from their (currently) low numbers. 
  • Interesting given how well they’ve managed to control spread before now with relatively mild control measures.  Shows what a kicker Delta + Winter is shaping up to be, and it’s early days yet for winter.
• Switzerland is both high in cases and short in doubling time which is a bad place to be, especially as they’re holding a vote on if they should drop all Covid control measures or not [2].  I don’t even.
• The end of the lockdown in Latvia presents as a pivot round towards growth (remember the rate constant measurements lags the cases rate measurement on these plots - a trade off between noise and immediacy on the leading edge of the data)  as it clearly prepares for another trip round the growth/lockdown orbit, and Romania is lining up likewise.    
• Austria is looping round to decay following its recent lockdown, but that’s a time-limited offer and then it’s Christmas.  Pretty clear what’s going to happen to to all the measures when the lockdown ends…
• Netherlands - growth is stalling, how much is down to their control measures and how much his down to exhaustion of their PCR testing capacity is an open question….
• Greece - case rates have stalled and are holding at a high level; I haven’t seen reports of specific new control measures nor any sign in the OWiD stringency index; but the onset is way too sudden to look like immunity thresholds emerging.  Perhaps this is another saturation point in testing?  Or something more interesting? Wait and see.
• Hungary - it looks like they’re going to exit the pandemic phase the hard way.
• UK - actual death rates are higher than much of Europe, but are falling, and the extrapolated rate is lower or many times lower than the extrapolated rate of most of the comparator nations, and is basically static unlike the rapid exponential growth we’re seeing elsewhere. 

Hopefully there’s going to be a very swift and successful adoption of the antivirals across Europe to prevent these extrapolated rates from being realised. 

Link to previous thread:

https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_53-...

[1] https://www.ukhillwalking.com/forums/politics/b11529-741492?v=1#x9552094
[2] https://www.bbc.co.uk/news/world-europe-59380745

Post 2 - Four Nations 1

A slightly different mix of posts this week as the focus shifts.  All 4 nations have trendiness showing cases now in decay; I tuned out to be over optimistic on this for England last week (and had my toes promptly put to the fire by Si dH, mea culpa).  There’s perhaps more provisionality at the leading edge right now - Scotland in particular looks like the last data point might not hold up.  Probably a weird few days ahead as people didn’t go for testing on Saturday due to the fallout from Storm Arwen.  It’s the longest power outage and most number of trees down I’ve seen since the Great Storm of ’87.

Anyhow, big picture - the top level cases have been more or less level or moving very slowly up or down over the last 4 months in all the nations.  The sands under these level numbers have been shifting though, which leads us on to….

Post 3 - Four Nations 2

Hospital admissions plots for the 4 nations show more decay over the last month or so than you’d expect from the cases curves. 

I look at the demographic data on this for England in posts below; I haven’t looked at Scotland this week but the same trends had been developing before within the more limited resolution of the data there.

In England it looks to be strongly related to the demographic shift driven primarily by 3rd doses but also in part by the age of both child and adult/household infections moving down a notch.  It’s early days for this shift to play out as big reductions in the burden on hospitals, but I hope it continues.

Post 4 - England 1

Typically hospital admissions crosses in to growth ~2 weeks later than cases on the rate constant plot 9e; we’re at three weeks now with no sign of the growth in cases landing in hospitalisations, and the gap is even larger for deaths which are now halving faster than at any time since cases first returned to growth in the Spring.   

Deaths look to be falling a lot faster than other measures.

Post 5 - England 2

There is no sign of the much hoped for decay in cases after the Guy Fawkes cold spell in the top level rate constant data, but as the splits plots show there was a prompt return to decay for over 60s in line with the weather relationship.

I have a theory about why we're seeing so much growth in cases in the last week when the weather relationship says they should have been decaying (it looks like one of the biggest violations of that).  As theories go, it's - at best- held together with blu-tak so take with a liberal pinch of salt….

• There was a big spike in under primary school ages from the looks of plot D1.c; I think the pandemic is finally running “hot” enough to drive signifiant growth in that age range with the effects of seasonality.
• This age is less susceptible to growth in cases than secondary, as seen from previous school-associated spikes, but now the immunity from the last big spike in secondary ages is damping that down. 
• Then, we’ve got child > adult/household infection going on with a lag; you can see something compatible with this in plot P1 which is a normalised distribution of cases - both the upper and lower “blue arms” are descending down the age range in recent weeks. 
• So, what we have is all age bands turning to decay in line with the weather, but then there’s a lagged bump added to the 15-59 age range caused by the spike in primary ages, that is cancelling out the decay for now.  So, we’d expect them to go in to decay any day now, but....

Effects of the current cold spell should start landing in the data in a few days.  Like I said last week, what this does is the point of maximum uncertainty.  Not long to find out now, unless there’s more to this than meets the eye.

An abridged set of posts subject to less proof-reading than usual; got lots of storm related things to be dealing with today...  Thoroughly enjoying the dark world outside without a street light or house light in sight.

Facemasks are back in fashion, together with self isolation, and PCRs for travellers....

https://www.bbc.co.uk/news/live/uk-59443504

That was quick. I was just musing that if we get lucky and Omicron only dents protection rather than caving it in completely then we are in the position of having lots of less intrusive restrictions to reach for before it gets into heavy lockdown terrain....

The plotiversary has gone and sadly reality breaks back hard again. So many thanks for this hard work and the importance looks to be relevant for quite a while now.

I don't get the extrapolation for NZ on the log graph... Is this a plot error or am I being dumb?

I don’t know, what don’t you get?  Hard to answer a generic question…

• Actual rate is low and falling (green arrow) very marginally (short green arrow)
• The middle of the extrapolated range for locked in death rate is below the highest past actual value from the last 60 days and so there’s a black tide mark for that actual high
• Extrapolated rate is low and falling (blue arrow) very marginally (short blue arrow).

I should have qualified this plot a bit more - with a stand out low rate and a low population the noise in the data is significant, and is bouncing measures around.  Which is probably why there isn’t a monotonic sequence of tide mark > falling actual > falling extrapolated.   Basically not many people are dying of covid in NZ and there’s not much sign of that changing in the immediate term.

Is Omicron a bad name for a variant?  

Perhaps I should start a thread about nice names and bad names for illness & conditions which kill us. ??   does it really matter?  Do people care anyway?  We'll see.

"Oh, my grandma died last week!  It wuz orrible !   called it Omicron I think.  They could have chosen a nicer name".  

Been lots of discussion about the name on other threads, I thought I’d get a snapshot of views… 

Yes, something of an issue in research and medical ethics, with all sorts of whimsical names being given to genes upon their discovery - see the past controversy section on the sonic hedgehog gene for example - https://en.wikipedia.org/wiki/Sonic_hedgehog

Mind you, the variant name hasn’t tended to feature in reporting of deaths, just “covid”.

More updates - https://www.bbc.co.uk/news/uk-59445124

"The health secretary is to ask advisers to consider rapidly extending boosters, including reducing the gap between the second dose of the vaccine and the booster"

It seems like quite a few of the precautionary voices from the last few weeks are now going to get what they've been asking for, now due to this variant.

It seems to me worth taking a lot of immediate steps in order to lower the demand on healthcare as well as to slow the potential rise-to-prominence of the variant; incase it does turn out to be really bad news, creating some space by using the hard won immunity against delta and more control measures to hammer it down seems sensible...  If it doesn't turn out to be needed for the new variant, I dare say it'll still be greatly appreciated.

Quite.  I don't know if we should be happy or terrified that the government are being so pro-active...

Yes, indeed.  

I hate to be the voice of pessimism again, but I think your point about the sudden action on the part of this stand aside govt, is on the money.

we never hear the advice they actually get in private. I worry that to provoke such rapid and decisive action against the tories natural impulses, it must have been genuinely terrifying. 

One could so easily form the impression that perhaps some conversations are never minuted.

That would be an entirely reasonable interpretation. 

Let's hope they're just learning from their time in the school of hard knocks about the benefits of a more precautionary approach...

ROFLMAOUICB

Have you ever played the video game quake?

There’s a gun in it called the BFG.

This whole series of events makes me think something has got the BFG and we’re about to see the words “quad-frag” on screen soon.

Quake? I see you, young man/lady* and raise you Wolfenstein 3D.
 

*edited as I know a (previously) young lady who was a big Doom fan and thanks to her input I am embarrassed by my initial chauvinism. 

I am choosing to believe that it is nothing more than that Boris’ fragile ego can’t take being photoshopped onto a picture of the grinch and labelled as “the man who stole Christmas” a second year running, and that he thinks this will buy enough delay to achieve that. Plus it’s a nice justification for relieving a bit of pressure in the nhs if omicron turns out to be all bark and no bite. In some ways it’s a convenient excuse that lets him get round his backbenchers if he is actually slightly more risk averse than the CRG loons.
 

It is more pleasant (not the same as more realistic, I accept!) to believe it is this which is driving him against his natural lackadaisical/libertarian/callitwhatyouwill impulses than the alternatives, particularly given that if the private advice is that this is terrifying then this response is pretty piss weak compared to what you could do (if you were really that scared - door to door surge testing and local lockdowns in the areas with the existing cases and move every country to the red list for non essential travel and damn the consequences, that sort of thing?)

You can’t have that straw, that’s the one I’m clutching.

In reply to minimike:

During my quality axe time splitting the log pile, when I get a 4-way split, I hear the Q3A chime and voice announce “4-way split”.  I keep thinking about having a go at some image processing code using the relevant CCTV camera to trigger an actual announcement.  Would need to recognise 3-way splits for it to be worthwhile…

Any good windfalls.last night? I got a huge chunk of Scots Pine which I dragged down the road. Not sure the neighbours were impressed.

Also,.why is splitting fun but sawing a drudge?

Ha! So true.

But I’ve a nagging suspicion it might be the same reason as why our PM likes winning elections and hates actual governing. Which brings us back to the straws we’re clinging to tonight.

A set of big willows came down on the road.  Farmer has sawed off at base and dragged clear, I’m not sure what the local etiquette is on removing wood from the remains, I figure if it’s still there I’m a few days…

I’ve a couple of big ash branches down and yes, I couldn’t get the enthusiasm together for the bow saw.  They’re not going anywhere…. I’ve banned myself from using the chainsaw this winter.

Possession  9/10ths of the law.

And finally we understand the pseudonym 

One lesson I’ve never forgotten from my younger days is that most farmers are in possession of shotguns…. On the other hand, the battery electric chainsaw is very quiet…

They must be thanking their lucky stars that COVID has jumped back to the top of the news agenda… 

OMICRON scares MORONIC government perhaps!

I’ve just been sent a photo of one of the local testing sites.  It was a tent on a sports field.  Now it’s a collection of torn canvas and plywood sheets strewn across the grass.  I doubt it’s the only testing site to have been destroyed.

That's like asking if Tiddles is a bad name for a cat.  It's not a bad name for a fluffy pet but it's a rubbish name for a tiger. We don't know how bad this variant is yet so we don't know if it is a good name yet. It's certainly one of the more ominous sounding Greek letters.

I await the arrival of the Omega Doom variant.

Breaking News

Moronic government still moronic!

https://www.theguardian.com/world/2021/nov/27/boris-johnson-ignored-my-plan...

The knives are coming out.

Bingham’s comments last week were very notable, particularly around embedding science within government decision making.

We had one on one of the piers in the harbour for arriving yachtsmen that got blown into the harbour a couple of weeks ago

Agree, if the ‘secret’ advice is really bad, this response isn’t strong enough. I doubt Whitty and Vallance know much more than what’s in the public domain, given Omicron got identified only a few days ago. What they might have done is some quick projections assuming a higher R and a bit more immunity escape. Given we were already sailing close to the wind, it won’t take much to completely upset the apple cart. 

Next will be Pi, I suppose.

Everyone likes a nice pi.

Interesting comments from Valneva about the UK government.

They are saying their factory in Livingston was taking longer to expand than planned because they couldn't get material due to Brexit!

https://www.bloomberg.com/news/articles/2021-11-24/u-k-threw-covid-vaccine-...

Interesting discussion. So what's it worth looking out for in the data in addition to the usual?

Whether the mask rules make any difference to the general trajectory over the next 2-3 weeks

Data from South Africa

Any sign of outbreaks in  Nottingham, Chelmsford or Belgium

Anything else?

P.S. I used to be partial to a bit of Quake 2. I used to go by the alias 'Super HPB'. You might be able to work that out. When it became obsolete I got pretty good at Q3A rail arena on map 17. A time when being accused of being a bot was a compliment!

Hospital admissions in SA - proportion of vaccinated people remaining the same might be an earliest suggestion that the vaccines still work.

She was excellent. No wonder she is highly regarded. 

Perversely it backs up what Cummins had been saying , but he is a nasty politically toxic character. 

Do you know if South African case and hospitalisation data is published daily on the web anywhere?

Hopefully the SGTF means data on this is going to be really obvious, although that’s not presented in any dashboards hopefully it’ll get regularly summarised.

Ages 15-25 have been very inert recently in the demographics and university conditions consistently produced some of the strongest growth in the past, so that might be an early sign.

If I ever open my restaurant/bar, “Map 17” is a contender for the name.  Proof that less is more.

No idea. Sorry.

The trouble with Quake is you get into the habit of throwing hand grenades before entering church as a precaution against zombies.

Sorry, I'll clarify... the extrapolation decline arrow for NZ starts higher on cases than the current decline arrow. Edit  I've got it now extrapolation arrow sits in the middle of the extrapolation range.

On a different subject I think one of the problems in the vaccination service needs some airing. They are struggling for jabbers locally in some areas and yet there is no national call for more trained volunteers (and more training) for the planned booster acceleration.

Personally if I had a tiger I would call it Tiddles. But I’m a contrarian.

Edit: I once had a goldfish called Sauron (it was always watching me).

That variant name has already been used. They even made a film about the life of that variant.

Could be hard to disaggregate from the other factors. We should see growth coming through in the coming days as a result of the cold spell which started last week and is going to end tomorrow, just as the mask mandate is brought in and some people generally start being more cautious - so we could expect the growth to stall from next week for both of those reasons. On the other hand, the Xmas party season is kicking off early this year… The Arwen disruption could also cause some unusual fluctuations, though whether that’s going to be significant is not clear. So lots of things going on.

Definitely. As for UK outbreaks, here could be all over the place. I bet there have been more than two import events already. 

Apparently there was a guy flew in from South Africa and had meetings in Westminster and they are contact tracing there.

We are probably screwed, if it gets in among those guys they'll spread it everywhere.

I had no problem with the name, until seeing a post on a local Spotted Facebook page. Someone, who loves to bang their anti-Covid restriction drum, pointed out that Omnicron is an anagram of 'moronic'. A fellow supporter commented that it was a 'level two troll' by those behind the New World Order. They really do walk among us.

How would 60 people on one flight have it? That's about  1 in 5. Did tbey spread it to each other during tbe flight?

Brilliant. I will be unashamedly plagiarising this when necessary

Yeah. That's because it's going to be the morons it will disproportionately affect...

Out of 600 people. Still a lot but must reflect high prevalence in that area of SA at the moment. I’d be surprised if infection on the plane would be picked up by a test a few hours later but I’m guessing here. 

More than you'd think.

I've been pondering my immediate and strong dislike to the variant name whilst shovelling the snow away this evening.  It's much easier to take an instant dislike to something than it is to figure out why.  I think it's three things..

• Omicron is a word massively overused by people writing Sci Fi technobabble (at least in English language works) and so it seems out of place with Covid.  I expect the passing familiarity and association this invokes in many feeds in to the insanity you saw.   
• It has more syllables than the disease it applies to; this seems backwards, counter to the natural order of things.
• It doesn't roll off the tongue in the context of "Omicron variant" - all the previous variant names ended in a vowel, following naturally in to the consonant at the start of "variant", where-as when actually speaking this, an extra pause is needed to re-arrange the vocal stricture from one consonant shape to the next.  There's a reason we put vowel sounds between consonants in a word, and all the greek letter prominently used to date naturally flowed in to the consonant at the start of "variant".  If I say them all out loud with "...variant" on the end of each, omicron is the odd one out.

Still, I can see why the WHO don't want to waste too many letters of the Greek alphabet, that's always seems a rather optimistic choice for the list of variant names...

Probably the single most pointless and diversionary comment I've made on Covid yet...  Better than thinking about the alternatives though.

Are the names not simply allocated sequentially, as significant variants develop?

Otherwise, isn't it like calling them A, B,C, D, O?

They skipped over "nu" and "xi", so there's clearly some level of thought going in to what makes a sensible and politically acceptable name.

Dingo Bongo.

They skipped past Xi.  Sounds nothing like the turd in China btw.

I know I'm not that familiar with the Greek alphabet, but I don't recall either of those...

There were two flights, but even so. And I think the Netherlands were still requiring pre-departure testing (at least they were for ex-uk) 

Danny Altmann, professor of immunology at Imperial College London.

“And yet, the soundings we’re getting from South Africa seem to be saying that it doesn’t look severe, and the people who are going to hospital are the unvaccinated, rather than the vaccinated, as if vaccination was still buying [them] some cover.”

https://www.theguardian.com/world/2021/nov/28/what-does-appearance-of-omicr... 

No Severe COVID Cases Among Vaccinated Patients Infected With Omicron, Top Israeli Expert Says 

https://www.haaretz.com/israel-news/top-israeli-health-expert-covid-vaccine...

Though it has also been pointed out that that doctor had only seen young patients, and the death/hospitalisation rates in SA are increasing quite quickly.

Yes, she seemed to be reporting an anecdote about one family, primarily. 

Indeed.  Unsurprisingly the deniers are seizing on it to misinform.

Heads up on latest covid misinformation doing the rounds (LBC, GB news and social media).

https://www.logically.ai/factchecks/library/99987978

Perhaps one for the other thread but here’s an explanation (where possible) of the various Omicron mutations from the Covid sequencing lead at the Sanger. Looks pretty bad in theory… See the thread for further details  

https://mobile.twitter.com/jcbarret/status/1463975708770897923

Government have pressed a Big Red Button as heralded in the news.

As big red buttons go, this one is very big indeed - 3rd dose on a 3-month gap to all over 18s, and second dose to 12-15 on a 12 week gap. 

https://www.bbc.co.uk/news/uk-59465577

The JCVI guidance on second doses for aged 15-16 was interesting reading, it seems the very low probability specific side effect that was causing concern is largely mitigated by the 12-week gap.  I haven’t read the guidance for 12-15 yet but I imagine it’s similar 

https://www.gov.uk/government/news/jcvi-issues-advice-on-covid-19-booster-v...

https://www.gov.uk/government/publications/covid-19-vaccination-resources-f...

Edit: An apology from me for this in my OP  "Switzerland[... is ....] holding a vote on if they should drop all Covid control measures or not".  That should have been "some", not "all".  Not sure how I got such a bad impression of the news reports, and can't check as they've been updated with the result - control measures remain in force.

Some updated rate constant plots for England.  Still having a Zeno's paradox approach to top-level decay.

The demographic splits show that decay has continued in ages 60+, growth is running out of stream in ages 15-59 and 0-14 is headed for decay. The timing of the various peaks combined with the "double bump" in recent weeks has me still thinking we're seeing a decay in 15-59 linked to the warm period after Guy Fawkes that's eclipsed by lagged household transmission from school cases.  

• If I'm right (it's a hunch, not tested theory) then we'll see a repeat of this landing very soon with the current cold spell - another big spike of younger school aged cases where immunity is lowest, then a downstream spike through household transmission.
• (I seem to have held out against catching it so far, but I'll be amazed if I make it to the end of the school term without the clobbering almost everyone around me has been getting...)

The weather passband plot gives a hint here - this shows the "passband value" for temperature and rate constant; here "passband" means that we're looking at the deviation from a medium term moving average (timescale of weeks), with day-to-day noise averaged out.  

• So, we see when the temperature is higher than a moving average the rate constant is lower, and a vice-versa.  
• The last week has been in violation of this usual relationship, with worse growth in the passband than expected, as shown by a red shaded area.
• Two more days on this plot before we'd expect to see a rising rate constant in response to the cold spell.  I've extended the weather data rather non-robustly by taking the average of the high and low daily values from the BBC 14-day forecast for the village of Maidwell (somewhere in the middle of the CET measurement zone).
• Given how close the top level rate constant is to 0 at the moment, and given that the passband shows deviation from the trend, it's hard to imagine we're not going see top level growth.  I expect we'll see big growth in 0-14, moderate growth in 15-59 and either stagnation or low growth in 60+.

At some point - probably soon - hospitalisation from rising cases in the upper end of the 15-59 range on the splits plot will outweigh falling hospitalisations from the 60+ range, meaning that the long running fall in hospital admissions and occupancy could go in to reverse.  Another 3 weeks of boosters have passed since the last cold spell however....

Right down to the wire...

Edit: A plot 22 update as well - there's been a bit of a rise in ITU occupancy despite falling hospital occupancy; not something I recall seeing before.  It could perhaps have been explained by a demographic shift to older people, but the cases data is shifting in the other direction.  Hospital data is not very granular but I might have a look later.  Strange, and perhaps a little concerning.

If hospitalisations have shifted demographically out of the 80+ age group a bit that might be the reason for increased ICU occupancy. I understand the ICU figures are only for people on mechanical ventilation and that people aged 80+ are less likely to be given mechanical ventilation as they might not recover from it.

The NHS England vaccine booking system is notable right now - it has a hold queue where a quick measurement suggests about 25 people are joining a second or 90,000 people an hour.

What's interesting is that the proposed changes haven't been actioned in to the system it seems, so nothing there has changed I think - except that suddenly a lot of eligible people who hadn't previously signed up (including 1st, 2nd and 3rd doses) have suddenly got vaccine fever.

Amazing what some wall-to-wall press coverage with the word "Variant" in it achieves.

Edit: unless most of those peoples are queuing up for the disappointment of rejection for trying to book before 5 months post second dose…

In reply to Si dH:

Interesting thought, thanks.  Edit: not the best news for the eventual effects of the current cold spell if so.

In response to earlier, yeah the hospitals and doctors aren't stretched at present, but that could change quickly of course, but at present there is slack in the system, admission and icu cases are low. 

They have two possible cases, folk returning from Africa testing positive, but some press are jumping the gun claiming omicron, even though it's not been sequenced yet. But sweden being sweden they aren't alarmed, most are too busy waxing their skis as winter kicks in!  

Regarding the Swiss referendum, it was to approve (or reject) the entirity of the existing Covid Law. In particular, it proscribes the Covid Certificate for vaccinated, tested or recovered people, and which one needs to eat in restaurants (of which a lot goes on, e.g. at lunchtimes during the week). The certificate requirement was the main focus of the debate, with regard to creating a divided society. Much hand-wringing still going on post result.

The law is here: https://www.fedlex.admin.ch/eli/cc/2020/711/en

Apologies for anecdote but I booked my booster a few days back... earliest slot over two weeks away in a big centre more like three for a convenient pharmacy. I simply can't see how all the extra  demand now being planned can be met before January, and even that is looking difficult in high demand locations.

As a city we have one of the worst vaccination rates in the country (and most of that is hesitancy but there is a denominator issue). We had a system glitch earlier in the year where the minimum age limit got left off: that got lots under that age trying to book early and the system crashed. 

As ever with long queues the most problematic to reach, usually the most deprived, end up being delayed most and the vaccination gap adds risk to everyone.

Is that true? I don't know across the board, but my mate is consultant  in A&E in Sheffield. He says average time to see a doctor on his last shift was 9 hours. He says the reasons are multifactorial. Maybe Covid cases in hospital aren't that significant (compared with previously), but the picture he painted wasnt one of slack in the system.

Summo is posting from Sweden I think.  

Sweden is really interesting.  Pre vaccination their trajectory has been quite close to the UK (but with lower control measures - a win for the Nordic lifestyle?).  

At present, I reckon Sweden in particular split the difference between the UK and much of the rest of Europe; good demographically weighted vaccination like the UK and a big post vaccination wave mostly in a younger demographic - but it’s perhaps 0.6x the scale of the UK’s and came pre delta - so more genetic distance from delta and more wanning but streets ahead of places that suppressed spread with measures short of knockdown until winter blew all that control away.

If anywhere in Europe beyond the UK is going to make it through the next 6 weeks without lockdown, I reckon it’s Sweden.  Wouldn’t like to call it either way.

Edit; that’s all written on the hopeful assumption that omicron isn’t a game changer - although already the threat of omicron is changing the game, regardless of how real it turns out to be.

“Javid says getting rid of almost all controls in the summer turned out to be the right move. He claims that some of his European counterparts wish they had done the same. 

We did take measures in the summer where we set out that we were removing almost all domestic rules and controls. They turned out to be absolutely the right measures. There’s many of my counterparts in Europe that now believe that they should have taken a similar route as well.”

Well, quite.

Whilst it hasn't been spelt out in 40-foot high burning letters that the UK has had a deliberate intent to the policy decisions over the last 4 months, it's not exactly been a secret either.

I feel now is a relevant time to link back to this thread from a couple of months ago:

https://www.ukhillwalking.com/forums/off_belay/why_is_our_infection_rate_so_hi...

Who I listen to on here is strongly correlated with who was on the ball in that thread.

I was surprised by the ferocity of the pushback to some of the early plots on here ~6 weeks ago showing the inevitable land in Europe; it's got to the point it can't be denied any longer.

What bitterly disappoints me in all this is that the same politics-over-science mentality seems to be behind the approach in a lot of other European nations as well; the number of times up-coming elections seem to influence things is uncanny.  I'd been holding to hope that some European nations would navigate their way through this pandemic consistently better than the UK, to give a solid comparator come the public enquiry; that increasingly looks like a forlorn hope as the gains from their earlier, better responses are now squandered by poorer vaccination (by demographic risk weighted  measures) compounded by an inability to accept that there's only one way a pandemic ends.

If Omicron turns out to escape all forms of immunity it will reset things however; it's become clear the UK is now in a better immunological position than most of Europe; that means we have more to loose with an escape variant.

As always, it pains me to say this but some can't wait to misinterpret.  Recognising that we are where we are does not mean endorsing every step of how we got here.  With these threads, I want to try and understand where we are and where we are going. 

Swedish measures were subtly stricter than they looked and not that different anyhow. Just compare the OWiD stringency index for the UK and Sweden throughout the pandemic.. Then remember they focused on what mattered most (for instance they let people meet outdoors, where we were stupidly paranoid long after it was known that wasn't a serious issue) but also because they knew there would be better than average (for the EU) compliance.

There is still hope with Omi (as the Metro call it) as it might be a good bit less lethal but more contagious...we just don't know yet: so take rapid precautions in case its just as lethal and more fingers crossed  X.

More contagious and less lethal is good (I thought). Would it not become the dominant strain taking over from delta but leaving less carnage in its wake?

Sorry, in my normal post then edit process, that was the point I was trying to make (but we don't know that yet and it could still be really bad).

I don’t really buy the idea that it’s less serious. We just haven’t seen the impact yet. SA has a younger population, as well as a poorer one - wonder if healthcare is free there. There is no real selective pressure for the virus to be less lethal - the IFR is pretty low as it is (in terms of impact on spread). Of course it could have evolved to be less lethal by chance. If it turns out to be more transmissible but less lethal, happy days. However that seems optimistic to me. 

One difference now is it's winter, proper winter, below-20 in North, just below in the very south. Life for most has very much swung indoors. 

Technically sweden already had a ban on non essential travel beyond the eu, but they were many exemptions like family visits etc.  I'm not sure how much impact it had at all. 

It might not be, if say, it was twice as contagious and half as lethal. The uncontrolled peak of infections would be much more than 2x higher and the health service would be overwhelmed.

Moderna CFO reiterating what Moderna CMO said at weekend ...

"Moderna CEO Sparks Slump Reiterating Omicron May Need New Shots

By Michelle Fay Cortez

(Bloomberg) -- 

The plethora of mutations in the omicron variant are likely to help it evade the protection provided by existing vaccines, making it necessary to develop new immunizations, Moderna Inc. Chief Executive Officer Stephane Bancel told the Financial Times, triggering a pullback in risk assets. 

Bancel effectively reiterated comments made by Moderna’s Chief Medical Officer Paul Burton at the weekend, that omicron may elude current vaccines, and if so, a reformulated shot would be available early in the new year. The CEO seemed to damp expectations new vaccines could be ready soon, however, saying in the FT interview it may take months for pharmaceutical companies to develop and deploy updated immunizations that they can deliver in large numbers. 

There is no way the current shots will provide the same level of protection against omicron as they do against delta, and there will be a material drop in their efficacy, he said.  

“I just don’t know how much because we need to wait for the data,” Bancel was quoted as saying. “All the scientists I’ve talked to . . . are like ‘this is not going to be good”’

Bancel’s definitiveness appeared to spook markets, with stocks in Asia retreating along with U.S. and European index futures and crude oil. 

Moderna said last week that it has already been studying booster shots that were designed to anticipate mutations such as those that have emerged in the omicron variant and will rapidly advance a candidate targeting this new strain specifically.

Current vaccines from developers including Moderna, Pfizer Inc. and BioNTech SE, AstraZeneca Plc and Johnson & Johnson are all able to help reduce the risk of severe infection and death from previous strains of the virus, though they work less well against the more transmissible delta variant. 

Research is still underway to determine if omicron causes the same level of illness as older versions of the virus, if it can evade protection from vaccines and previous infections, and if it will be able to outcompete the existing strains as the pathogen continues to circulate throughout the world. 

Moderna is striking a more pessimistic tone than Pfizer, with Chief Executive Officer Albert Bourla saying earlier in an interview with Bloomberg Television that omicron will know in two to three weeks how well its current shot holds up against omicron, and even in a worst-case scenario he expects the existing formula will retain some efficacy against the heavily mutated strain. 

Bourla said Pfizer will be ready with a vaccine targeting omicron in 100 days, should it be necessary. 

Chinese vaccine maker Sinovac Biotech Ltd, whose inactivated Covid shot has been widely used in China and much of the developing world, said it’s also evaluating its vaccine’s performance against omicron and the necessity for a new shot. The company said it can rapidly come up a new vaccine and manufacture it at scale quickly. Meanwhile, Chinese company CanSino Biologics Inc and Japanese drugmaker Shionogi & Co have both said they’re working on new vaccines for the variant. "

This makes me wonder if it's worth waiting for a different booster. I am very pro vax, but am slightly skeptical about the new decision to allow anyone over 18 and 3 months since last vax to have the current booster. I can't see that they have the knowledge yet to know that it will be effective?

I share the concern over the recent move with increasing the booster age range and reducing the interval between them, but why someone who is 'very pro vax' would be 'skeptical' about it is a bit confusing to me. It's either an evidenced decision made by experts we trust, or you have to remove at least one of those three words in that phrase (evidenced, experts, trust). Otherwise your skepticism is unwarranted.

I've to seen very good English language summaries of the timelines and control measures further East.  Be interesting to understand more about what kept it under control over the summer; climate as much as weather I expect, and the downstream effects on the ways people live and interact.

Well that's a cherry way to start the day!

It's highly effective at driving delta in to decay in the oldest age ranges, so it's likely it would more or lass halt the delta pandemic if everyone got a booster tomorrow.  

If I consider the spectrum of possibilities, it makes sense to me:

1. Omicron is just like delta immunologically speaking
   • 3rd doses for all will wrap up the current high hospitalisation rates far sooner than otherwise  
2. This is partial but reduced cross-immunity with alpha- and delta- induced immunity and current vaccine induced immunity
   • 3rd doses will help compensate for the reduced cross-immunity
3. There is no cross-immunity with alpha- and delta- induced immunity and the current vaccines don't work
   • This is the bastard scenario
   • In this scenario, omicron doesn't out-compete delta, it just goes on to be a different pandemic happening at the same time.
   • 3rd doses will wrap up the current high hospitalisation rates for the old pandemic, making much needed hospital space 

In practical terms I don't think the posters are going to happen much on shorter timescales as the logistics are looking like the limiting factor...

In terms of waiting for a different booster, having run through the scenarios above I'm happy to get my 3rd one as soon as I can.  Which is looking like +6 months...

I think there's some confusion that the most recent changes are purely in response to omicron.  I don't think so. 

Just as the inclusion of 12-15 year olds for a 2nd dose could be anticipated by the pre-omicron decision over 16-17 year olds now getting their 2nd dose, I think the move to a shorter gap (I've been banging on about that for a while...) and younger ages for the 3rd dose was coming regardless; omicron has sped things up a bit out of precaution but given the evidence piling up about the efficacy of the 3rd dose it would have been madness not to do this; my guess is omicron has taken another month or two off the gap beyond what was planned...?

In addition to what WT said, and putting my cynical hat on, the CFO of Moderna is likely making a play for advanced funding from worried governments so that he can develop his new vaccine at no risk. He is incentivised to paint a negative outlook.

Not sure why you’re collecting downvotes there… 

A reduction of protection from severe infection from 95% to 90% (for example) also seems small but it would double the number of people going to hospital, again overwhelming healthcare.

The UK is one of the places leading the way in terms of having lower control measures enabled by very high population wide levels of immunity; this means we have more to loose if immunity weakens.  Especially as we can only just keep up with the low levels of demand the virus is creating (compared to pre-vaccination waves) right now, much immune escape is a disaster.  

Edit: when you look at how the UK got here, “leading the way” is not the same as “winning”.  I say this to stave off the kind of response any recognition of our position has been generating recently…

Maybe the down votes are from people in denial about how close to the edge the NHS is. We just don't know enough about Omi yet and can't do much about it other than lockdown if it turns out to be more contagious but puts the same number of people in hospital and the morgue per infection as delta... and that's scary.

I'm going to suggest a take on climbing grades.

So Covid variant Alpha becomes C1 then Beta C2 etc.

Mild ones could be HVS (Hardly a Variant of significance)

With a technical lockdown grade of a ('ardly noticable, business as normal) b (betta get a mask) c (Christmas is cancelled)

I am pro vax and happy to have the booster, but yesterdays news gave me cause for concern, hence the post. My concern is that I take a booster vaccine tomorrow, and then find out I need another vax in 6 weeks time for Omicron.  I also wonder where the evidence based decision has come from for yesterdays change in policy when there have only been a handful of cases globally and the pharma companies have admitted it will take weeks to get a better idea. I have heard big pharma have all "war gamed" various scenarios over the summer with different potential variants, and that might be why we have seen this reaction. I just don't know. 

Wintertree's answer re killing off Delta rather than protecting against omicron is a good point that I hadn't really considered, but still feel we haven't had an explanation why 6 months wait was considered perfect last week, and now 3 months is fine. 

It'll be pretty effective against delta which will be circulating at high levels for some time yet however competitive omicron actually is. If it's really bad, capable of re-infecting easily and significantly evading the vaccines we'll inevitably be adding winter social control measures to avoid a hospital battering re-run of spring-2020. That will slow down the replacement of delta but of course also reduce the opportunity to catch it. If omicron is not as competitive as it seems, if it turns out to be something we can live with in wide circulation that'll be because existing vaccines are pretty effective so worth having and the replacement of delta will take a while anyway.

I suppose the unknown is whether we have to wait x, y or z months after the non-omicron booster before getting an omicron tuned booster delaying the protection we'd have got from that. All a bit speculative given such a thing doesn't even exist in a lab yet.

I can't see a clear reason to skip it.

jk

So is this a safety concern? Or a concern for the inconvenience of having to get 2 boosters?

I would have thought someone who is self proclaimed 'very pro vax' would not be worried about minor inconvenience? So what is the problem?

Maybe.

But selling a billion doses of a product he already had for boosters would also look pretty good in next quarter's numbers.

I think they'd have been happy to say 'our stuff is brilliant, buy more of it and you'll be fine'.

They're thinking 'oh f*ck what can we do in the next few weeks' and noticing they've got a ton of vaccine in storage and thinking WTF it may as well go in people's arms before the sh*t hits the fan, if it does no good it will do no harm.

Even if Pfizer turn round a new jag in three months it would be another two or three before they've made enough, it has been distributed and the NHS have actually injected it.  I can see round two of the 'which country gets their orders first' game being played and this time the UK being further down the queue because the mRNA jags are made in the US and EU.

What's your concern?

We know that there isn't sufficient data to make a perfect decision, it's a best guess made on incomplete evidence. I thought the concern about receiving a less effective shot than if BiS waited was obvious? If a new shot is available, it could take 6 months or so to get it if you're not a priority group. 

The point of changes to the age range and boosters timing is presumably just to increase population immunity as fast as possible if we're satisfied that vaccinating the vulnerable can't be sped up further. This is assuming we're not already jabbing at full capacity - I don't think we are?

I don't see where a valid concern would arise. 

It is possible to be pro vax, but not want to be taking new vaccines monthly as viruses adapt , which I think most people would agree with. Why do you find this a hard concept to imagine? Just apply a little bit of nuance to "pro vax" and hopefully what I said will not be so black and white for you and might make more sense. Pro vax does not mean "loves vaccines, wants more vaccines"

The drop to younger ages and a shorter period was already anticipated as the data on 3rd dose efficacy comes through loud and clear, along with the data on the effects of winter.

Omicron has clearly sped up decisions and probably shaved another month or two off the minimum gap.  I suspect actual gaps won't drop as much due to scaling the logistics..... 

On the other hand AZ and Novovax have production facilities within the UK, and both can be eminently adapted to new variants - a process already underway for Novovax at least [1].

I suspect that the next variant adapted AZ vaccine will have addressed the cause of its particular very low risk side effect, given the published findings over the splicing site issue.

I am curious as to why you think we have to buy the mRNA vaccines; you do always seem to return to those.  The UK's decision to back a production plant for Novovax seems quite sensible - I assume the contract for 60 m doses already placed puts us at the top of their propriety queue, and it's a technology readily adaptable to new variants that is reasonably suspected to produce lower side effects and that has none of the complex cold chain logistics of the mRNA vaccines. 

[1] https://www.reuters.com/business/healthcare-pharmaceuticals/novavax-testing...

BBC live feed is reporting a spokesperson from Oxford saying that they can adapt the Ox/AZ, but implication is that work isn’t yet underway…..

Those quotes are very apt... Is that 'rapid' in terms of conventional vaccine development timescales, or 'rapid' as in being able to deal with 'oh shit' timescales...?

I think before this pandemic most people would agree with that statement, yes. In our current scenario I'm not so sure where people stand. 

If monthly vaccines were deemed necessary and safe, being pro vax you'd be obliged to take them wouldn't you? Otherwise by definition you'd be 'anti-vax'.

Terms like pro-vax and anti-vax are devoid of nuance, hence my issue with people using them. If you ask for nuance to be applied to the former, you must also apply nuance to the latter which most don't/won't/can't. So really both should be discarded, especially as the need for nuance grows.

I am currently booked in to have my third dose of a vaccine in about a week and after just receiving my results from the ONS Covid study I am pleased it’s happening. According to the results I don’t have Covid and now I don’t have antibodies either. I had my second dose (of the Oxford vaccine) in June so for me it looks like antibodies only last about five months.

Maybe the thinking's not quite so emotive - it might be more like - this could turn out to be really bad, is there anything we can do now that might help if it does turn out to be that bad.

The gap originally being 6 months (and the lower age limit) is not wholly scientific, it's partly political and partly supply/demand situational (as I'm sure you're aware).

Really struggling to see what your point is.

As far as I can see, we've got different degress of 'anti-vax' from 'it's a microchip conspiracy' to 'I'm not sure about the potential health risks, I read some stuff on facebook that was scary' (these people might not want to be tarred with the 'anti-vax' bell-end brush); and then everyone else, who will participate in the effort to control disease by getting vaccinated according to what's offered.

If the choice was between monthly vaccination and society being crippled by disease (healthcare unavailable, lockdowns, economic collapse) then obviously it would be rational to get vaccinated every month, wouldn't it? But vaccines don't work like that. What is your point?

Do you believe there's room for members of the public to have "valid concerns" about the vaccines they're offered after all the advice and analysis from the JCVI? I.e. a rational possibility that someone declining such a vaccine is acting in their own best interest, and/or that of wider society, on a predictable statistical basis (not "I'd have been better off if I hadn't had that vaccine"). No one is going to want a vaccine that hasn't been shown to be the best way to control disease. No state is going to want to pay for vaccines that haven't been shown to be the best way to control disease.

"I'm not anti-vax but..."?

You must have given a lot of blood to science of the course of this pandemic...

The disposal of antibodies after an infection is the normal order of things mind you; the information lives on inside you in immune memory cells, ever alert for the call to action.

Personally I'd be quite happy to be getting a boost to my antibody levels in about a week from a jab...

LOL, not really, the ONS only need a few drops which is a tiny fraction of what I ‘lost’ whilst recovering from my last angiogram and then there are the three vials every six months that my doctor takes because of my heart condition.

I have wondered what Oxford University (and partners) does with these ‘gifts’. Is it only tested for Covid then discarded or are they using the opportunity to accumulate a massive blood database for study?

I think previous scandals involving unauthorised retention of body parts/tissue samples probably means that samples can only be used for the stated purpose, and can't be used beyond that scope.

But...

Well, that little displays of xenophobia has proved rather wrong in an egg/face kind of way.

https://www.bbc.co.uk/news/uk-scotland-59473564

All nine cases of the new Omicron variant of Covid are linked to a single event, the first minister has said.

Nicola Sturgeon told MSPs that all those affected had been tested on or around 23 November and had been self-isolating since then.

She said the cases all traced back to a "single private event" on 20 November.

She added: "We fully expect that there will be more cases identified over the coming days that are also linked to this event."

Five of the cases are in Lanarkshire and four are in the Greater Glasgow and Clyde health board area.

People spread Covid everywhere.  It really doesn't matter if it's "those guys" from Westminster, or people form Glasgow, America or Xanadu.

Well, in the permissions form I signed for one of their studies, they asked if it was ok for them to sell on any "leftover" blood to whatever third party company fancied getting their paws on it. I said no.

That got me wondering… What does informed consent look like for the sewerage studies being used?  I suppose they’re only amplifying viral material…  “By flushing this handle you hearby consent to transfer any and all faecal data to OmniConsumerProducts”…

Its amazing what tissues are sold on these days after surgery.  Sounds like type 2 diabetes feeds a thriving business in repurposing amputated limbs. Just don’t ask what the final product costs.

The paperwork states that the samples are a gift to OU (but for a bit of snot I get paid!) and it’s all voluntary so I can’t see it being a problem if the data is retained. I hope it is. Some people will become very ill or die during the survey and there could be monthly record of the progression of the illness. I can’t see that an opportunity like this has happened before and who knows what could be found by studying the data in the future.

That's a nice ideal. But unless the specific 'research' purposes are declared in any consent form, or genuine anonymity guaranteed (not 'pseudonymity'), I would adopt johnny taylor's stance and decline.

Who knows what nefarious insurance-based purposes some unspecified buyer could use your samples for? It's bad enough that people send their DNA for commercial 'ancestry testing' without consulting their siblings, or reading the small print about additional 'research' uses, without legitimate medical research ending up along the same murky path.

My nom-de-net is sometimes justified...

Unless they've got a sampler in my downpipe, I'm hoping that turd samples are fairly anonymous...

Related to the omicron variant:

"That look-back exercise has examined PCR test samples dating back to 1 November to identify any with the S gene dropout" [from https://www.theguardian.com/uk-news/2021/nov/30/scottish-omicron-covid-vari...]

I had rather assumed that after the Alpha variant they would be monitoring for this routinely. Or perhaps there are always a few dropouts and they're just meaning they prioritised those for sequencing to confirm omicron in some...

I suspect that depends on whether you’ve ever given your genome to one of those family tree companies..

You’re right. There’s always a background dropout rate (c. 0.1% iirc) which is basically random testing failures on that gene, not mutation driven. I imagine it’s the same on the other 2 genes taqpath uses but we don’t hear about those!

That lead me to this:

https://www.theguardian.com/commentisfree/2021/nov/30/anti-mask-blitz-war-p...

which contained this:

"Being told by the state how many ounces of basic ingredients you were allowed per week feels a bit more of a pisser than being told to wear a mask while you load up your trolley with pounds and pounds of the stuff in Asda. (I know it’s kilos these days, but I didn’t want to send them really off the dial.)"

LOL...

You didn't see my comment about siblings, then...?

I haven't, but my siblings DNA will be very similar to mine...

I didn’t.. I think you’re in the sewage, so to speak!

I guess when you flush a sh*t you are turning ownership over to the water company like when you chuck rubbish in the bin you are turning ownership over to the council/bin company.

So it isn't your sh*t anymore and they can do what they like with it.

I had this argument with a dentist once after having a tooth extracted. I wanted to keep it to show my kids and illustrate why they should brush their teeth and I got told in no uncertain terms it wasn't my property it was clinical waste and I wasn't getting it back.  I never signed anything to turn over ownership of the tooth and if something which was an integral part of your body doesn't belong to you what does?

The reality is it’s at least 3 months until an Omicron booster is produced (and approved, presumably) and then many more months until it’s easily available, unless you’re in a high risk group. So I’d get the current booster (which is what I’m doing next week) and the there might be an Omicron one in 6-12 months’ time. 

How was it xeonophobic to point out that people were walking off planes from South Africa in Heathrow with zero tests or quarantines and that people who came to Scotland from South Africa would have gone through Heathrow or Schipol but that Schipol seemed to be doing a better job of finding folk with it coming off flights.

Now there is new information that the virus was in Scotland 9 days ago. That doesn't change anything about how it got here, assuming the original source is South Africa. In fact, you could argue if there had been more testing of arrivals at Heathrow from outside the highly vaccinated countries we could potentially have spotted this a week or two ago and be in a better place.

All the way through this the Tories have been determined not to upset Heathrow's place as a global travel hub by adding any inconvenience to travelers and have accepted the increased risk to the UK.  

Yeah, I agree. US processing lab = sold to highest bidder. Or any bidder, come to that...

Not so good a job of keeping them quarantined in a robust way

https://www.bbc.co.uk/news/world-europe-59473067

You may be right about that.

Were the testing requirements any different in Scotland? Seems as if day 2 lateral flow tests were in place, same as England.

No idea. The point is there are no flights from Scotland to South Africa. The place it needs stopped is the airport with the long haul connections, which would be Heathrow or possibly Schiphol.  

The Scottish Government have had slightly different and tougher restrictions than England on airport arrivals at a couple of points but I've never seen the point when there is an open border to England.  Nobody is going to spend £2k on an airport quarantine in Scotland when it is p*ss easy to dodge.

Good point; there seems to be no link between any of those in the 'private function' outbreak and South Africa. I bet some bastard from Westminster flew to SA, deliberately got infected, and secretly snuck into the private function, and licked all the Tunnocks teacakes... There is no end to the evil those Westminster types will do to f*ck over the Scots. 

There were private flights for COP, haven't all the Scottish infections been traced as secondary, which 'could' tie in timeline wise? 

I don't know. But if it goes all the way back to COP and this is the first time its been noticed I guess that gives some ground for optimism that all the jags and previous infections here mean it can't spread as fast as it did in South Africa.

I'd have thought the official COP delegates in the private jets would have been tested to hell before they were allowed on site with all those rich and famous people and world leaders present.  

We can hope. Based on zero evidence, I'll predict this mutant a near miss, we'll still have some protection and it'll be anti vaxers suffering. Hopefully causing the west to not rest on their 1st and 2nd dose, and start doing more to protect those in other countries. 

If we can jail folk who glued themselves to the m25, the anti vaxers should be inside too! 

Not leaders, but crew mixing whilst enjoying a week in Glasgow? 

The setup crew (mostly from UK I assume) were there for weeks before COP so timing would point more to heads of state, UN staff, delegates, activists and media.

Everyone on site had to do a lateral flow test daily and I heard from someone working there that the COVID rate was lower than that of Glasgow (an element of positives diluted when everyone is testing?).

Overall COP was a huge news story but a small proportion of people entering the UK in the last month or two. COP only equivalent to a day or two of airport arrivals even if airports were running at only 10% of normal.

Correction:
Overall COP was a huge news story but a tiny proportion of people entering the UK in the last month or two. COP only equivalent to about half a day of Heathrow passengers or a full day of Heathrow arrivals.

Heathrow Airport managed to hit three million passengers in October 2021
https://www.independent.co.uk/travel/news-and-advice/heathrow-airport-passe...

The People's Covid Inquiry report is out.

The summary pdf is here:

https://36085122-5b58-481e-afa4-a0eb0aaf80ca.usrfiles.com/ugd/360851_62aeec...

The full report is linked here:

https://www.peoplescovidinquiry.com/

Roy Lilley's take on this:  "Jaw dropping"

https://myemail.constantcontact.com/Jaw-dropping.html?soid=1102665899193&am...

Well, I thought that might be interesting, but the exec summary to the summary report (yes, that's right) is over 20 pages long! Who in their right minds...?

Anyone who writes a 20 page executive summary has never dealt with a busy enough executive!

In reply 

Research news that finds serious covid infection significantly increases subsequent mortailty risk, so further stressing the importance of vaccination:

https://www.theguardian.com/world/2021/dec/01/severe-covid-infection-double...

Clearly you haven't read many independent public inquiry reports, and their summaries.

I linked Roy Lilley as he has a quick readable take on the matter (as an ex health management advisor for a previous tory govenment).

It's hard to see any learning matters anymore when, with all the trouble we may face over winter, our PM throws sensible advice from the at times cringeworthily loyal head of the UKHSA under a bus.

https://www.theguardian.com/world/2021/nov/30/boris-johnson-contradicts-exp...

As Peter Cook famously said:

"I have learned from my mistakes, and I am sure I can repeat them exactly"

We’ve certainly been busy reading the guardian this morning to be suitably outraged.

The “independent” report looks about as biased as you could possibly make it. Lots of talk about elimination too. Absolute guff.

People who are vulnerable enough to got a serious case of Covid are more likely to die soon? No sh@t Sherlock. Next you’ll be linking the guardian article which explains that 90 year olds are more likely to die than 40 year olds and telling us how outrageous it is.

Finally a government that doesn’t want to trash the economy when they don’t know how serious Omicron is yet. Boo how evil and despicable.

I was thinking more of flight crew, but maybe also aides, advisors etc...  either way, it's a small peak detected in a city that recently had lots of international travel, I'm a big believer in proven causation and correlation, but this can't be chance.

There are cases proven to have existed in the Netherlands a few weeks ago too. In the early stages the mutation numbers were likely so low it probably didn't stand out much. 

COP was tens of thousands of people so a tiny fraction of those entering the UK in the last month. However it might have been about half of those coming to Glasgow in the last month.

All nine cases of the Omicron variant of Covid in Scotland are linked to a single event on 20th Nov so it is VERY random.

If one person had been a bit more careful/lucky and not caught omicron, if that person's car had broken down, if the ventilation had been better, if they'd been an anti-social bunch and not got together or if the event had been cancelled for some other reason there may have been zero detected cases.

Funnily enough the authors of the work thought of that and presented both “raw” results and results adjusted by factors indicating vulnerability.   See table 3; that suggests for severe covid they perhaps 2/3rds of the increased risk is down to consequences of the infection and 1/3rd is because covid is biassed towards the more vulnerable.

The Kaplan-Meier curves are interesting; most of the increased risk falls in the first 150 days or so after Covid then it stabilises close to the No covid risk analysing the plot “by eye”. 

It’s very interesting in terms of determining the “true” death toll but in terms of its association with mortality risk and that attributing of deaths needs extending out to 150 days; this I think won’t be possible at an individual level but analysis such as this could be used to contextualise the national level death count if supplied with some national level statistics on vulnerability.  Given how low the KM curve falls it’s not a small adjustment.  The excess mortality around waves has rather foreshadowed this.  

Always worth reading the paper rather than commenting on the guardian headline…

Your slating of the Guardian does get a bit dull you know...

Edit - Offwidth - if they can't write a short (1-2 page) exec summary so that more than 10 people actually read it, the authors shouldn't have been given the job. I have just finished a 160 page report covering almost all of my regulatory work over the last two years (that's 70% the length of their full report). The exec summary is 1.25 pages. It's not hard.

(The title of the report also leaves something to be desired. No-one who disagrees with their position will pick it up.)

It's not luck It's probability. If you have slightly less than optimum covid testing, distancing, ventilation, mask wearing etc.. you increase the odds of an infect person passing it to an uninfected person. Repeat through multiple meetings over everyday of cop, eventually covid breaks through.

The only other possibility is oil and gas workers coming home from some regions of Africa, as it's likely Scotland has a higher proportion residing there. The earliest African cases appear to have been in Nigeria. 

Flights, if it was purely volume of passengers, the first cases would be where most Heathrow passengers in November went home to? I'm guessing it's not Glasgow. It's pretty obvious the Netherlands would have cases, as it's a European hub for so many southern and central African flights. 

Disagree, I find it quite appropriate. I was going to say something myself and VS saved me the job. It's comical how often and exclusively Offwidth links to the Guardian. It's like a meme at this point, a bit like tom_in_edinburgh with the Tory hate.

Yes… adjusting the raw data to account for a comorbidity model.

A model which says if someone has x they will live on average y more years.

Is it not possible that those who are susceptible to serious Covid would skew heavily towards the “would have died sooner rather than later” end of the spectrum?

Anyway I would imagine if you get a bout of anything especially nasty it isn’t very good for you.

Yes, and that’s what the authors control for using the known risk factors for Covid; there is still a large effect here clearly due to the infection not their susceptibility to it.  That’s why the process full medical records for all people in the study,

The shape of the K-M curve makes it abundantly clear much of this is not a selection effect, as the steeper gradient (enhanced death risk) does not persist after 150 days.  Clearly tied to the infection.

Indeed, but given that there’s been an awful lot of covid about it hasn’t been very good for an awful lot of people.

Hmm okay I see your point about the shape of the curve.

Fair enough.

This was reported in the Guardian, it was a study published here:

https://www.frontiersin.org/articles/10.3389/fmed.2021.778434/full

And what do you know, they controlled for comorbidity. Well I f*cking never, who would have thought that? 

Your over-confidence in your understanding of scientific research is embarrassing. You regularly criticise research you haven't read, saying that the data doesn't justify the conclusion and you know why. This is pure arrogance on your part and totally devoid of any knowledge.

You seem hellbent on spreading ideas that are both completely untrue, and extremely unhelpful for making any progress on the practical problems of whatever it is you opine on.

Give it a rest Jon. You lost - I know that’s what winds you up.

You’re an elimination fantasist and a sore loser. Not a good combination.

I'm not fussed with the puppy,. The attack on all liberal institutions for just being that (rather than actual consistent content problems) is front and cenre of the populism cause. False equivalence and dead cats are a crucial tools for them, truth is the enemy. Cherry picking bits of genuine science that suits their arguments is just part of the game (it's pretty obvious what they are when other less convenient genuine science gets attack rhetoric).

The dear old Grauniad linkage is accessible by all, doesn't break over the years and links well internally to similar news (including future additions)

For the report, the main benefit for me is at long last the millions who have lost loved ones get a collective voice. I'm not fussed with 20 pages summaries for massive investigations. My bigger concern is the structure could have been better (eg get rid of the CVs from the summary).

The problem is that many, many people are transfixed on dying of covid and (quite wrongly) think that as long as they don't die they'll be OK. Without publicising these sorts of studies they'll carry on in their own little world to the detriment of their own health and that of society.

Anyone who has paid any attention will know that you're incorrect. You can only see whatever suits your retarded narrative, and if you have to see the opposite of what's there, that's no problem either.

I’m not sure anyone is proposing to trash the economy. Some additional measures could be taken though, particularly around travel. Experience to date shows that acting decisively early one has paid off for other countries.

I get a sense of deja vu. Omicron cases are low and appear to be spreading slowly. Just like Covid in late Feb, early March… Nothing to worry about, move on.

Me too. I'm hearing the same 'lockdown or the economy' bollocks as in 2020. We'll be getting the 'waiting for the optimum point in the curve' next.

Not that were anywhere near lockdown yet... Hopefully, if people adopt the mandated measures, we won't need to go back into lockdown.

A few plots that didn't get out of the door on Saturday.  Generated with today's data.

Week-on-week rate constant - still having a Zeno's Paradox approach to decay; I've marked last Saturday as a likely anomy - depressed sampling due to severe disruption from Storm Arwen in parts of England.  If it is, there will be a false high 7 days down the line from a week-on-week comparison.  Behind the scenes decay adults 60+ continue to have significant decay, and all other ages are now reaching decay; but tomorrow is when I'd expect a rising signal to start landing from the cold spell... We'll see...

I've put in a plot showing the probability distribution of cases vs age for two recent times 3 weeks apart.   This shows what fraction of cases (regardless of actual number) are in each age band, regardless of the total number of cases.  The third dose is hammering down rates in over 60s, and a few other things are going on.  Assuming omicron doesn't hit a big reset button, at some point infection in younger children will run out of susceptible people - as we've seen in ages 15-25 -  and cases there will drop down also, removing some of the pressure driving cases in ages 30-50.  With an optimistic hat on, that tangibly close point almost feels like the end of pandemic Covid in England.  We wait and see what omicron turns out to be now.. I'm also wondering if it's going to accelerate a decision on lower volume single-dose vaccination for under 12s, as for example authorised in the USA.   

Plot 18 - regional rate constants - the right edge of all plots is provisional and cases are biassed down a bit by Storm Arwen's disruption as well as day-of-week effects when updated now (hence why I normally do Saturday, seems to be the best day) so I expect the decay won't remain this strong with more data.  London stands out has having a higher rate constant (more growth in cases) over the last couple of weeks; I would have put that down to noise and not commented, but... the hospital admissions signal is showing a similar trend.  One to keep an eye on for another week or so...

Lilley on the vaccine expansion (a clue to his view is in the headline).

https://myemail.constantcontact.com/Trollope.html?soid=1102665899193&ai...

Overall, given the ramp-up time, we will need over 700,,000 jabs a day, including over xmas and new year (who wants to get vaccinated on those days or risk hampering a special day by a potential bad reaction from vaccination just before). I suspect we will be saved by the can't be arsed as a clear individual incentive just isn't perceived to be there for many vaccinated younger adults. It's proved hard enough to get that demographic vaccinated where there is an individual incentive.

Government ministers loudly proclaiming that everything's fine and there's nothing to see here while scientists make increasingly concerned noises...

We are well beyond concerned noises. This is major leaks and Boris humiliating the senior scientist in charge of England's Public Health responses.

Germanys number of deaths over the past few days are clearly a concern- as you forecasted.

Weather forcing people from moving via the streets and into the tube?

Germany has gone over the cliff now. France rapidly becoming the one to watch.

Hold on, how does that fit with your "remember that thing you were wrong about?" vendetta? I thought you wouldn't have it that demand dropped off at younger ages...

It looks like cases are tapering off in Germany, but there's still a lot of growth in the death rate locked in.  They'll need to sustain it at that high level for the next few months if - as their health minister has said - the plan is "vaccinated, recovered or dead".

Worst doubling time on my comparator plot.  Looks like Macron was wrong to claim the vaccine passport would see them right.

Well, it was the worst doubling time.  I added South Africa.  I'm just going to tell myself that this is the kind of doubling time we've seen in the UK in areas when cases were very low and people were being incautious, and that the usual behavioural loops are going to close to moderate the exponential rate.  I might also tell myself that this is probably in part due to everything but the kitchen sink being thrown at testing due to the fears around omicron.  

It would be easier to believe myself if they were going in to winter like Europe rather than going in to summer...

Still, we wait and see.  Lots of data is needed - and expected - on the new variant.

How confidently can this be said? Just looking at cases, their huge weekly reporting oscillation makes it a bit hard to interpret, for me. 

Either way they're now past (or very close to passing) the point of guaranteed ICU overload. They're at last doing something about it, but this reads an awful lot like Austria+2 weeks. Anyone betting against a full lockdown following shortly?

COVID: Germany set to approve curbs on unvaccinated https://p.dw.com/p/43jEx

I was feeling more optimistic about omicron until I read this today.

https://www.theguardian.com/world/2021/dec/02/omicron-variant-fuelling-expo...

Some positive news though.

https://www.theguardian.com/global-development/2021/dec/02/omicron-may-caus...

 “We believe the number of cases will increase exponentially in all provinces of the country. We believe that vaccines will still, however, protect against severe disease.”

Anne von Gottberg, an expert at the National Institute for Communicable Diseases in South Africa

I argued the numbers in the 18-24 group would not saturate at 50% vaccination whatever the data implications were at that time, as it just didn't seem possible with ONS intention surveys, and as there were significant issues with double counting on the denominator due to students. Something you never apologised for getting wrong, despite being pretty aggressive towards my views. Even if they meet ONS intention numbers (they haven't yet), they are still disappointingly low, as they are in all the younger adult categories (even when you take out numerator problems).

I'm pretty confident that it's happening - see the plot below.  (*). It doesn't look like a saturation effect as both the minima and maxima of this cycle are lower than the last.  It also ties up with the timing of control measures ratcheting up.

That does appear to be their intent given the heath minister's quote from last week.  

In reply to elsewhere:

Lots of speculation whilst we wait for the hard data to come in...

===

(*) this plot is raw data on a 0-to-max scale per-nation with the filtered curve also show.  This should not be used to compare case rates between countries, because absolute levels have been deliberately removed to put a focus on the trend and on any biassing effect caused by day-of-week sampling effects.  It's a diagnostic plot and is not useful for anyone seeking to play a doubly pointless game of Top Trumps over case numbers.  

I'd add Belgium as a bigger EU concern. Even allowing for the most honest counting of covid deaths in the EU they have handled the pandemic awfully almost throughout and seem to be doing so again.

There is an OWiD plot  combining per capita cases, admissions, ICU and deaths and Belgium has significantly higher admissions per capita (which probably means more younger admissions, given deaths and ICU  are similar to Germany).

I was certainly proved wrong with my optimism about German government response.

More news of bad actors.

https://www.theguardian.com/technology/2021/dec/02/facebook-owner-meta-take...

Yes, Belgium don't seem very interested in changing course just yet.

Some of the political comment at the UK from across the water over high case numbers during the summer/autumn could conceivably have given many people the idea that there was a better solution, and that Europe was going to show the way.   Turns out it was just more politicking at opportune moments followed largely by silence on the issue a few months later as the inevitable slams home. 

Early on in the pandemic, someone posted a letter to the Lancet they claimed offered support that we were close to herd immunity through asymptomatic infections.

The Lancet are one of several journals to dress letters up with a formatting and DOI strongly reminiscent of peer reviewed content.  It is not.

I tried to make that point that such letters are not of very high value.  Today when looking for good examples of physicists gone off the rails, I found this letter from some of Hoyle's network of astrobiological epidemiologists.  It makes that point about the letters quite well I feel...

SARS: It Came From Outer Space!

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(03)13440-X/...

You couldn't make this stuff up.

I like this bit "Mathematical modelling of epidemics such as the one described invariably involves the ad hoc introduction of many unproven hypotheses—for example, that of the superspreader."

Followed by: "The recognition of a possible vertical input of external origin is conspicuously missing in such explanations."

The Lancet are taking the p*ss with that and it is a disservice to the many journals in other fields where a letter is a basically a short paper with a fast review cycle.

They have had a serious election this time and its a realistic assesment that the powers that be may have had their eye off the ball for sometime especially with Merkel moving on.We tend to underestimate the impact of these issues on decision making at the top.

Its like Johnson and Brexit at the start, political eyes were elsewhere and it costs needless lives.

Thats one view anyway.

I've been very disappointed with the way what is in effect the agony aunt's column in both the BMJ and the Lancet have been (ab)used during this pandemic.  Turns out it's been going on for quite some time...

Some people literally do !!!

Could be; most of this came to pass before omicron could have had more than the slimmest toe-hold I think so I wouldn't look to that.

The trend firmed up a bit with today's plot; what was a very weak growth signal in deaths has firmed up a lot today; as ever this is the provision leading edge, and there's a lot of small number noise in regional deaths.  But, it does tie in with the increasing hospital signal and also a recent uptick in ITU occupancy.

One to still keep an eye on.

With the odd piece like this: https://www.thelocal.fr/20211126/analysis-will-frances-new-covid-rules-boos...

Parts of the British media – even parts of the BBC – are revelling in the new Covid surge in Europe. They ignore the fact that this is the continuation of the “Delta variant” wave which started in Britain in the summer and produced inflated levels of British cases and deaths while most of Europe was spared.

Could have been written by one of our own, that

Well I have cycled, as usual, from work to Paddington at the end of the afternoon today, and then spent 5 minutes getting through the hot aches in my toes and fingers. I am hoping that my resolution to stay out of the potentially-plague-spreading Tube will hold up over the winter, but it is just a reminder of the way the weather drives us indoors.

Re: London - like several other big cities it has had lower than average case rates through most of the last few months and has missed out on some of the temporary rises that occurred in that time period too. I think what is probably happening is that these cities including London are now catching up with rural areas and towns because of young adult cases gradually rising again? (I haven't looked at young adult cases for over a week, is that hypothesis supported?)

I’m not sure it was just politicking to criticise the UK’s approach. I think the criticism was reasonable at the time. It’s always easy to say in retrospect that so and so took the right decision but it was far from clear at the time. From a healthcare overload point of view we’ve been sailing close to the wind and a number of things are not clear.

Would we have got through without some additional measures even without Omicron messing things up (although another lockdown would have been unlikely - not so sure now but it’s a different ball game now)?

Who will have the highest cumulative death rate?

Who will spend the longest time in lockdown overall?

Was there a third way for us since July, with relatively light touch restrictions which might have put us in a better position (fewer deaths and hospitalisations in the short term but relatively little ‘payback’ in the medium term)?

Is our relatively better position due to our relatively worse cumulative position up to Freedom Day, our policy since Freedom Day, our higher vaccination rates among the vulnerable, our 12 week gap policy,  an earlier booster rollout, our milder autumn weather compared to some EU countries or all of the above to varying degrees?

Lots of questions… I think the answer to the last question is all of the above but I’ve no idea what the relative weighting of the factors might be. I doubt that our currently relatively better position is simply due to our relaxation of measures over the last few months.

It would be interesting to compare vaccination and death rates by age bin between different countries.

Yes, I've always maintained that the right way was far from clear, and that is why it was not appropriate for either side to criticise the other - policy on both sides of the channel was informed by different parts of valid scientific advice traded off against a veritable sea of unknowns.  

Your "who will" questions - if asked post-delta, post-vaccination, the UK is looking like it's going to have a relatively easy time of it compared to basically everywhere else in Europe; assuming omicron doesn't hit the big red reset button.   If asked over the whole pandemic, it's a different answer but considering choices made since vaccination - my mantra that we are where we are - I think we're doing okay.

I think the evidence is pretty clear that the massive difference is in our population level immunity (the LSHTM paper) and given waning timescales and genetic drift, I suspect that the order of precedence is vaccination, then post-delta spread then (more weakly) alpha spread then (even more weakly) wild type spread from the start.  The 12 week gap will undoubtedly be helping, and the 3rd dose is making a massive difference - but a 3rd dose isn't going to help the situation in countries where large numbers of older people haven't accessed their 1st or 2nd doses.  Cultures adapt to their climates.

No, it absolutely isn't.

 But that managed relaxation is a key step to easing out of the pandemic phase, and it was only accessible to the UK because of a very high rate of vaccination in older and otherwise more vulnerable people.  I think much of Europe had been unable to access that level of relaxation because off the large remaining pools of vulnerability - something winter is now forcing to the fore.  So, they're going to crank through it at maximum hospital occupancy going through winter with a lot of lockdowns.

It's not clear to me that the price the UK has paid post-delta is worth the difference, but I maintain that it's never been one-sided "high cases bad".

I've repeatedly said that I thought messaging could have been clearer on the risks for the more vulnerable, and that there should have been stronger legal and practical protections for the more vulnerable during the last few months.  Having said that, with masks returning it's been instructive watching supermarket after supermarket announce that they're not going to enforce mask wearing and expect the police to do it, and the police seem to have little interest.  Perhaps I live in a pipe dream where people would make little adjustments for the vulnerable.

In reply to Si dH:

The devil must balance his books; interesting take on London.  I don't tend to look at the demographics on a regional basis because the data gets pretty noisy at that point.  

The larger cities have certainly had somewhat lower rates over the last few months - very obvious on the dashboard map. I assumed they was due to higher cumulative rates and hence more infection immunity. However your point about demographic case rates is a good one. The counter to that is the rates were previously driven by children and I’d have thought there are roughly as many children per head of population in the large cities.

The other factor in London is more office workers being encouraged to get back to the office at least a couple of days a week.

All these questions and more will be answered in next week's episode of...

..Soap... sorry, Friday Night Covid Plotting

That’s a good way of looking at it I think - our higher vaccination rates where it matters enabling us to sustain higher care numbers over the past few months and those two factors combined placing us in a better position currently (not least to face Omicron if it’s as bad as some fear).

As you say, the devil must balance his books and it remains to be seen whose cumulative fatality numbers will be worse over the whole pandemic (a rather morbid race to the bottom). Perhaps it won’t be that different for much of Europe in the end…

Cases reported ticking up again, with a significant rise today (by eye). Right on cue for the cold weather impact from last week. Perhaps a bit of bunching due to Arwen disruption but that should sort itself out over the next couple of days.

Almost certainly a false low then false rise from Arwen.  Will be interesting to see what the next couple of days bring; the fall in hospital admissions is almost halted - demographic shift running out of steam in the critical ages as rates in older people have crashed down about to the level of the pre-delta lockdown.

With older people disengaging from spreading the virus through boosters, school aged child are taking control of the top level cases, and their rate constant is less affected by the weather than adults it seems.  Could delay the changes by a few days.  Who knows what the messaging and rule changes notionally did to omicron have had.  Still keeping an open mind on how omicron is going to pan out…. McGuffin or big red button?

Meanwhile… Omicron is saying hello. Twitter thread about SGTF numbers. Key quote: “in the last five days (24 – 28 Nov), the level of SGTF has gone up from its usual ~0.1% to ~0.3%. These are not huge numbers of cases — this represents about 60 more SGTF cases than we would expect to see in these data given the background prevalence of ~0.1%. However, this number will probably go up, as the last 2-3 days of data are still filtering in“

https://twitter.com/_nickdavies/status/1466204384921071624

So low numbers for now and not outcompeting Delta yet but give it time…

Doesn’t seem to say where the data come from. 

The view from South Africa.  Hockeysticks.  And it reinfects people who had Alpha or Delta Covid with no problem at all.

https://twitter.com/DrEricDing/status/1466485884568670209

I was about to post this..

https://twitter.com/twenseleers/status/1466501989500653568?s=21
 

very thorough analysis to drive my paranoia (and insomnia!). WT - about those dark red bulbs.. 

Very odd how the SGTF peaks in the SA data seem to repeatedly herald a bigger outbreak without SGTF…

Thoughts

• Much SA immunity is likely infection granted from Beta, so you could grasp at a straw that this drove immune escape and Alpha and Delta will have better cross immunity.  Haven’t looked for expert opinion on this; it’s time we had matrix of genetic drift between variants…
• Hopefully immunity from severe infection is much less disrupted, this is the natural order of things…
• Looks like we’re not going to have to wait much longer to find out how this pans out for the UK…
• If it does spread much more through immune escape but has immunity blunted consequences, it’s a disaster for countries relying on immunity to keep society open but with significant pools of zero immunity people. Even for high immunity places it would go on to raise healthcare demand a fair whack.

Can’t have any red bulbs though, Northern Powergrid are still using them all for their status boards. Some places around here are in to day 7 with no power.

'Thelocal' in which ever country is usually dire. They run primarily on add revenue, producing selectively edited articles, often Google translated from bigger articles in the various countries. 

Does that imply S69-70del mutations are somehow less fit for transmission (but avoid previous immunity)?

that hypothesis would seem to explain the high level effect, apart from first wave where clearly there were many early variants, minimal sequencing in SA (presumably) and no one knew what was happening). 

what I’m thinking is this:

1) wave of S positive sars-cov2 occurs in a population. Some natural immunity results.

2) selection pressure to evade antibodies results in S69-70del (alpha) which is (relatively) less fit for transmission. Other mutations compensate for this.

3) small alpha wave occurs and selection pressure for S69-70del wanes with immunity from the first wave.
 

4) Any new variant without S69-70del can flourish and is inherently more fit as S69-70 is important. Eg Beta in SA or delta in UK.

5) bigger wave due to fitter more transmissible variant, but S69-70 antibodies build again in population due to non SGTF variant.

6) rinse and repeat..

all of which means omicron is ‘relatively unfit for transmission’ due to its S69-70del mutation driven by the need to avoid delta and vaccine induced antibodies.

two scenarios present:

a) vaccines keep pressure on for S69-70del and omicron happens as now (in well vaccinated populations)

b) pi..

Edit: this is purely a HYPOTHESIS and is purely mine. I’m not a virologist and I hope I am totally wrong.

That plot more than hints at that kind of interesting coupled dynamics, doesn’t it?

Tick, tock, tick, tock, tick, tock, bang?

Edit; or tick tock tick tock tick tock, where’s the earth shattering kaboom?

Yes it’s basically the first time I’ve seen plots of SGTF over any extended period. Are you aware of any uk public data on that? I’m not.

Re-infection is a lackluster term at this point. Severity of infection/re-infection is all that matters now really, as we should be accepting endemic virus as the only logical endgame. Causing panic about mild-moderate infections will do no-one any good.

Doctors taking to Twitter and spamming CAPS LOCK with FASTEST SURGE EVA and OMG TEH YOUNG does not scream carefully considered, holistic view of the situation to me. 

I haven’t looked for a definitive source but there’s an occasional poster or two who might be able to point you in the right direction…. Random plots I’ve seen snow a much simpler behaviour for the UK.

If it grows here the way those curves show it growing in South Africa the time delay between 'ho hum, not much happening' and totally f*cked is very short.

In that situation, when there is uncertainty about how bad it is if you wait until you know for sure it will be too late and if your plan is to protect yourself with 3rd jags then you aren't going to get them done in time unless you also have a plan to really slow it down.

The people being silly are the UK media and Tories pretending that the worst outcome from this is 'missing Christmas'.  

On the highest level it seems broadly similar to me.. albeit with less waves

wild type (S), alpha (SGTF), delta (S), Omicron (SGTF), …

I think the relative peak sizes since alpha are strongly vaccine moderated (unlike SA)

I agree on the cyclical pattern, but ours looks one choice per wave, their looks like one always heralds the other in each wave.

What are the odds of either situation arising without some deeper mechanic than chance?  Pretty low at this point.

That's totally dependent on what sort of covid cases this new variant produces. I also think it's fair to say South Africa's population immunity, through either vaccination or prior infection, is considerably lower than ours, not to mention myriad other social, political, health, economic, cultural factors, so a bit silly to suggest what happens there will happen here.

I would have had some sympathy for pre-emptive short term border closures of the UK as a whole to give time for a more thorough assessment. However it's already too late for that, and targeting South Africa alone for travel restrictions is pointless as you'll just get cases via third countries. Correct me if I'm wrong, but I don't think any countries have opted for total border closure in light of this new variant have they? So I can't really agree with the specific Tory bashing on this occasion.

Again with the deja vu, unless you are willing to implement military level preparedness for closing borders and other actual preventive measures in the face of unknowns (I personally think this is over the top but just saying) then all you're doing is playing pretend with all the pantomime restrictions we're seemingly obsessed with.

The link above that minimike provided  clearly demonstrates almost certain vaccine escape and also given that SA percentage total deaths is pretty similar to the  estimated IFR, the vast majority in SA will have infection immunity. It also shows hospitalisations are now rising fast in SA, so even if it is a less serious variant it is almost certainly not less serious enough. 

The UK simply doesn't have capacity for any significant rise in hospitalisations. That is the result of our government idiocy of letting things run a bit too hot for too little benefit. Plan B should always have been Plan A as we have nowhere to move with a new variant that increases hospitalisations other than a really damaging lockdown. I think if the data in that link pans out here (as it's very likely to do) we must restrict more now and even then we are probably just delaying another lockdown. 

One day later and I've had to expand the y-axis range again for South Africa.  This is the kind of trajectory only really seen in the UK in the early part of 2020 and in university student outbreaks pre-vaccination.  

Our world in data show hospital admissions for SA, reported weekly, and the last data point has an up-tick, the next one will be informative.

At least the doubling time seems to have stopped getting worse...  To get much worse than 3 days would be a strong hint that it's fundamentally more infectious than previous variants, rather than (just) immune evading.  Which seems a bit like commenting that at least that thermonuclear device wasn't coated with Cobalt-59.  Always look on the bright side of life, dum de dum de dum...

Is it?  The suggestion in the link from minmike are for population wide spread of the virus inferred from deaths.  

Sadly I think we might yet again be at the point where we ask ourselves do we feel lucky with Dirty Harry's gun facing us. Delta based immunity might give us extra protection but that's far from certain to be enough. Part of South Africa's lower death rate and hospitalisation rate was always about demographics (they're a young country with a medium age about 28). We simply don't have spare NHS capacity and even if the UK hospitalisation hit is a quarter as bad as that linked SA data, it will be serious and at the worst possible time... January and February. Prospects for Europe and the US look even worse but they will have much more ability than us to whip up nightingale style responses (we are brexit blocked with staff capacity.... I've loved the B5 asides but this might be more NHS Gandalf realising there is a balrog coming).

The only good news if this scenario pans out is deaths should be a lot lower as vaccine protection is high and medication has significantly improved.

I think that’s probably just timing. Their waves overlapped. Ours didn’t so much.