If you want to save some reading time, this week's commentary is basically a repeat of last week's.
Starting with the 4 nations plots... The case curves for Scotland and Northern Ireland are wobbling up and down - suggesting periods of growth and decay - which may be noise by this point or may be real, some is probably down to asymptomatic LFD data but I don’t know how much. Plot 9x is using a 17 day, 3rd order polynomial filter to get smoothed rate constant lines; over that smoothing period, the trend under the wobbles in recent data for Scotland and NI still amounts to decay, along with England and Wales. It’s hard to tell that from the cases plots perhaps, as the wobbles are larger than the drop.
NI had sustained growth a few weeks ago enough that its rate constant turned positive for a while, the others remain in decay. It's back in decay now perhaps. It's notable that the Republic of Ireland has also seen decay in cases just about stall, it may be that NI is as tied, or more tied, to it's land neighbour than to the rest of the UK when it comes to cases.
It seems like the most rapid halving times seen in March are behind us and we’re in to more stubborn chains of infection now. Hopefully the ongoing vaccination will continue to help out here. It seems like this is where the biggest differences between the nations are creeping in, with Scotland and NI in particular struggling to make progress, and with Wales being the lowest of all.
Link to last week's thread: https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_23-733980
Now measures are so low, I’ve switched to a log-y axis for these plots; on such an axis, the gradient is proportional to the exponential rate constant and it’s easier to compare this “by eye” between regions of high and low measures.
Admissions and deaths can both be seen to be moving off the previously fixed rate exponential - the curves become less steep on the log-y plot. The cases curve is all over the place with the addition and subtraction of LFD data at various points so isn’t the most helpful to understand why the halving times for admissions and deaths are rising (decaying less aggressively). I think this is in part down to the demographic blip I’ve noted over the last couple of threads where we had a return to growth in cases in older adults a couple of weeks back, combined perhaps with more stubborn chains of infection being almost all that’s left.
Hopefully that stubbornness is down to demographic and social factors and not variants. One poster suggested on plotting #23 that almost all UK positive PCR cases are now going for sequencing. If we take that as fact, and going off the data here , there were about 380 variant cases (excluding the "Kent" one) found in the last week in the UK out of about 5,000 cases total (although I don't have PCR-only numbers for the UK) . That is not currently a large enough number I think to itself account for the stubbornness but it's notable that the weekly number of new variants detected is going up, whilst the case count is going down. If indeed most cases are being sequenced, "surge testing" is no longer a way of contextualising this to be less concerning, although "screening at borders" still comes in to it. I really hope to see more information published on the variants soon so that the data can be more meaningful, for example for each variant, how many cases came from border screening and how much from pillar 1 and pillar 2.
No sign of the latest round of re-opening causing a failure of decay of PCR cases - there’s a PCR only plot for England in a later post. This is great, and it’s a a couple of weeks yet until the next round of unlocking’s notional date. That’s the big one in terms of risk IMO as it covers more indoor things. By the time it happens, the phenomenal vaccination effort will be even further ahead, and the weather factors will hopefully be more in our favour - although there was lying snow not far from us this morning….
Deaths look like they're about to stop happening on a daily basis, but I'd caution that we're seeing very low numbers so noise can be a significant effect at the leading edge of the data and the demographic breakdown in a later post isn't going to look quite so positive, but it's still a big change so soon after the winter.
One interesting thing has happened this week - there has been a big outbreak in a warehouse run by a company called Clipper in Selby. Around 50-70 people tested positive I think. The local rates temporarily shot up quite quickly - some graphs for the local authority below, the demographic one is particularly stark; also the two MSOAs which make up most of Selby town itself are both over 300 cases /100k over the last week.
They have put in surge testing and the local authority top-level cases graph suggests they are probably getting things under control. What this shows though is what will still happen on a much bigger scale around the country if we let our guard down too fast.
On D1.c, the period of growth in cases in those aged 70+ has remained intact as it comes out of the “provisional zone” on the right; this I think came at a cold spell in the weather and is perhaps related to the slackening of decay of hospital admissions and deaths, but it’s hard to see it in the demographic deaths data as the numbers are now so low, noise is a major factor. Plot 18 has a similar period of growth in hospitalisations in a couple of southern regions - an island or orange growth at the top of the hospitalisations sub plot. It could be that a couple of outbreaks are showing trough now the baseline is so low but it does suggest to me that we're not far from a reversal of fortunes if caution is lost; thankfully the government continue to hold the line on a cautious, progressive unlocking and it seems to be working.
Plot D3 showing the changing rates over recent weeks has the oldest ages returning to decay from the brief period of growth, and has the school ages going in to growth which is I think mostly the uptick in asymptomatic LFDs associated with schools going back after Easter. It's notable that the island of orange emerging in the bottom right of D1.c is not as vivid this time as for the first return of schools; perhaps the improved weather is helping, and background symptomatic case rates are low.
Looking at demographic deaths in the new cropped take on D5.lin, decay has perhaps stalled for working aged adults and those aged up to 69, but the numbers are so low that I'm wary of reading much in to the most recent 10 days or so. It feels compatible though with the bigger picture though. The vaccine continue to work down the age ranges in working aged adults so I would hope we see this continue to decay, but it's clearly approaching insignificance in terms of total daily deaths in the UK; however the recent islands of growth in cases and hospitalisations suggest to me that it's not insignificant in terms of where things could go if caution was abandoned.
Thanks, had been wondering what was going on there as it showed up on the dashboard map.
The final grab bag of plots
Plots 22 and 22r have very nearly closed the loop on hospital occupancy back to 0 people by both measures. I've added a new sub-plot to 22r. This normalises both axes to the maximum hospital occupancy (x-axis) value for each region. The maximum value of a loop on the y-axis shows what fraction of the hospital admissions become ITU admissions. For most regions, this is between 8% and 10%. It's notable that London is closer to 16%. I remarked some threads back on the steeper curve for London - that twice as many people go in to intensive care seems frankly remarkable and it's not something I've seen discussed in the media. Social and demographic data on ITU admission is hard to come by so I can't offer much insight.
There's a rate constant plot using my new method (week-on-week changes) for PCR-only data for England. We continue to see decay on every day of 2021 apart from those affected by the Easter bank holiday weekend under-sampling (blue lines). Decay seems to be back in a "slow mode" now with a rate constant of ~-0.02/day. I did not expect to see PCR data remain in decay for so long, and I'm very happy that it has.
The vaccines plot seems to have settled in to a weekly cadence. There's another 5 weeks or so before the big spike in first doses from mid-March lands due in the second doses. It looks to me like there's just about headroom in the current total rate to accommodate this with a brief pause to first doses, assuming no other changes to supply. There are changes to supply expected however, but it seems that's always a bit volatile.
Next up is the variants plot.
I think fair to say that the return of schools and the reopening on the 12th hasn’t had much of an impact so far. It may have contributed to the decay slowing down but it hasn’t led to an increase. This suggests to me that, in the context of a relatively low case load overall, retail isn’t really an issue (masks, fairly socially distanced, relatively short duration), outdoor hospitality isn’t really an issue (despite people sitting close together at tables) and schools don’t seem to be an issue in terms of driving wider spread via parents. The relatively nice weather recently must have helped as well.
Worth noting that in England not only PCR cases are still falling - total cases seem to be falling week on week as well, though only very slowly. We have two more weeks to lock in a further reduction before the 17th...
> What this shows though is what will still happen on a much bigger scale around the country if we let our guard down too fast.
Thanks for that post; interesting and indeed a sign of why vigilance is needed still. It's disappointing that we're still seeing outbreaks in warehouses when so much is known now about transmission control measures; enforcement seems pretty toothless. It'll be interesting to see how the limited nightclub trial this week ends up; the requirement was a negative Covid test for entry I believe.
(From plotting #23)
> Ironically more cases of b.1.617.2 have seemingly already been sequenced in the UK than in India...
I've wondered before how much our border screening is turning in to sentinel screening for some other countries, and if there is a systematic way for countries to share screening data on cross-border travel back to the originating nations.
As local cases continue to fall, we could "donate" our excess capacity to countries that are having serious problems to help them better understand the situation. This would take the form of samples being sent in to the UK for processing. I mentioned this before, someone (Toerag?) rightly pointed out that effective control measures are basically the same regardless of the variant; this is true to a point but we don't know that this remains the case for future variants, and the first sign of trouble can be one variant rising in proportion.
Almost unbelievable isn’t it? Such a change in a few months. Explains why I’m struggling to find much new to say each week...
Looking at that and at the data coming out on the first vaccine dose reducing transmission, I struggle to see why more nations aren’t moving to a longer gap between doses.
> > What this shows though is what will still happen on a much bigger scale around the country if we let our guard down too fast.
> Thanks for that post; interesting and indeed a sign of why vigilance is needed still. It's disappointing that we're still seeing outbreaks in warehouses when so much is known now about transmission control measures; enforcement seems pretty toothless. It'll be interesting to see how the limited nightclub trial this week ends up; the requirement was a negative Covid test for entry I believe.
It seemingly wasn't very limited (!), there were 3000 people crammed in for 2 nights, it was absolutely packed out to the limit of what would be allowed in normal times with lots of people going fairly mad (it looked like the sort of thing I'd have loved 20 years ago.) Everyone had to take an LFT beforehand at a location nearby, but obviously that could let a few cases through if unlucky. Rates in Liverpool have been very low, down at about 12/100k per week I think.
There was also a business conference with 400 people a couple of days earlier. This is all 3-4 miles from my house so I'll be watching rates around Liverpool closely for the next few days! There is also a big gig planned today I think with a few 1000 people in Sefton park (other end of Liverpool.)
Interesting so see Sweden so high up there, having been heralded as the success story for not locking down!
Thank you for persevering, wintertree, even though there's little to say. I feel a great sense of foreboding as we watch what is happening elsewhere, alongside gratitude for a period where this country, for now, is in a good place.
Thanks for the details. It’s always happening in Liverpool it seems. With the numbers so low it seems like the value in these trials might be more about testing the logistics of running the events than the transmission risks, I’d want to run about 10x as much before considering stats on transmission.
In reply to girlymonkey:
> Interesting so see Sweden so high up there, having been heralded as the success story for not locking down!
Interesting, but not surprising.
In reply to BusyLizzie:
Indeed, we have a lot to be thankful for right now and I hope we don’t loose sight of that. Yet even as we achieve the status of least affected nation in Europe, a few of our high status academics are lobbying hard to undermine public and political support in any sort of control measures. I’ve been surprised that PCR cases have remained in decay all year, and that the 5-week gap between unlocking stages has been adhered to against a background of everything improving so rapidly. This more cautious and progressive approach has my thanks, and I hope those who convinced leadership of its necessity have their efforts thoroughly vindicated, and that this sets a more cautious note going forwards. I remain convinced the being more cautious is the best way to achieve the net lowest level of restrictions over longer time periods.
> We have two more weeks to lock in a further reduction before the 17th...
Two more weeks to lock in effects of vaccination as well - doses already given developing in to protection against transmitting the virus as well as against illness, and hopefully two more weeks of 1st and 2nd doses to be given, ready to develop in to protection.
Vaccination is now open down to age 40 in England; as that bracket completes, its half the working aged population offered the vaccine. It’s really getting in to the ages where most transmission happens now so that’s going to take a big chunk out of the exponential rate constant, along with the next swing of the weather cycle back to high pressure and dry warmth in a couple of weeks. That’s hopefully enough to prevent a return to growth after May 17th, and if not cases will hopefully be so low that the consequences of the hopefully moderate growth are very minor for a long time, giving ample chance to reevaluate everything and for more vaccine doses to be given, chopping more off the exponential rates.
So, even the worst case result of the 17th doesn’t seem very bad. But we’re approaching the crunch point where new variants are either going to break through and take all that hope away, or not. Cases are falling, variants are rising. I’m really not qualified to understand what’s going to happen there, and if I asked someone qualified I think they’d hedge and say we won’t know until we know. Still, we’re going to be in close to the best possible state to meet such a challenge and to try and contain it if it arises; a baseline of very low cases, with testing and sequencing apparently running like clockwork with field experienced enhanced contact tracing teams. Should there be a variant that evades vaccines enough to be a problem, we’re as prepared as we could hope to be IMO other than tougher border closures and managed isolation and quarantine...
Hospital admissions after vaccination are almost but not entirely soon after vaccination.
> Interesting so see Sweden so high up there, having been heralded as the success story for not locking down!
Only by the anti-lockdown brigade...
That’s a great link, thanks. Good to see some of the longitudinal results on the vaccine and hospitalisation; compelling stuff too.
Following elsewhere's link I came across a series of more recent sage papers from their meeting of 22/04. It was a treasure trove of information:
- an update of the analysis that elsewhere linked. Conclusions broadly unchanged. They did note that this early analysis now suggests that mortality is still high for people in vulnerable groups who are admitted to hospital despite having had a vaccine> 21 days earlier (ie cases of vaccine failure.)
- a separate paper containing lots of information on hospitalisations that we would have been very interested in a few months ago, might still be of interest now. Lots of longitudinal information and various graphs showing outcomes as a function of age that I think you might like for your arguments with big bruvva.
- the best until last? a paper with loads of information on variants, especially the first of the Indian ones and it's tracking, for example the graph below showing exactly what you said would be interesting in the last thread. Graph below. It also breaks down all the variant cases (VOC and VUI) in to travel or not travel related, and shows locations where they were detected. And various other stuff, eg growth model estimates for all the variants.
(and a couple of other things)
Fantastic, thanks. A lot of reading to do.
A couple of comments on the first link:
A couple of comments on the second link:
I had a mini-epiphany the other day when somebody in the medical trade said something that now seems obvious.
Travelers can be quarantined, sure. But then when they get sick and need hospital treatment, they get it. When the inevitable happens do the people who catch it in the hospital know they've been near someone who traveled? How would they answer if asked?
Yes, keep forgetting that the vaccination drive must be having an effect on transmission by now as it’s down to the working age groups.
I’m a less optimistic on the situation after the 17th. The vast majority of people under 45 won’t have had their jabs for 3 weeks by then and the vast majority of those under 40 won’t have had a jab at all. So I think we will see growth returning but slowly and with significant regional disparities (some areas are already stubbornly refusing to drop). Hopefully as the weather warms up people will continue to favour meeting outdoors, which should help as well.
In a way, if cases rise again that could be helpful in the medium term as BoJo might be less likely to go for the full unlock on the 21st? Suspect that’s not how these things work in Westminster... Good to hear Raab saying today that there will be something around SD and face coverings after the 21st.
Re vaccine evading variants, if they escape local surge testing etc, I fear we will see ‘too little, too late’ yet again in terms of measures. If we can get through autumn and winter without significant restrictions, that would be quite an achievement. We shall see...
This is where it would be usefully to further stratify the community cases between medical / in hospital and everyone else. Although I wonder whether anyone catching it in hospital after a traveller is admitted is already noted as a contact of a traveller. Depends how sophisticated the contact tracing is.
So various variants roaming in the wild... Numbers are low (even on the assumption that the real numbers are several times higher).will they break through the vaccine shield and remaining measures? Not sure anyone knows.
Thanks again for the work you do, I have been enjoying my new found freedoms and work is really ramping up but will continue to come back for your weekly updates.
Some potential good news with regards to the Indian variant coming out of Cambridge University this week.
I am continuing to remain optimistic with regards to our reopening schedule and how well our vaccine program is going, it appears that the vaccine efficacy in the real world is much better than anyone could have hoped for with more evidence appearing that they work well against the variants.
Gibraltar and Israel also continuing to be the benchmarks for what life here could be like by the end of Summer.
This news from Cambridge is incredibly important and on balance appears to be good news long term. Extrapolating and hypothesising in a way they can’t (would be considered speculative) it is what, 6 months since E484K first appeared? In that time none of the newer variants seem to have done ‘better’, with other mutations or combinations thereof. To me this suggests we have seen the rapid adaptation to a new host phase and now can expect the typical slow mutational pattern of most coronaviruses. IF I’m right (huge if) then even the mark1 vaccines we currently have will make a vast impact on deaths and hospitalisations globally, if not on cases per-se. Moreover, a mark2 vaccine covering the common mutations would be effective for a reasonable duration. IF...
It’s almost the best possible news perhaps as have been previous studies on variants and vaccine induced immunity - the emerging picture over various studies is that the change is enough to evade some neutralisation responses, but serious illness and death is largely prevented. As the immune up- and down- regulating compounds emerge from clinical trials (more good news there this week) much of the remaining illness should hopefully be blunted. At that point, we can perhaps contemplate dropping the vaccine arms race and letting it circulate mostly “below the radar” updating immunity as it goes (the threshold where it hospitalise a disproportionate number of people to other seasonal respiratory viruses.).
Edit: I imagine the vaccines would remain for the more vulnerable, as with the flu. If we can get to a “just another winter virus” state it’s a big mindset flip for many of us.
> To me this suggests we have seen the rapid adaptation to a new host phase and now can expect the typical slow mutational pattern of most coronaviruses
It feels to me like it’s been thrashing around it’s genetic space and has found one good route out of its entry point to the species. The question is, where does it go from there? Is it a dead end or is there some lucrative change in reach from where this passageway is going? If it was a Nelder Meade simplex it’d be all scrunched up rubbing elbows on the tunnel as it thrashes about. Is it about to pop out in to a big valley and expand its search space? If it does it feels more likely that it could increase lethality or transmissibility more than it could evade the other immune responses than neutralisation.
> IF I’m right (huge if)
An even bigger IF on my interpretations
Love a good Nelder-Mead Simplex.. to switch analogies, let’s hope the passage in question ends harmlessly in a sump or a high aven.
The EU are really hitting the pace on vaccine manufacturing and deployment now.
14m doses delivered to member states Jan, 28m Feb, 60m Mar, 105m April, projecting 125m May and 200m in June. 200m doses in June is pretty much half the eligible population of the EU. With what they've already done and taking account of some people being too young to vaccinate and some refusers once that 200m doses goes into arms they'll be pretty much finished.
Not only that the EU have already exported 160 million doses to other countries with that number expected to be 250m to 300m doses before the US starts to seriously export.
The Tories can brag about how clever they are and how the EU is a failure but the numbers say different.
> The Tories can brag about how clever they are and how the EU is a failure but the numbers say different.
> Or.... not
It's up to the individual nations to get the jags into arms but the EU program to get vaccine supply now seems to be sorted and working better than the UK one.
Looks to me from going through the rest of that thread like the French are doing pretty much the same amount of jags per day (i.e. sum of first and second dose) as the UK now but their curve is rising steeply while ours has flattened off. Which means they are now catching up but from a fair distance behind.
Hopefully the improved vaccine situation in Europe will stop the current wave.
But the EU's initial problems with vaccine procurement has cost lives, in the same way that the delays with various other decisions in the UK have cost lives.
The question this leads me to ask is, does one country/region getting vaccine earlier necessarily lead to more cases/deaths in other countries/regions?
Obviously if everywhere had the same case levels and growth at the same time the answer would be yes, but that isn't the case.
> Obviously if everywhere had the same case levels and growth at the same time the answer would be yes, but that isn't the case.
It's a bit more complicated than that I think. Even if everywhere had the same case rates and 'need' for the vaccine at the same time, it would be too simple to say that one country having more vaccine supply definitely reduces that available elsewhere. Actual vaccinations are limited to differing extents in different places by logistics, by resources to store and administrate them and by population uptake, not only by supply.
(Edit: so I would say possibly, but not necessarily)
> The question this leads me to ask is, does one country/region getting vaccine earlier necessarily lead to more cases/deaths in other countries/regions?
I don't see why.
For example the UK getting EU manufactured vaccine early in Dec/Jan/Feb didn't actually damage the EU. They were still doing approvals, weren't ready to deploy it and they didn't had low infection rates. It was a win win that the output of EU factories could be exported.
You could also argue that getting a technically advanced region under control with vaccination is going to speed up the availability of vaccine because the industries which make the vaccine will operate more efficiently.
The problem I have with the UK/EU thing is what happened later when the Kent strain started to cause major issues for the EU and for a time there was a vaccine shortage in the EU. At that point the decent (and smart) thing to do would have been to allow AZ to export vaccine from the UK to the EU.
> Obviously if everywhere had the same case levels and growth at the same time the answer would be yes, but that isn't the case.
My gut feel is the pramgatic way to do it is to build out from the richest to the poorest countries with travel controls at the boundary and gradually expanding the region which is under control and operating normally.
The first line of defence against Covid outbreaks should be lockdowns, social distancing and so on and with vaccination coming in after that to keep it under control long term. The strategy has to consider how to protect the efficacy of the vaccines and having a population with a large amount of Covid in circulation and a steadily increasing number of vaccinated people might be setting up circumstances for the virus to evolve.
> The first line of defence against Covid outbreaks should be lockdowns, social distancing and so on and with vaccination coming in after that to keep it under control long term. The strategy has to consider how to protect the efficacy of the vaccines and having a population with a large amount of Covid in circulation and a steadily increasing number of vaccinated people might be setting up circumstances for the virus to evolve.
This is my biggest concern with the current strategy in many EU countries, which are opening up or planning to open up because of improved confidence in the speed of the vaccine programme but with infection rates still significantly higher than they are/were at the same stage in the UK. As well as presenting enhanced risk of new variants cropping up, it's also questionable at this stage whether the strategy will achieve the basic aim of keeping infection rates low enough that healthcare capacity is sufficient. Fingers crossed that summer weather helps out and the gamble pays off.
> Fingers crossed that summer weather helps out and the gamble pays off.
Given the apparent levels of vaccine skepticism and refusal around western Europe I'm not sure if it's a gamble or just hastening the inevitable by a few months. I certainly hope for everyone's sakes that it doesn't take things back to healthcare overload or elevate a new immune evading variant, but it seems significant vaccinate and unvaccinated populations will intermingle in France and Germany as a result of refusals, not shortages, so we're going to find out how real that risk is, one way or anther.
Don't know what the French are doing but in Germany the intermingling should be limited as the current lockdown is being eased by in some ways more stringent meaures. Shops for example are opening but only with a negative test (or a vaccine pass etc) and still with masks, distancing etc.
It's a bit complicated economically, socially and legally as the legislation used for lockdowns is specific regarding whether one is combating an infectious disease, protecting the health service isn't there. One has to work within the legal framework and what the public will support, nothings perfect.
Hopefully those countries might see some increase in predicted uptake as the process continues, people realise the benefits a vaccine could provide them and they see their family and friends taking it up, as has happened to uptake in the UK albeit from a better starting point.
As jimtitt points out, seems they've chosen the vaccine passport route as the easy way to address the low uptake. "You wanna go to the bar? Oh, that's a shame. Well, your choice."
It'll be interesting to see if that kind of carrot approach works, or if it backfires by driving more people in to socialising in private venues without any sort of regulatory oversight of ventilation measures.
It's a pretty strong carrot when shops are included. It almost looks like a stick...
> It's a bit complicated economically, socially and legally
Does Germany have many academics betraying the evidence based principles of their background in order to push incorrect bullcrap against control measures, or is that limited the English speaking world?
It's a stick. It's definitely a stick. A very effective stick, because there's both jealousy and fomo on the end of it.
Also does Germany have many newspapers running front pages like "WHY WAIT SEVEN MORE WEEKS?" only a few months after they themselves, on the very same front page, shat on the government for unlocking too early? Probably not.
We have all sorts of crackpots, one of the larger political parties are Covid deniers to start with though as their supporters slowly die that's changing.
> As jimtitt points out, seems they've chosen the vaccine passport route as the easy way to address the low uptake. "You wanna go to the bar? Oh, that's a shame. Well, your choice."
Actually for Germany the last survey by the RKI only gives 4.4% who would refuse vaccination and 72.6% who would vaccinate under any circumstances. Maybe it's other countries with a problem though once the EU Passport comes on stream and the people can't travel etc I expect it'll fade away. Principles rarely overcome pleasure.
A few more sizeable outbreaks starting to pop up. A pretty big one in Hyndburn which I think is mostly from a school in Accrington but may have spread outwards, and a significant increase continuing in Bolton. I'm starting to think we might be seeing the precursors to a more general uptick. Might be worth pulling out some variation on your Utla plots again? I'm only spotting these via the dashboard map, so a few days behind.
> perhaps it’s a case of undiscovered chains of infection perhaps starting with in infected inbound traveller who tests negative, and our control measures snubbing out the undiscovered chains of infection.
Which is fine until you de-restrict your internal population.....oh look, guess what's about to happen in the UK...........
> So it looks like travellers are producing a fair chunk of further cases through community transmission. Unless we have mandatory whole household quarantine around returning travellers or MIQ it's hard to see how this is going to change.
> It's not going to be long before importation events outnumber cases being generated within the borders. At this point an interesting question of ethics arises... We might be asking the majority of the country to abide by restrictions when the majority of cases could be coming from a very small minority of people travelling, and the chains of infection they start.
There's going to be a lot of wailing and gnashing of teeth over the summer as people with their 'personal shield of vaccination' (irrespective of how effective it is) clamour to go on holiday or open up internal restrictions even though the science says it's too early to do so. We're seeing it already on social media 'we should open up now, all the vulnerable have been vaccinated!''we can't stay cooped up forever!'. They've got down to vaccinating 38yr olds here now. Interestingly, people on social media in Jersey are asking for a delay in opening their borders for a month or two to allow an unrestricted local economy (like we have here in Guern) for a bit before the inevitable importation of cases and ensuing restrictions.
Just read a comment on Manchester Evening News: last year there were clear linkages of cases in parts of Grter Manc who had family in this parts of Lancashire. The same thing could be happening now. And it may be Ramadan related (families breaking the fast etc). Bolton has seen a weekly increase of 58%. Fully get that when you have low actual numbers then it’s easier to get a high % increase, but Wigan borders Bolton and we’ve had another small decrease.
Stated this is one of my earlier rants, but religion and behaviour may have had a bigger negative impact than many folk care to admit.
>> perhaps it’s a case of undiscovered chains of infection perhaps starting with in infected inbound traveller who tests negative, and our control measures snubbing out the undiscovered chains of infection.
> Which is fine until you de-restrict your internal population.....oh look, guess what's about to happen in the UK...........
You might have a point there... The next set of releases are the first ones to be really concerning, and there's bit a bit more noise about more travel coming along after them. Let's hope that test and trace is up to the task.
In reply to Si dH:
Sporadic outbreaks, rising in frequency and then merging in to a rising baseline is a familiar story from late last Summer.
> Might be worth pulling out some variation on your Utla plots again?
I'll give it a go; they're very erratic with the off/on/off/on nature of the LFDs but we'll see how they work out.
In reply to Longsufferingropeholder:
> Travelers can be quarantined, sure. But then when they get sick and need hospital treatment, they get it. When the inevitable happens do the people who catch it in the hospital know they've been near someone who traveled? How would they answer if asked?
Well, there's the test and trace app... About which I don't recall hearing a single thing in 2021.
Not quite finished given the need for second doses. It’s great to see that it’s ramping up there - they need it given they’re starting to reopen now while cases are still high in most cases. It’s going to be a vaccine race to prevent yet another wave there.
I suspect vaccine hesitancy will reduce over time. There have already been polls to that effect in France. A small minority will continue to refuse but I think a lot of people are just a bit worried / unsure as opposed to actively anti. Once they see lots of other people and particularly their friends and relatives get it, a lot of these people will be happy to take it as well.
Possibly but don’t underestimate the impact of schools, hospitality and the general sense of Covid being ‘over’. All it takes is a small outbreak, which then spreads relatively quickly given there are fewer restrictions now compared to back in March.
The way I see it, there are two issues at the moment. Firstly, local outbreaks. There’s a chance for these to be controlled through T&T and testing. Secondly, the pockets of relatively high case rates which refuse to reduce, mostly in the Manchester to Leeds belt, plus Leicester, Luton and Slough (the last three have finally turned light green on the map).
I’m really puzzled by the Lancashire / Yorkshire / Lincolnshire situation. Here in the West Midlands the rates in the 7 local authority areas range from 12 to 25, with Birmingham (obviously) in the middle at 19. Our level of social deprivation and so on can’t be that different to L-Y-L (probably lower but not massively and there are certainly some very deprived areas). Liverpool is another good example - you’d think it’s a similar sort of area but the rate there is much lower.
> I think Liverpool got their act together late last year. They’ve had walk in lateral flow testing for months, and people use it. Even a few weeks back when i needed to go up there, best case in London would have been to book a test at a not particularly convenient location. Instead, I just dropped in when I arrived. Slightly different now with the home tests, but i was glad it was there at the time.
The testing availability late last year probably helped a bit, and I think in autumn the local population were more cautious than most of the country because we got hit with a big wave in September through early October while most people were still outside of any restrictions. Hospital capacity here in late Oct / early November was pretty tight, much more so than in early 2020. However, come December onwards I think complacency must have set in, because in the new year we got hit with some of the highest case rates anywhere, over 1000/100k per week despite not apparently having much of the Kent variant at the time. I do wonder whether immunity built up in susceptible (ie key worker) populations in that period here and in other hard hit areas like London, the SE and parts of the West Midlands may have contributed to our low case rates now. In contrast, Lincolnshire and South Yorkshire had some of the lowest rates in the country around new year (Manchester was middling I think, but I don't think their 3rd wave peak was as high as their 2nd wave in November.)
The north west has basically had three waves, November being the worst. In Grter Manc and Lancashire, at the start of each wave, the areas of highest Covid matched areas of highest South Asian communities. Overcrowded housing, poverty, issues around low wage economy and religion (and associated behaviours) all played a part. Other geographical areas did catch up (eg Wigan). Last year politicians (eg N Sturgeon) correctly called out Eid celebrations as being a potential problem. Families travel to break the fast and to celebrate - it means so much to them. So it’s no surprise to some of us that the current outbreaks are following the same geographical pattern. Wigan is three times lower than Bolton yet we border each other.
> Sporadic outbreaks, rising in frequency and then merging in to a rising baseline is a familiar story from late last Summer.
This was reasonably inevitable with the reduction in restrictions now running some significant number of weeks ahead of the vaccine delivery to the younger half of the population. The obvious gamble is not enough of us will get sick and or die fast enough to overload the health services, that the delivered vaccine will keep the older population hospital admissions and deaths down and that the ongoing roll-out will eventually whittle away the big reservoir of infection and hospital load we're likely to build up into autumn. That's fine where the government has genuinely closed the feedback loop and is willing to pause or roll back measures if things gon't run smoothly but does anyone really believe we're not now just ticking dates and events off a calendar. If the delivered vaccine and demographics of the un-vaccianted don't sufficiently mitigate hospitalisations and deaths who knows what happens, we now have a precedent for the press and population accepting huge death rates, high expectations of the vaccine and huge frustration at so much disruption. The government will be incredibly reluctant to restrict the economy again into a third year. Yet if the autumn is still bad the winter will very likely be worse. It's a race at this point to get the young vaccinated, and a gamble on that pulling the winter-R under 1, the fraction of the more-vulnerable for whom the vaccine is less effective still threaten the health service/economy if covid runs riot again. Also I think more importantly the vaccine needs to be getting cases falling again significantly before the winter arrives so seasonal spread isn't inviting disaster as we would if we started with a high baseline.
> I suspect vaccine hesitancy will reduce over time. There have already been polls to that effect in France. A small minority will continue to refuse but I think a lot of people are just a bit worried / unsure as opposed to actively anti. Once they see lots of other people and particularly their friends and relatives get it, a lot of these people will be happy to take it as well.
Just saw these numbers for vaccine take up in Scotland for various demographics. It's amazingly high (really amazingly high in some cases because its gone over 100%! Presumably this is an artifact of the way the number is calculated, maybe the number of people in the category changes over the data collection period).
> The north west has basically had three waves, November being the worst.
The highest rates ever experienced in the north west were around Liverpool region in early January. Agree with you about three waves tho. The autumn wave was also a lot more drawn out.
Vaccination numbers appear to be dipping to about 200,00 per day. Including yesterday so not just the bank holiday.
3rd May 79,304 (1st jabs) & 129,058 (2nd jabs)
One thing I’ve never got to the bottom of is: why has Wigan had such a high death rate (over 1,000 total deaths)? Nearby authorities have had higher case rates but us (and I think Tameside) have had highest death rates. I know in the past we had legacy health issues due to our industrial past, especially breathing issues. But these have by and large faded away.
> One thing I’ve never got to the bottom of is: why has Wigan had such a high death rate (over 1,000 total deaths)? Nearby authorities have had higher case rates but us (and I think Tameside) have had highest death rates. I know in the past we had legacy health issues due to our industrial past, especially breathing issues. But these have by and large faded away.
I agree it's difficult to fully understand, there is quite a big disconnect between case rates and death rates at LA level. I'm sure legacy health issues and deprivation could come in to it, as well as age demographic and also ethnic backgrounds (since we know that for whatever underlying reason people of some ethnicities are more vulnerable.) We actually have a similar issue in Sefton where the cumulative death rate is the highest in the (Liverpool city) region, despite lower case loads than the rest of the region except Wirral - which incidentally has the second highest death rate. Both Sefton and Wirral have a mix of both very deprived and very wealthy areas, but I think they are probably bottom of the list in the region when it comes to overall concerns about deprivation or background health issues, and they are not very ethnically diverse. I wonder if the root cause here is mostly age related (the coast being a nice place to retire to) and/or related to a high number of care homes, but I don't have any data on that.
The fact that the Indian G7 delegation have had positive cases today does raise questions about the efficacy of travel testing. You would hope that government delegations would be tested as stringently as possible, especially as this G7 conference was intended to show that face to face diplomacy can now take place.
If we can't even prevent cases travelling within this 'elite' group of people, what chance do we have of prevention in the great unwashed masses...?
Of course, it could be that the 'elite' think they are above measures for the great unwashed, and actually weren't tested as stringently as you might expect; that exceptionalism again...
Some headlines from a couple of recent stories about flights from India.
30 People On Air India's Flight Test Covid Positive Upon Arrival In Italy
49 passengers on India-Hong Kong flight test positive for COVID
I reckon there will be alot of very annoyed people in the diplomatic arena, anybody from the G7 will be livid.
Just remind me of the events in Cornwall and in Glasgow this year.
> If we can't even prevent cases travelling within this 'elite' group of people, what chance do we have of prevention in the great unwashed masses...?
Very little I imagine but unfortunately all those who think a foreign holiday is a basic human right will be packing out every flight to anywhere that will have us. And a lot of them won't be vaccinated due to their age and due to their age may also have more risk averse behaviour when out there.
However, on a personal note, we've agonised over this issue as my wife is German and by June/July won't have seen her family for 18 months - so getting her back there is becoming a pressing matter. I appreciate that wanting this to happen but not wanting to see planes packed full of partygoers is also largely hypocritical.
As things stand, we don't know when Germany will be "safe" to visit and any trip would not be before she and the family have all had both jabs (as well as making the trip long enough for any quarantine issues) but am still very torn (and I wouldn't be going) between the potential problems of travel opening up so soon yet also the possibility of getting her home for a few weeks.
I agree with all of that.
I don't think any good can come of having the health service overloaded again for the coming winter. There's so much backlogged work to get through, as well as the human side and the effect on the staff.
> we now have a precedent for the press and population accepting huge death rates,
Yes, expectations have been massively renormalised, and as other countries fall at basic hurdles of century out public health knowledge on pandemic control, it doesn't help make the case that we can do better, and that doing better isn't just about saving lives but ultimately getting the economy to recovery sooner, too. Short-termism is never good, but right now it's particularly bad.
A lot of unknowns ahead and May 17th is fast approaching.
In reply to captain paranoia:
> Of course, it could be that the 'elite' think they are above measures for the great unwashed, and actually weren't tested as stringently as you might expect; that exceptionalism again...
I don't think we need to invoke exceptionalism to explain this; anyone who just got infected is going to test negative for some time, so immediate pre- and post-flight testing is gong to miss a fair bit I think. Especially as the whole travelling process is going to expose people to the virus at various pinch points. This doesn't make me particularly happy given the shift in the news towards green listing various destinations sooner rather than later.
In reply to groovejunkie:
At some point, if you're agonising over choices well within the spirit and letter of the rules, you're probably making far more effort across the whole of your life to avoid spreading this virus than many, and you're going to put much more care in to this when travelling than most. Difficult if you feel strongly about travel opening too soon (I know I do) but you're not going to be the ones making things worse I suspect... A lot of other concerns around sudden imposition of quarantine etc. If I had a pressing reason to travel I think I'd rather do it sooner than later although who knows if the "cases are holding low" windows for the UK and Germany are going to have much overlap.
> As things stand, we don't know when Germany will be "safe" to visit and any trip would not be before she and the family have all had both jabs (as well as making the trip long enough for any quarantine issues) but am still very torn (and I wouldn't be going) between the potential problems of travel opening up so soon yet also the possibility of getting her home for a few weeks.
My daughter is working in Germany at the moment and my wife's family are there. They are going crazy with the vaccinations - 10 million first doses in the last two weeks including one day where they did 1.1 million. My wife's parents both got two doses of Pfizer within the last month. At the rate they are going they'll catch up with the UK very quickly.
> so immediate pre- and post-flight testing is gong to miss a fair bit I think
My comment about stringent testing was meant to refer to a more prolonged pre-flight testing and isolation regime, rather than at the departure gate...
Oh f*ck. A FB post from PHE just turned up on my timeline because my sister responded to it (she's a vaccinator), explaining her centre's arrangements for late opening to cater for Ramadan (in spite of religious leaders insisting being vaccinated isn't breaking fast).
And I got exposed to the base level f*ckwittery of the internet that I normally try hard to pretend doesnt exist...
However that does not explain why these areas are seeing a resurgence / failure of decay, whereas places like Birmingham and London are not (yet), despite also having areas with a high proportion of ethnic minority people.
You are right but it’s interesting that Ferguson now thinks Covid should be more or less under control going into winter. I think a lot depends on government willingness to reintroduce measures if need be and no vaccine resistant variants popping up. On the first point, I think most people and indeed politicians now get that it’s better to go early with less stringent measures rather than leaving things too late. As to the second, who knows...
Great data. Over 100% is due to the population being an estimate, I suspect.
This might give you an idea why some areas of West Yorkshire (Keighley, Bradford, Batley) still have high infection and low immunisation rates.
> My daughter is working in Germany at the moment and my wife's family are there. They are going crazy with the vaccinations - 10 million first doses in the last two weeks including one day where they did 1.1 million. My wife's parents both got two doses of Pfizer within the last month. At the rate they are going they'll catch up with the UK very quickly.
Been meaning to say this for a while, but you should have took my offer of a wager - l think you may have won!
Impressive. And UK well over half a million just reported.
You’re right. I’ve not looked at much Covid data recently (I was obsessing with it which wasn’t good). But a few months ago, when it was being pointed out threat people from BME backgrounds where x times more likely to die of Covid I did compare some key areas. Tower Hamlets, highest Bangladeshi community in the UK and possibly one of the highest south Asian communities and considerably lower death rates than equivalent areas in the NW. This was why I challenged the ‘people form BME backgrounds are x times more likely to catch/die of Covid’ and the reasons usually cited, because there are huge disparities. And Wigan has a very high death rate and very small BME population. Complicated, poverty and housing must play a part, but I think we underestimate attitudes and religion (often linked) and this doesn’t get discussed through fear of appearing racist. Probably a complex blend of issues (terraced housing and a culture of being in and out of each other’s houses won’t help, and high numbers of people in low paid, risky ions compared to other parts of UK?
Anyone got any speculation (or local insight) into what's going on in Moray? https://www.bbc.co.uk/news/uk-scotland-north-east-orkney-shetland-57010292
Sounds like it's a cause for concern among the local public health people, but that BBC article doesn't really say much about what might be driving it. Hopefully somebody among them has a candidate explanation, even if they're not saying...
Bolton is also one of the places where several cases of the Indian variant had been detected according to that SAGE paper I linked a few days ago. Hopefully that's not significant. The next update of variant numbers was due out today but has been put back until tomorrow.
Eek, no. The headline numbers reported in your bbc article are about to get a lot worse too, looking at the grey bars on the right hand side of the cases graph (see link). The absolute numbers per day are pretty small though, so I guess it's a combination of a couple of outbreaks, surge testing and a small population that highlight the problem.
I think it's focussed on a school in Elgin. Hopefully containable.
> Bolton is also one of the places where several cases of the Indian variant had been detected according to that SAGE paper I linked a few days ago. Hopefully that's not significant. The next update of variant numbers was due out today but has been put back until tomorrow.
> The next update of variant numbers was due out today but has been put back until tomorrow.
The notice of today’s delay was the first actual confirmation I’ve seen that there’s an intended weekly release cycle on Thursdays; the webpage settled down to that a while back from erratic updates but the schedule has never been formally announced unless I’ve missed it.
I read the delay due to technical reasons text and thought “oh really?”, then chastised myself for being so cynical. Then, from your link:
The latest update of case numbers of these variants was due to be published on Thursday. But leaked emails seen by the Guardian show the announcement was delayed until at least Friday because of the local elections.
I wondered a thread ago and so again if this variant was behind the burst of rising cases in the south in the older age ranges a couple of weeks ago. From the article:
In London clusters have been located in care homes
Clusters of the Indian variants of Covid-19 have been found across England, including in care homes
Ominous that today’s update is apparently political enough to get delayed; there’s one more update due before the May 17th notional date for the next round of unlocking.
In reply to Si dH:
Manchester Evening News flagged it yesterday.,.
And Bolton has second highest rate, after Hyndburn in Lancashire....
In a ‘comments’ section, someone stated this has happened before in these two areas and was (partly?) attributed to large families living in both areas and mixing. I also saw another article about another Asian wedding celebration last Feb, 60 guests. Been quite a few of these often slipping under the radar. The attendees must have known they were wrong but carried on anyway. Then there was the Bolton councillor who travelled to Pakistan for a wedding. He got suspended. Like I said, this stuff isn’t getting discussed.
One difference between the Indian and SA variants I suspect is the size of the sub-communities they "plug in to" in the UK; in particular the communities most likely to be affected by the Indian variant here are some of those at greater risk from the virus in the UK, and where some of the vaccine hesitancy seems to be concentrated.
> Like I said, this stuff isn’t getting discussed.
The key thing to me is community engagement working with community leaders and that seems to have been taken seriously with the vaccination program for example.
Some difficult issues for the authorities.
The Hyndburn outbreak is mostly from a school in Accrington. Not sure how but quite a few kids and teachers tested positive (LFT) to the extent that they decided to PCR test everyone in the school (again, both kids and teachers) regardless of LFT test or result; this uncovered a bunch more asymptomatic cases, which is why there is a big spike in infection rates. It's well covered in local news. The spike in Hyndburn has now gone and daily cases for the last 3 days (still grey on the dashboard, so not captured by any of the seven day average figures) are back at normal levels. I think Bolton is much more troubling because it looks to be in continuous growth, and rates have increased in all adults rather than just school ages.
I do wonder what the agenda of people pushing this rubbish is. I’m not sure they actually believe this but who knows.
I like this bit in the article:
<<In February Tom Ratcliffe, a GP in Keighley, encountered 'vaccine hesitancy' among a group of street drinkers in the town.
Even though some had previously injected themselves with "all sorts of things", they won't take the vaccine, he said.>>
That still doesn’t explain why X community in place A has lower rates / deaths than X community in place B. I get that x y z religious groups might be associated with higher spread. Israel had an issue with Ultra Orthodox communities and there were some reports of large weddings etc among the Ultra Orthodox community in London. There was a large Easter gathering at a Polish Catholic church which was broken up by police. There were reports of orthodox Christian gatherings in Eastern Europe driving spread. However what doesn’t make sense is to suggest that say Muslim practices in area A somehow drive spread but in area B they somehow do not (although religious / social practice could vary from one community to another despite a common religion.
What is it about Yorkshire and Lancashire. Weather? It’s colder up north. Yet Newcastle is in a better position than Yorkshire. Something to do with former mining communities (underlying respiratory conditions)? Yet there are plenty of other former mining areas which are in a better position. Your point about jobs might be closer to the mark, yet there are areas elsewhere with similar working population profiles and similar deprivation levels. So I’m puzzled. No doubt someone will do a study eventually. I just hope it’s not due to variants...
Today’s 7 day average rates:
’Dark green’ Yorks, Lancs and Lincs areas on the map are all over 50, some significantly so.
> Even though some had previously injected themselves with "all sorts of things", they won't take the vaccine, he said.>>
I'm working on a project with an engineering team in Pakistan at the moment. When I mentioned I'd got vaccinated I didn't hear any qualms about vaccination at all, more a desire to get themselves vaccinated as soon as possible.
It's interesting that the position from some communities in the UK on vaccine seems to be more extreme than in an actual Islamic country.
> Ominous that today’s update is apparently political enough to get delayed; there’s one more update due before the May 17th notional date for the next round of unlocking.
It's been released now:
As rumoured, quite a big increase in numbers of the second Indian variant, which has also been designated a VOC. No info on distribution. This is the one without the E484Q mutation interestingly.
> In London clusters have been located in care homes
> Clusters of the Indian variants of Covid-19 have been found across England, including in care homes
What's more, plenty of vaccinated residents caught it and required hospital treatment (although not acute).
That screams 'vaccine escape' to me....
I've updated the variants plot with this week's delayed data release.
I know you know this, but it's stated for the thread: As well as the usual extensive riders that apply to this plot, fitting an exponential function to two data points as has been done with the new Indian VOC does not in any way imply that the data is rising exponentially - basically any function can be fit perfectly to two data points. Still, it's a way of asking "If the data is rising exponentially, what is Is it's doubling time?".
> This is the one without the E484Q mutation interestingly.
The "best" way out of a local minima doesn't have to be the most accessible.
In reply to Toerag:
> That screams 'vaccine escape' to me....
Indeed; partial escape - likely from the neutralisation antibodies but not from other antibody and T-cell responses? It's very bad news for the recovery if this variant has the potential to hospitalise large numbers of care home residents even as the weather is warming, let alone going in to winter. A lot of unvaccinated care home staff caught it, so one seemingly obvious suggestion is to legislate to protect employers agains dismissing staff for vaccine refusal.
One more update of the variant numbers before the notional data for the next round of unlocking. I drove over to Hawes and back today for my first vaccine dose and so listened to a lot more radio than normal. The presenters were full of what they're going to do come May 17th and the travel changes due today; it seems the public momentum has already built behind these measures; it would take a strong, charismatic leader with unassailable support from the electorate to delay for a week or two to allow the situation around these variants to be understood, and then enlightened decisions made accordingly.
People were streaming in to Hawes from far and wide for their jabs today - even North of the Tyne. To get away from the traffic I came back the direct route - nearly got brained in the hail storm doing the 4 gates on route, and had a chance to reflect on how well suited a RWD convertible is to a borderline dirt track getting buried under snow and hail. Nice part of the world, the Yorkshire Dales and the council have built a lot of new, very large roadside lay-bys outside many of the villages which seems remarkably sensible.
Well done getting your dose, don't let any side effects put you off tomorrow's data update
Thanks; it's quite a relief - I'm aware the actual risk is very low now, but I want all the immunity I can get for where I worry we could be going. AstraZeneca for me. I'd been planning a swimming tour of the various nearby waterfalls on the way out but the snow line was close enough to put me off...
> don't let any side effects put you off tomorrow's data update
I'm just going to blame my usual grammar errors and transpositions on the side effects, real or otherwise...
> Given that India is now on the red list for travel and that we know the mechanic of the virus is exponential, it's not the daftest question in the world to ask.
Okay, maybe something even dafter - if predictable - could explain the very large rise without calling on rapid exponential growth through community transmission...
Nick Triggle has something to say on the matter, although - to my reading - he does not delineate clearly between what his PHE source says, and what he says, but the gist is perhaps a load of people rushed in from India ahead of the red-listing. As with my post above, he's suggesting we need a couple more weeks of data to understand this... Although I imagine PHE don't - they have the data on where these cases have come from, so hopefully that's reflected in what the sources are telling Triggle - but I've not always sure that choice, anonymous comments from PHE and the data square off as well as might be expected.
Come on PHE, put someone senior's name to an interpretation of these numbers, preferably backed up by some data.
There are some early signs in the data, Public Health England sources say, that the increase may be coming to an end, meaning that it may reflect that rise in travel rather than significant community spread.
Two key factors are in our favour - the vaccines appear to work just as well against this variant as the dominant virus circulating in the UK (although uptake in the Indian community is a little lower) plus there are still significant social distancing restrictions in place that should help to limit spread.
Lots of testing and contact tracing in different areas are taking place - and some surge testing is expected to be announced later in areas where there is most concern.
It will be a couple of weeks before we know for sure. The message is clear - this needs to be taken seriously, but there is no need to panic.
> a load of people rushed in from India ahead of the red-listing.
I'm betting on this. The airlines were asking to put on extra flights ffs. News was awash with "person can't find a ticket home in time to dodge quarantine and infect everyone, isn't it terrible, sob sob" that week. It's this. Totally this.
Edit: given the infection rates, number of seats on a 747, and number of people in a household, I reckon you can do some very simple multiplication and get to 200.
I'm sure that had an effect but if it was the main cause I think we'd have seen a similar rise in the first Indian variant that they like to call the double mutant - but we haven't.
Depends on the relative prevalence in the areas of India that people are flying back from.
In other good news, if we're wearing our 2-points-is-a-fit glasses, have the other two variants started to go sub-exponential??
There were a couple flights from India to Hong Kong & Italy that had 30 to 50 of the passengers testing positive for Covid on arrival.
10% or more prevalence amongst passengers on those flights.
> In other good news, if we're wearing our 2-points-is-a-fit glasses, have the other two variants started to go sub-exponential??
Plot below with residuals to an all-timepoints non-linear least squares fit of an exponential. The residuals are normalised to the square-root of the fit as an estimate of Poisson noise; this keeps the plot normalised in dynamic range whilst the absolute numbers rise, and shows that as with P1+p2 daily case counts, the real noise is worse than Poissonian.
It looks like both the SA variant and the UK local variant (VUI-21FEB-03) have been falling on to ever slower exponentials for the last 5 weeks; I wondered a while back if this is what it looks like when enhanced contact tracing is put on to a reservoir of live cases and chases through them faster than the infection is spreading - initial fast phase then a curve over to match the wider case behaviour - assuming the variant is no more prolific.
Edit: the noise is non Poissonian for very different reasons to pillar 1 & 2 I think. P1 & P2 it comes largely from day-of-week sampling effects I think and here it comes from lots of factors around surge testing etc.
So, provisionally and highly qualified good news indeed. Manus variant is still close to a fixed-rate exponential rise however, but at lower numbers.
I'm still on the fence about whether the Manaus thing can be sustained, at least in the main, by imported cases. People are getting very creative with their itineraries. I know what I want it to be.
Although if you think about the mindset of someone willing to be so creative, and the legal penalties they’ll want to hide away from, it’s not a stretch to imagine them failing to quarantine sufficiently let alone to go for a test if symptomatic unless they end up hospitalised. We’ll see what the next two weeks bring.
I can only speak to West Yorkshire's problems here, but I have a few clues to what's been going on, and think that a combination of mostly though not completely unrelated factors are at play.
There are plenty of other areas with similar deprivation levels as you point out, but few large county-level areas containing so many densely interlinked cities and towns. If you look at this IMD map - https://fryford.github.io/imdmap/ - you see that there are lots of cities and towns in W Yorks covering a total area similar in size to Greater Manchester, all with very highly-deprived urban centres. I'd hazard a guess that a commuting map for this area would look much more chaotic than the same for an area with one large urban centre; it would have lots of random interaction between widely-dispersed areas rather than a majority commuting into a centre, then out again along suburban 'spokes'.
Then there are the underlying health conditions. COPD is mainly a disease of the over-50s here, but not solely linked to mining. There's a much larger female population of ex-mill-workers with COPD, and it seems to me they've been hit hard. A younger working population is still being affected by the fact that asbestos has not yet been removed from their workplaces, so COPD isn't yet a thing of the past.
Then the behavioural differences are, I think, huge. The Sunni Muslim population is largely poor, religiously more conservative than elsewhere (remember the London bombers came from Dewsbury), vulnerable to disinfo, and live multigenerationally. All of these factors exist elsewhere too but probably not in such virulent combination.
Similarly the subsequent generations of immigrant populations - Poles, Kurds, Hungarians, Romanians, Lithuanians - include significant numbers of human-trafficked people living in their workplaces, usually bed factories, and none is integrated; they speak no English, live and work together within very small local areas, and are vulnerable because of their poverty and precarity.
But the white working class in the same areas combine nearly all these elements - they live multigenerationally too; are very right-wing (remember the murderer of Jo Cox in Batley); are poorly educated to the point that it's equivalent to a language barrier; and have been targeted, it seems to me, by disinfo campaigns. Walk around a white council estate here and the Qanon/Joe Biden is a pedo/Covid is a hoax stuff is rife; join a local FB group and you find the same.
So compliance with mitigation measures like masking or social distancing has been woefully low across the board. There's no single sub-community driving high prevalence, as far as I can tell: we see outbreaks alternate between MSOAs where one or another of the above live, like embers repeatedly sparking off new and recurring firezones.
> it would take a strong, charismatic leader with unassailable support from the electorate to delay for a week or two to allow the situation around these variants to be understood, and then enlightened decisions made accordingly.
We'll be fine,then; the electorate seem to think we have a wonderful leader...
To be honest, I think you are staring at tea leaves a bit. Yorkshire has not generally been badly hit in the pandemic - the LA with the highest cumulative case load (per 100k population) in Yorkshire is Bradford, which comes outside the top 30 in the overall English list. It warrants investigation and thought as to why South Yorkshire and the Humber areas have held on to higher case rates in recent times, but the explanation can only be something that has changed or happened more recently during the pandemic because those areas have not had high cases generally when compared to urbanised areas in much of the rest of the country.
Having said all of that, the deprivation map you linked was brilliant - thanks. I've never seen anything like that before.
> To be honest, I think you are staring at tea leaves a bit.
Wrong phrase. What I meant was, I think you're looking for the wrong type of cause.
Re extra flights. You’d think by now the muppets in charge will have realised that the way to deal with this is red listing overnight. The hotel quarantine could be free for the first couple of weeks.
> I'm still on the fence about whether the Manaus thing can be sustained, at least in the main, by imported cases. People are getting very creative with their itineraries. I know what I want it to be.
Importation could be from anywhere, doesn’t have to be from Brazil itself... France had not insignificant levels of the Brazil variant, I seem to recall from reports earlier this year.
Thanks. That’s a fascinating map and, going by my local knowledge of Birmingham, fairly accurate on the whole, though it does give some odd results. I particularly like my brother’s apartment block split half way down the middle into different colours (he tells me it’s because the map is based on LSOAs which were designated in 2004 whereas his block was built post 2004 and was right on the border of two LSOAs). Also some very affluent streets aren’t as ‘green’ as I’d expect but that’s due to LSOA level dilution - a couple of streets with huge detached houses isn’t sufficient population for a separate LSOA. It could also do with a different colour for non-residential areas, though I do find it amusing that my apartment block is apparently less deprived than my office (or what used to be my office...).
Anyway, interesting analysis. I hadn’t considered the cross-cross commuting angle and I can seen COPD being a local thing as well. As to the other points, in principle these are all possible reasons but I would question whether it’s that much worse in Yorks than say in the West Mids. Perhaps it’s just grim up North...
Another interesting comparison is Leicester. Stubbornly high for most of the last year and of course the first area to be placed in local measures last summer. Finally turned light green on the map about a week ago and now at 36 and falling. Factors such as dodgy working conditions in textile factories and a high ethnic minority population were previously cited in the media by they seem to have turned a corner in the end. Perhaps being a relatively isolated urban centre helps (your commuting point) - there is some commuting into Birmingham but a lot of that is white collar employees who would have been WFH through lockdown.
Liverpool has just gone yellow. Amazing for a large urban area Anne well done to the Liverpudlians but, again, why is it so much better there? Some comments on this upthread but I’m not sure we have a clear answer.
Is this important? I think so, as the dark green will turn blue and then start to spread...
So what you’re saying is there’s less herd immunity in Yorks? Would be interesting to see some kind of heat map plotting death rates up to end of August say vs subsequently by area (I say death rates as case numbers for most of the first wave obviously won’t be reliable). Or perhaps cases to end of November vs subsequently.
> So what you’re saying is there’s less herd immunity in Yorks? Would be interesting to see some kind of heat map plotting death rates up to end of August say vs subsequently by area (I say death rates as case numbers for most of the first wave obviously won’t be reliable). Or perhaps cases to end of November vs subsequently.
Well, it's certainly true that those areas had relatively very low infection rates in December and January, they never hit the really high infection rates seen in other areas, so will have fewer people still with antibodies from that period than other urbanised areas of the UK. Whether that difference is significant enough to cause the different behaviour we are seeing now, I don't know.
Argh, went over 30 minutes trying to edit my post.
Here are some screenshots of the infection rate map from the period 27/12 through to 24/01, ie through the peak of the 3rd wave and the early part of lockdown. Eastern bits of G Manchester/ Lancashire and Yorkshire/Humber were unique amongst urbanised areas of England I think in not really hitting very high case rates through this period. They had stayed under Tier 3 through December and lockdown came in time for them, unlike elsewhere. They were worse hit in November, but not as badly as some other areas in Dec/Jan, and presumably immunity from that period in autumn will have been wearing off more.
> Whether that difference is significant enough to cause the different behaviour we are seeing now, I don't know.
Small differences to an exponential rate constant compound under both decay and growth.
White working class women from deprived areas in and around Calderdale are the main people who care for my father-in-law who is severely disabled and receives care at home. 6 people visit every day and the job has about 20 regulars but with quite a large turnover. He's been receiving care for about a decade. From all my conversations with them I think you are exaggerating the behaviour of the white poor in the area. Aside from my massive respect for their work on minimum wage (often looking after a family at home as well) I have grown to really respect their views... mostly being funny, astute and more politically aware than I thought possible (for some nearly everything comes through their phone but they seem to 'know' what's bullshit). They have become an important part of my political barometer. Some of the carers are from poor Muslim families... two of them were young, well educated and ambitious and just doing the work to earn some cash for the family and gain experience relevant to possible future NHS careers. The nutters are indeed out there but they also live in nice white middle class areas, like where my parents are based in a village in Northants. Some of the behaviour and attitudes of their neighbours during covid beggars belief: full on hoaxers and blatant ignoring of regulation.
No, I think you had it right first time - reading tea leaves is not far from what we're all doing. Agree about Yorkshire generally, but I'm not looking at Yorkshire generally - too large an area, with very affluent towns like Harrogate and vast tracts of sparsely-populated farm and moorlands. I'm more looking at those MSOAs within W Yorks that have stubbornly continued to have sustained high prevalence despite special measures, surge testing etc. At a local level that comes down to the same MSOAs within one UTLA consistently having dramatically higher prevalence than others. What covid has done is to bring those areas and their non-covid problems into sharper relief - from this point of view covid prevalence has been a symptom of pre-existing disparities that needed addressing long before covid.
Quite - I too know a majority similar to those you know. That doesn't mean that there are not areas such as I describe, or that I'm exaggerating. I'm not generalizing, which would be to exaggerate, but doing the opposite. I'm trying to identify specific local MSOA (and in many cases sub-MSOA) level areas where prevalence has been consistently high and compliance has been low or non-existent, without simply ascribing their problems to the presence of "nutters"; these areas have been historically disregarded as hotbeds of nutters by the majority and the LAs, but to do so doesn't help us to understand or solve their problems.
I appreciate what you are trying to do but go back and read what you actually wrote and see if you really are happy with those rather sweeping generalisations.
Aha. That may well explain it. Whereas places like Merseyside and West Mids got hit hard. So it’s almost like a series of aftershocks, except they are in a different place compared to the main earthquake. Having said that, to get a proper view on this you’d need to look at infection rates in the first wave (hospitalisation rates would be a better measure) and then over the period from October till now. There is also the possibility that immunity from last spring has now faded. The picture is certainly complex but I find your theory more credible than “area A has X Y Z demographics contributing to the spread (but we don’t know why the same demographics aren’t contributing to the same extent in areas B and C)”.
I agree that the analysis needs to be at MSOA level (being the most detailed info available for cases, not sure about hospitalisations) but I think looking at things at a higher level as with the screenshots above is helpful to get a general feel for things. I’m ignoring the ‘rural’ bit of Yorks. The other UTLAs are pretty urban.
I also agree that Covid has highlighted long standing issues. But the presence of long standing issues which are present in many urban areas does not explain the current situation.
I'm happy with what I wrote. It's pretty clear that I'm talking about very specific areas which have within them Sunni Muslim, eastern European, and British white working-class communities, and which are particularly deprived on the IMD map . If you're reading "sweeping generalisations" into my statements you're misreading.