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Coronavirus in the UK - news, lockdown and discussion

My concern was not that immunity would evaporate between 4 and 12 weeks, it was mostly about a lack of data at the time as to what effect a longer gap might have on the levels of protection finally obtained after both doses.

Mistakes I may have made in terms of rigidity is that I like evidence-based decisions, and so I found it unhelpful that we were using timing that didnt match the timing used in the trials which provided the early evidence and data. I thought that introduced uncertainty, and I didnt know if it was safe to make assumptions.

There wasn’t trial data supporting administration to the over 80s either. A little knowledge can be a dangerous thing.
 
There wasn’t trial data supporting administration to the over 80s either. A little knowledge can be a dangerous thing.

Maybe it is useful to try to take me down a peg or two at times, it should reduce the chances of me making pandemic mistakes. I'd rather it happened in the form of discussing detail though. For example I'd like to better understand what knowledge enabled you to be confident in dismissing the concerns about proceeding in a manner that didnt match the timing used in trials. I'm assuming there is some, and I've never fully understood what it consisted of. If there wasnt anything in particular that made such assumptions safer, and it was mostly a case of looking at the upside in terms of number of people jabbed then that is also understandable.
 
If anyone is still interested in the detail of UK concerns, judgements and balancing act in regards the 12 week timing of the second dose and the situation at the start of this year, this is one of the papers I read at the time:


A few relevant summary quotes:

For both vaccines approved for use in the UK, the virus neutralization titres and efficacy are higher after two doses than one. There is therefore a higher risk of virus replication under partial immunity after one dose than after two doses, so in the short-term, delaying the second dose would be expected to somewhat increase the probability of emergence of vaccine resistance - but probably from a low base.

Whilst the neutralization titres seen after one dose of vaccine are lower than the median titre of convalescent plasma, they are within the lower range of responses seen following natural infection.

In the current UK circumstances the unquantifiable but likely small probability of the delayed second dose generating a vaccine escape mutant must be weighed against the measurable benefits of doubling the speed with which the most vulnerable can be given vaccine-induced protection.

It is a realistic possibility that over time immune escape variants will emerge, most likely driven by increasing population immunity following natural infection.

I dont like unquantifiable risks and so although I took on board what they said, I didnt have a means to judge whether their approach would actually stand the test of time.
 
According to my parents, the Swiss are doing this: If you have had covid (meaning if you know you have had it) then you only get one jab of vaccine. If you haven't had the covid you get both. Is that likely to be driven just by shortage of supply?
 
According to my parents, the Swiss are doing this: If you have had covid (meaning if you know you have had it) then you only get one jab of vaccine. If you haven't had the covid you get both. Is that likely to be driven just by shortage of supply?
Its another example of a balancing act where supply realities are part of the picture, but where they try to be clever using available evidence.

If there is evidence that levels of protection offered by natural infection and then one vaccine dose are in the same range as protection offered by two doses of vaccine, then it makes plenty of sense. And I think there have been signs of such evidence, though I havent studied the details in depth myself.

edit - oops typed infection when I meant to type vaccine! Reminds me of the time in a press conference when Johnson said the virus needed to be kept in a freezer.
 
TBF, elbows, it wasn't just you expressing concerns about the 12 week gap, that was the majority view on here.

I was one of a few, in fact it may have just been me, that was agreeing with platinumsage, and getting shot down over it, because I trusted what my SiL had discussed with me.

I am looking at the details of the balance of decisions, including long conversations with my SiL, who is a scientist, and has been discussing the delay between the 2 doses over recent weeks with colleagues, and based on what I am hearing, and the fucked-up situation the UK is in, on balance the 12 week gap is the right decision.

I think it was fair for people to have had those concerns, because of how the trials were done using the 3-4 week period, perhaps it the situation hadn't been so urgent, those early trials would have tested the longer period, but, that was then, and it all worked out OK, so I am not sure it's worth revisiting that point in time.
 
Cheers.

I wonder if we will end up having any similar disagreements when it comes to the time where questions about how long immunity lasts will become a more pressing concern.

I expect that at the moment there is a mixture of historail knowledge and assumptions, combined with some bits of contemporary data that offer some clues and so some people who figure they know abot this stuff will have some ideas about this already. But in terms of a wider body of evidence, as JVT mentioned in the press confrence recently, we cannot fast-forward time and only time will really tell. Obviously this topic already comes up when we hear current stories about trialling booster jabs.

Perhaps some of the disagreemnts relate to a different form of binary thinking about vaccines than the one I usually draw attention to. Confidence is an important part of ensuring a successful vaccine rollout. Uncertainty could get in the way of that, making it tempting to take a simplified stance in order to diminish concerns that could impact confidence. I expect we will see some of this when it comes to vaccines effectiveness against new strains - the last thing the government want is for lots of people to become defeatist about the vaccines and not bother with doses because they think it doesnt work well enough to bother. So they may be very tempted to oversimplify the message and talk about vaccines still working. I am bound to be interested in the detail, and when I talk here I want to discuss uncertainty and changes to levels of effectiveness properly. There are some circumstances in which my view becomes more binary, in the most obviously indisputable areas or in the direst of circumstances, but I mostly trust peoples to be able to cope with the nuances.
 
Not sure there's much scope for disagreements over how long immunity lasts, because both the virus and the vaccines are new, trying to second guess longevity would be pretty dumb, until real world data becomes available, everyone is saying 'only time will tell', including my SiL, even when I've pushed her on what would be her best guess/bet, she refuses to go down that road. :D
 
Yeah thats my presumption but its only a presumption so I thought I would test it to see if there are other stances out there.

I suppose it somewhat ties into my inability to really understand where the views on confidence about not having a big third wave come from. If its not simply wishful thinking then I want to understand that evidence that underpins it better.
 
The other bit of the Spector video that seemed a bit controversial was the suggestion that lockdowns haven't actually had much of an effect.
 
Yeah thats my presumption but its only a presumption so I thought I would test it to see if there are other stances out there.

I suppose it somewhat ties into my inability to really understand where the views on confidence about not having a big third wave come from. If its not simply wishful thinking then I want to understand that evidence that underpins it better.

I've kept away from discussing a third wave, my gut feeling is we will get one, but I hope the vaccines will prevent it being a big one, so I remain cautiously optimistic, which probably has a lot to do with how hard this lockdown has hit my mental health, but I am prepared, thus only cautiously optimistic.
 
The other bit of the Spector video that seemed a bit controversial was the suggestion that lockdowns haven't actually had much of an effect.
I've tried to resist going into detail about that because it will involve lots of tedious waffle from me including about changes to behaviour that came in the buildup to the lockdowns, including peples taking matters into their own hands and adjusting their own sense of risk before the government got round to acting. I also need to update my understanding of the various studies on this topic so far.

At least when it comes to platinumsage not being on the same page as me in regards some aspects of third wave risk, he made it clear enough that thats partly based on not agreeing with the vaccine effectiveness figures the modellers used. With Spector I dont really have a good sense of where his confidence on this comes from, except that he seems to treat the '70% of the population gaining immunity' as a magic threshold. There will be a threshold like that somewhere, but I dont think I'd be that specific or attach that much confidence to it at this point, nor do I understand the reasons for being so relaxed about the Indian variants potential.
 
I had a very brief dig around to get a slightly more rounded view of his current stance.



I do have some sympathy with that position, but I think he may be going too far.

For example before this pandemic I did tend to spend quite a bit of my influenza forum talk time pointing out the excessive nature of some newspaper etc reporting on 'Australian flu' and suchlike, and how such concerns would not necessarily translate to the UK seasonal influenza picture at all. So it is not a good idea to ignore the media hype aspects of infectious diseases.

But given whats happened so far in this pandemic, and some of the largest mistakes that were made, it does seem rather stupid to me to become as confident as he is at this particular stage. His learning to live with Covid stance is also rather too perfectly in tune with certain interests and stances that I consider to be incomptaible with an appropriate public health response at this stage. If months go buy without problems then my position will gradually shift, and eventually we do need to make all sorts of adjustments to our sense of risk from this virus. But this soon after the last wave, with the current valid concerns about variants still being explored, and vaccination not yet complete? No, I cannot do that at the moment, far from it.
 
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According to my parents, the Swiss are doing this: If you have had covid (meaning if you know you have had it) then you only get one jab of vaccine. If you haven't had the covid you get both. Is that likely to be driven just by shortage of supply?

Oh and I just found this when looking at things Spector has said on twitter in the past.

 
The thing is,that it could, say, lead to a 60% risk that a dangerous mutant will arise in a population of X million, and we have just been lucky (so far) that it hasn't happened.
Sure. We have an order of magnitude idea, though, in that we now know that it is possible to vaccinate 20 million people at a 12 week interval in the teeth of a wave and not create a variant that ruins the process. We can calculate that a certain level of luck is extremely unlikely. And that's practical evidence that can inform, for instance, India's response to its current wave.
 
Maybe he should remember to mention more often what he said about predictions in April.


It's a question of what you want from your predictions, though. In this case, a new variant has been allowed to seed many times across the country by a particularly stupid and avoidable government decision wrt border control. So his prediction may well have been right without that specific event, an event that clearly hasn't (yet) happened in Israel.

It's one of the problems with the many models. How do you incorporate Boris Johnson into your covid models?
 
What I want from predictions is for them to cover the likely range of things that will actually happen, and not be used as an excuse to act late.

I continued to travel backwards along his twitter timeline and was unsurprised to discover that his negative feelings about lockdowns are not new.

Just one example:



So I am partly at odds with him in some important areas. However, since I have been going on about the important role of hospital infections for a very long time, there are some things he highlights which are very much in tune with my thinking. And this stuff is a balancing act too - I would suggest that if we had a perfect grip on hospital infections including during dangerous periods, we could get away with fewer draconian measures in other areas. And I'd assume that hospital infection control is one of the areas where vaccines reducing transmission will be very important. Vaccines can be a gamechanger in that setting, but this also means I will be alert and worried about any indications that new variants start to hamper the vaccines ability to reduce transmission.
 
What I want from predictions is for them to cover the likely range of things that will actually happen, and not be used as an excuse to act late.
How do you model Boris Johnson? Do you look at the list of countries he wants to make trade deal with and factor those in to your predictions? There's an argument that you should, that models of future UK covid waves aren't going to be much good without factoring in the idiot at the head of government.

It's also ok imo, and I think more useful, to say 'well if X doesn't happen, I predict this, but if X does happen, I predict that', where 'X' may be anything, including something like politically motivated border control measures.

And that's where Twitter can be the problem. It's not the best medium on which to express nuance and conditionality.
 
I'm only using twitter to find examples of what his stance on lockdown and the future was like in the past.

The modelling I'm interested in is quite narrow and specific. It models things like expected cases, hospitalisations and deaths in different scenarios. So modelling Johnson doesnt really come into it, except to say that the modelling I tend to get to see is based on scenarios that are compatible with the governments plans for unlocking steps etc. Which is why SAGE looks at those model runs in particular and then we get to see the papers. And they arent supposed to be predictions of exactly what will actually happen, just indications of what we might expect from different scenarios and different ranges of parameters. I'm always going to moan at people who try to turn particular model runs into confident predictions about what will actually happen, although I suspect I've ended up in that territory myself on a few occasions despite my attempts not to go that far.

Anyway I found a lot more things that Spector said along these lines but I wont bore everyone with all the lockdown-related ones. Instead I'll just use one more of a different sort, to make a point I havent made for a while:



If you want actions based on science you have to look at things from more than one angle. I've always said that one of the reasons closing schools is a measure which ends up being taken at very bad stages of the pandemic is actually nothing to do with levels of infection and transmission in certain age groups and within the schools themselves. Rather its because if you close schools then it causes a lot of disruption to adults normal routines, contact mixing patterns and ability to attend workplaces. Stuff that needs to be disrupted big time to cope with bad waves.
 


I do have some sympathy with that position, but I think he may be going too far.

It's a very parochial viewpoint. We can stop worrying when >=70-80% of all countries' populations have been fully vaccinated. In the meantime, in unvaccinated, partially vaccinated, convalescent and even vaccinated cohorts the virus has an opportunity to explore advantageous point mutations from a perspective of fitness and degrees of immune escape and improved transmission (which would of course nudge the aforementioned target percentage higher).
 
The modelling I'm interested in is quite narrow and specific. It models things like expected cases, hospitalisations and deaths in different scenarios. So modelling Johnson doesnt really come into it, except to say that the modelling I tend to get to see is based on scenarios that are compatible with the governments plans for unlocking steps etc. Which is why SAGE looks at those model runs in particular and then we get to see the papers.
I have to disagree. Modelling Johnson has to come into it if you are to provide meaningful estimates of which scenarios are likely. The most recent example is the perfect case in point, I would have thought. So what would have happened if we hadn't imported a new variant in that way? Would the Kent variant have continued to decline? If the answer is yes, then you have to factor in Johnson to come up with any meaningful idea of when and where the next wave will come as it is conditional on decisions made by Johnson.

In reality, all predictions are necessarily conditional. It's just that some state their conditions while others don't.

Regarding Spector, generally his positions are much closer to those of someone like Anders Tegnell of Sweden than those of the likes of Neal Ferguson. Sweden gets much maligned because it's done worse than its Scandinavian neighbours, but it's had about half the number of excess deaths of the UK. It's not absurd to question the effectiveness of the lockdowns that have been imposed just as infection levels have peaked or even passed their peaks.
 
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It's a very parochial viewpoint. We can stop worrying when >=70-80% of all countries' populations have been fully vaccinated. In the meantime, in unvaccinated, partially vaccinated, convalescent and even vaccinated cohorts the virus has an opportunity to explore advantageous point mutations from a perspective of fitness and degrees of immune escape and improved transmission (which would of course nudge the aforementioned target percentage higher).
It pains me that such attitudes still persist despite how many times such approaches blew up in their face earlier in the pandemic, including at the start when I couldnt quite believe how much scope I had to get a better grip of reality than some of the people who do it for a living.

It pisses me off. Some of his other comments about lockdowns in the past are along the lines of "we shouldnt do national lockdowns, we should go for options that are more 'efficient'". And vague sentiments about how we will be ok if everybody behaves sensibly. I find that stance hard to take, especially when there arent too many signs of these people having a good hard think about how sensible their own attitudes really are.
 
I have to disagree. Modelling Johnson has to come into it if you are to provide meaningful estimates of which scenarios are likely. The most recent example is the perfect case in point, I would have thought. So what would have happened if we hadn't imported a new variant in that way? Would the Kent variant have continued to decline? If the answer is yes, then you have to factor in Johnson to come up with any meaningful idea of when and where the next wave will come as it is conditional on decisions made by Johnson.

In reality, all predictions are necessarily conditional. It's just that some state their conditions while others don't.

Regarding Spector, generally his positions are much closer to those of someone like Anders Tegnell of Sweden than those of the likes of Neal Ferguson. Sweden gets much maligned because it's done worse than its Scandinavian neighbours, but it's had about half the number of excess deaths of the UK. It's not absurd to question the effectiveness of the lockdowns that have been imposed just as infection levels have peaked or even passed their peaks.

Do you actually read the modelling papers that come via SAGE? They model specific scenarios at specific moments in time, to match up with contexts that require SAGE offer the government advice at a particular moment. So the ones a few months ago were looking at the likely unlocking timetable, and what might happen after each step. They have to leave various unknowns out of the picture, or deal with them by creating a range of additional generalised scenarios, such as what a third wave might look like if vaccine effectiveness is only such and such a percentage.

Given how long it takes to find out what impact a particular variant of concern ends up having in practice, I dont see much point in also trying to guess which countries might seed which variants widely around the country in future based on guesses about what travel & border policies Johnson will follow at any given moment with any given country. At most there are a few scenarios that I would model to try to cover some of those bases, but the models are not supposed to be a crystal ball, they arent supposed to give one single answer as to out future plight.

For example none of the modelling made public in recent months allows me to make a confident, assured prediction about what will happen with a third wave. They offer strong clues about the expected impact of the unlocking steps, and some guide as to the magnitude of wave potential that still exists under a nrage of possible scenarios. I can use that to urge caution or to warn people about how much protection we can expect from a wave via vaccination, or to criticise aspects of the unlocking timetable. I wouldnt expect them to be able to enable solid predictions, to enable me to be able to say 'we will have a wave with x hospitalisations per day in the middle of July'. They can help me to avoid ruling such possibilities out, or inappropriately developing a sense that such possibilities are outlandish.
 
Just a few small examples of things one of the Warwick modelling papers came out with that I found useful. Note the fact that they can offer ranges, depending on how various factors actually turn out:


The size of the third wave is most sensitive to the speed of vaccine deployment, vaccine efficacy and the level of transmission (and hence population-level behaviour) in Step 4 (Fig. 17). These three elements could combine to generate highly optimistic scenarios with 6890 (CI 1540-23,800) hospital admissions over the third wave, or highly pessimistic scenarios with 186,000 (CI 88,200- 346,000) hospital admissions (Fig. 18).
England remains extremely vulnerable to novel variants with either higher transmission or that can partially escape existing immunity (Fig. 24). A variant that is 30-40% more transmissible than B.1.1.7 is projected to generate more total hospital admissions than the first wave. Variants that escape immunity (either from infection or vaccination) could generate outbreaks larger than the second wave unless immunity confers a significant degree of protection against severe disease.

And there is heaps of info about what thigns they do and do not include in their considerations, and the areas of greatest uncertainty.

In terms of variants of concern, this is the first part o their explanation as to what assumptions they used for this particular exercise, including the seeding amount, geography and timing:

We consider three different scenarios of a variant successfully invading the UK in early March 2021, but in very low numbers. To understand the role that NPIs play in controlling these novel variants, we consider a situation in which relaxation is halted at Step 2, one in which only Steps 2 and 3 occur (compare to Fig. 1), and one in which relaxation proceeds through Steps 2 to 4 (compare to Fig. 6). In general, the majority of the third wave of infection (from June 2021 onwards) in these scenarios is attributable to the novel variant. We assume that the VoC has been introduced to England at very low levels on 15th March 2021 (at one infection per NHS region), and it grows from this small seeding.

But I always feel like I've done a disservice to the papers as a whole when I try to zoom in on little chunks, there is so much detail in them!
 
Plus there is usually more than one model to choose from. So just to provide a final example, here is the new variant scenario that the London School of Hygiene and Tropical Medicine described in their modelling which was considered by SAGE early in May at the same time as the Warwick modelling I already mentioned:

We also consider scenarios introducing variants of concern. We consider two scenarios related to the characteristics of a VOC: an escape mutant with 80% transmissibility relative to B.1.1.7 and 50% cross protection from prior infection with other SARS-CoV-2 variants, and an increased transmissibility variant with 150% transmissibility relative to B.1.1.7 and 100% cross protection from prior infection with other SARS-CoV-2 variants. Each of these variants is introduced into the model by seeding 5 daily infections with the third virus variant (which is modelled explicitly) from 1st January 2021 onwards. We base our assumptions around vaccine effectiveness for the escape mutant variant of concern scenario on limited evidence available related to vaccine effectiveness against the B.1.351 variant (Table 4). For the increased transmissibility scenario, we assume vaccine effectiveness values shown in Table 1.


Using those parameters and all the other assumptions and details they fed into their models, that particular exercise came up with this, which I have probably posted before:

Screenshot 2021-05-22 at 15.57.49.png

I dont know how close to reality either of those might turn out to be. But when I see that stuff, it certainly informs my opinion about whether it is wise for the likes of Tim Spector to say the things he has been saying recently.
 
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Regarding Spector, generally his positions are much closer to those of someone like Anders Tegnell of Sweden than those of the likes of Neal Ferguson. Sweden gets much maligned because it's done worse than its Scandinavian neighbours, but it's had about half the number of excess deaths of the UK. It's not absurd to question the effectiveness of the lockdowns that have been imposed just as infection levels have peaked or even passed their peaks.
Per million covid deaths reported, UK 1873 -v- Sweden 1415, and you think that's about half?

Their current average covid death rates are running at about 7 times that of the UK, adjusted for population.
 
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I have now seen enough of Spectors track record to conclude that I will not be listening to his opinion on variants of concern.

Not that I have a brilliant record either, since I spent a fair bit of the first pandemic year trying to tell people not to take pandemic mutation cliches in the media (eg 1918 stuff) too seriously, and had no way of initially judging whether the UK government were hyping up the Kent variant risk when they first started going on about it and hiding behind it when having to u-turn over restrictions, Christmas etc.

All the same, I am concluding that Spector is a bit of a pillock.

 
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