Coronavirus in the UK - news, lockdown and discussion

[platinumsage]

I'm sure it's not the concern of "most scientists", which is why I said virologists.

most virologists then

SARS-CoV-2 has so far only explored a fraction of its mutagenic space, and that, in the wild, in a relatively short time. Besides RBD mutations, the spike has an unusually high degree of conformational plasticity and that even contributes to antibody evasion through concealment of key epitopes in the NTD, where the virus has been playing with a lot of deletions. Now we are seeing co-infections, sooner or later we are probably also going to start seeing recombination events as well.

There's plenty about the spike protein that is highly conserved across species, and it's plasticity is as expected given it's mechanism as a fusion protein. The idea that it's going to suddenly start evading the current vaccines such that these vaccines cease to be effective at preventing serious disease and death is a big stretch.

Absolutely, but that unfortunately cuts both ways (eg vaccine sera variant efficacy studies).

Here it still applies, as vaccine sera studies don't tell us about the T-cell response which is likely to be polyclonal to a variety of spike protein epitopes outside the RBD and thus not comprised by the mutations under discussion.

I think the fact that both the media and many virologists unused to the public understanding of science have in their public pronouncements focused on standard vaccine effectiveness as measured in phase III trials using "disease", rather than "severe disease and death" has lead to fear and vaccine hesitancy in some quarters which could prove highly damaging.

There's no indication whatsoever that current vaccines will not have a considerably beneficial affect against the so-called South Africa strain.

Sure we need to update vaccines as time goes on, but the idea we should withhold current vaccines for lack of efficacy against current variants, or that we shouldn't extend the gap between doses due to concern about mutations are mistakes that are 100% likely to result in many deaths.

 

[IC3D]

The UK govt are the covidiots of Europe. Hoarding a vaccine that may very soon be useless.

 

[andysays]

According to the BBC, the Irish government has said anyone crossing the border from NI will be fined.

Garda carrying out random vehicle checks...

 

[elbows]

Interview on Sky's Sophy Ridge on Sunday show.

There is nothing in that interview with Dr David Nabarro that says the WHO have changed their position. Yes he made a lot of positive noises about the bravery of British scientists, and how we are learning as we go along, but he also spoke of how the committee that deals with such things will look into it. And he acknowledged the 'so far' aspect.

He spoke of plenty of other things too, like the subject of sharing vaccines with the world.

His remarks are consistent with someone whose career involved international civil service, being nominated by the UK government to become WHO Director General some years ago (unsuccessfully), etc. His comments early in the pandemic were a mixed bag too, given both the correct emphasis on test & trace but also comments that were easily construed as being against national lockdowns. His stance was actually more complicated than that, but certainly demonstrated the limitations of putting too much faith in the words of one person in the pandemic, no matter their position and knowledge.

 

[elbows]

My advice remains:

Dont listen to anyone who has to resort to appeals to believe in the wisdom of arbitrary authorities.

Dont treat vaccinations as a silver bullet if you want to stay safe from the possibility of crushing disappointment arriving at some point.

Dont make reassuring claims about mutations and strains that may not stand the test of time. Especially do not do this just because you are worried about the negative implications of people losing faith in vaccines, since no matter how valid such concerns about public attitudes may be, such aspects cannot overrule the fundamental scientific truths that will emerge. And if you've destroyed your own credibility by talking shit at this stage, nobody will listen to you later, you end up being part of the problem not the solution, just another peddler of false reassurances that will contribute to the loss of faith if such a stance is found wanting later.

Dont listen to people who try to pretend that science is all about counting how many scientists hold a particular view.

 

[elbows]

And absolutely dont treat phrases like 'there is currently no evidence' as being a guide as to where our understanding of a matter will eventually end up.

 

[elbows]

And by all means pay attention to what sort of detail is involved in the reassurances that authorities are prepared to give. Carefully chosen language, what they are not saying, deflection, reframing etc.

Covid: Scientists developing vaccine boosters to tackle variants

An early study suggests the AstraZeneca vaccine may be less effective against the South African variant.

www.bbc.co.uk

 

[elbows]

If anyone out there is still wondering whether my emphasis on hospital acquired Covid infections has been over the top and excessive throughout this pandemic, this article contains some figures which I believe demonstrate the huge scale of the issue:

Hospitals defy coronavirus rules to protect staff as 35,000 patients infected on wards

Exclusive: Hospital supplying higher grade masks to staff amid concerns about exposure

www.independent.co.uk

An analysis of the latest NHS data by The Independent shows more than 35,000 patients were likely to have been infected with coronavirus while already in hospital between 1 August and 31 January.

NHS England has estimated as many as 20 per cent of infections could be due to spread within hospitals. Outbreaks at some hospitals have seen whole teams of doctors or nurses affected, in some cases leading to wards having to be closed.

The Independent has learnt several hospitals are now supplying higher grade masks to staff working in general wards, despite Public Health England saying only surgical masks are needed. Research this week suggested staff exposed to coughing were at greatest risk of infection from the virus.

Theres quite a bit more detail in the full article, including things certain trusts have done such as give out better masks and using Covid marshals on wards.

The solution to these things is a mix of the correct infection control protocols and staff protection, but also if you want to avoid this stuff you absolutely have to keep the level of infections in the broader community down below a certain level. Because there are tipping points, beyond which hospital outbreaks become rather inevitable.

 

[IC3D]

'there is currently no evidence'

 

[elbows]

Since their figures broadly match my interpretation of that hospital data, here is a graph of those hospital-acquired cases per day since August 1st. This is for England only. Total for this period so far = 36,414.


Comes from interpretation of data from Statistics » COVID-19 Hospital Activity

 

[2hats]

The idea that it's going to suddenly start evading the current vaccines such that these vaccines cease to be effective at preventing serious disease and death is a big stretch.

Hence the repeated mention of degrees of escape from both natural immunity and vaccine efficacy (of some given type).

Here it still applies, as vaccine sera studies don't tell us about the T-cell response which is likely to be polyclonal to a variety of spike protein epitopes outside the RBD and thus not comprised by the mutations under discussion.

T-cell response appears to play a major part in asymptomatic/mild cases, whereas increasing antibody expression appears to be a feature of increasingly severe cases (DOI: 10.1016/j.cell.2021.01.007, DOI: 10.1016/j.cell.2020.08.017, DOI: 10.1016/j.celrep.2021.108728). The escape concern isn't just focussed on the RBD but in deletions in the NTD as well, wherein the plasticity could also potentially hinder epitope recognition.

 

[elbows]

The UK govt are the covidiots of Europe. Hoarding a vaccine that may very soon be useless.

I wouldnt lean too strongly towards it being completely useless at this stage. I try to keep my expectations somewhere in the middle, although even since the earliest trial data that particular vaccine didnt look like it would end up as the very best one, even without pesky new strains. It does have some practical advantages so I shall be sad if its effectiveness is much diminished.

 

[cupid_stunt]

There is nothing in that interview with Dr David Nabarro that says the WHO have changed their position. Yes he made a lot of positive noises about the bravery of British scientists, and how we are learning as we go along, but he also spoke of how the committee that deals with such things will look into it. And he acknowledged the 'so far' aspect.

It wasn't me that posted the WHO have changed their position/advice, that was someone else misquoting what I had posted, which in my haste to respond with a source I didn't correct them on, I had originally posted, 'the WHO [as in their Special Envoy on Covid-19, Dr David Nabarro] has now congratulated the UK scientists on this move [to delay the second dose]'.

Professor Sarah Gilbert, who heads up the Oxford vaccine team, on the Marr show also explained that their research shows it is best to wait 12 weeks between the 2 doses of the Oxford/AZ vaccine, as it'll give better protection than having the second dose after only 4 weeks. She was also asked about the pfizer vaccine, and expressed the view that she didn't see any reason for concern about the 12 week gap between doses, because immunity doesn't suddenly 'drop off a cliff edge'.

Research based on the Israeli roll-out indicates the pfizer vaccine provides up to 90% effectiveness by day 21 after the first dose, and there's no reason to think that would suddenly drop off thereafter.

So, it comes back to if you want to protect say 10 million people to a level of 90% or only 5 million to a level of 95% in the 8 weeks difference between the second dose being given 4 or 12 weeks after the first.

 

[elbows]

I didnt like the 12 weeks decision because it wasnt based on data, wasnt bassed on the way things were done in trials, and also because escape mutants are very much a focus of attention these days. As data comes in that demonstrates effectiveness with longer gaps, I can at least relax more about one side of that picture. The strains and mutations side of things is more complicated and will give me reasons to fret for probably a long time to come.

 

[elbows]

As for this:

It's a bit silly to rightly attack the government for not following advice from SAGE, and then attacking them for actually following the advice on vaccination.

What a load of shit. Dont pick a side and blindly follow them as if they get everything right or can even be said to represent 'a side', look at the detail and all the factors that go into the balance of decisions for crying out loud.

 

[2hats]

It wasn't me that posted the WHO have changed their position/advice, that was someone else misquoting what I had posted, which in my haste to respond with a source I didn't correct them on, I had originally posted, 'the WHO [as in their Special Envoy on Covid-19, Dr David Nabarro] has now congratulated the UK scientists on this move [to delay the second dose]'.

Some people are getting confused.

It is the [US] CDC who are advising that the dosing interval for mRNA vaccines should be no more than 6 weeks (where the manufacturers' dosing intervals can not be met).

 

[cupid_stunt]

I didnt like the 12 weeks decision because it wasnt based on data, wasnt bassed on the way things were done in trials, and also because escape mutants are very much a focus of attention these days. As data comes in that demonstrates effectiveness with longer gaps, I can at least relax more about one side of that picture.

BIB - it is in respect of the Oxford/AZ vaccine, have you not watched the interview with Professor Sarah Gilbert on the Marr show yesterday?

* it's just over 30 minutes in.

Also explained in this good interview with Kate Bingham.

" What the Oxford data has shown is that by extending the time between two doses, they can improve the immunogenicity. And remember, they got data to show for it because they, like J&J, were planning to do a single dose regime, but it was when they have had two doses arm and when they looked at the two doses arm, they then realized that they got much better immunogenicity after the second dose. So they went back to that the trialist and said, "Would they come back please, for a second dose?"”

“Because many of the trials had started in April. By the time they had a second dose, many of them had got to 12 weeks. So the AZ data has a spectrum of data of people who had their second dose after four weeks all the way up to those up to 12 weeks. And what they have been able to show is that the immunogenicity goes up with an extended time between doses. So it is correct that there is data to justify and extended period between doses for the AZ vaccine. I think it's the right public health response, which is to show that you try and vaccinate as many people as possible, as soon as possible. Better to protect everybody a bit rather than to vaccinate fewer people to give them an extra 10 percent protection. I think it is the right public health response. If I was making that decision, I would have made the same decision”.

Kate Bingham: Why UK strategy on Covid vaccines has been a great success

An exclusive interview by "Die Welt" and "La Repubblica" to the former Chair of the UK Government's Vaccine Taskforce: what Boris Johns…

www.repubblica.it

 

[cupid_stunt]

Some people are getting confused.

It is the [US] CDC who are advising that the dosing interval for mRNA vaccines should be no more than 6 weeks (where the manufacturers' dosing intervals can not be met).

The WHO's advice is currently the same too.

 

[elbows]

And I'm sorry if I am going to end up being rude again at the moment. I'm afraid its inevitable if people are intending to mark the anniversaries of various authorities fucking up their initial response to the pandemic by refusing to learn all the lessons about when to place trust in various compartments of the establishment. Or at least the limitations of that approach.

Also my break is cancelled. It turns out it was just a looming migraine that made me feel exhaused, and that migraine came last Friday and now I am filled with energy once more.

 

[cupid_stunt]

What a load of shit. Dont pick a side and blindly follow them as if they get everything right or can even be said to represent 'a side', look at the detail and all the factors that go into the balance of decisions for crying out loud.

I am not blindly following a side, and 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.

 

[elbows]

I am not blindly following a side, and 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.

Then dont tell people its stupid to agree with SAGE about one thing and disagree with them about something else. Because, detail.

Look, I've got a bee in my bonnet today in part because Nabarro used the word bravery in that interview. How it was a brave decision by UK scientists. Bravery is a complex thing that can also mean recklessness, arrogance and unnecessary risk. Which word is the best fit is usually decided with the benefit of hindsight. And the worlds of public health and medicine must often deal with these themes. Its complex and can be ugly since often the person making the decision is risking, or being brave about the possibility of losing, their reputation. Whilst for others the conseqneces are more a matter of life and death.

Its tricky stuff. I moan at Whitty when he goes on about all of medicine being a balance of risk, not because he is wrong about that, but because of which way the balance tends to be tilted in this country, and also because he was usually bringing it up in order to make some excuses for grotesque failures. Beyond that I do have sympathy with the very tricky balancing of decisions. Its not like there are often easy options, eg if I tried to make such decisions in a risk-averse way, this would introcude other risks of its own, the risk is unavoidable.

If I remove my venom then I suppose all I really want is for people to say stuff that is consistent with looking at the detail each time, as you have mentioned, rather than default to trust in the substance based on the authority of the person coming out with it. We know there are slippery aspects to these issues and the way they are discussed, especially by those 'in a position of responsibility', and there are usually more questions than answers, and so much that remains unknown. I look forward to more data over time, as ever.

 

[cupid_stunt]

Another good day -

First dose vaccinations now just over 12m

New cases - 15,845, overall a drop of 24.3% in the last week.

New deaths - 373, which is down 214 on last Sunday's 587, that brings the 7-day average down to 901 a day, a drop of 23.3% in the last week.

Well, the news continues to get better, from a fucking shit situation, we continue to move in the right direction, but still some way to go yet.

First dose vaccinations now just under 12.3m

New cases - 14,401, overall a drop of 25.3% in the last week.

New deaths - 333, which is down 73 on last Monday's 406, that brings the 7-day average down to around 891 a day, a drop of 22.4% in the last week.

 

[cupid_stunt]

Just a reminder, press conference at 5pm today with Hancock joined by Jonathan Van-Tam and Dr Kinni Kanani, the Medical Director of Primary Care for NHS England.

 

[2hats]

The WHO's advice is currently the same too.

Not quite.

The WHO recommendation (8 Jan) for BNT162b2 is 21–28 days between the doses, though the "interval between doses may be extended up to 42 days (6 weeks), on the basis of currently available clinical trial data" in "exceptional epidemiological circumstances".

The WHO recommendation (26 Jan) for mRNA-1273 is 28 days between the doses, though in "exceptional circumstances ... the interval between doses may be extended to 42 days."

The CDC advice (21 Jan) on both (US regulatory approved) mRNA vaccine dose intervals is simply on the basis of "if it is not feasible to adhere to the recommended interval".

 

[Pickman's model]

Well, the news continues to get better, from a fucking shit situation, we continue to move in the right direction, but still some way to go yet.

First dose vaccinations now just under 12.3m

New cases - 14,401, overall a drop of 25.3% in the last week.

New deaths - 333, which is down 73 on last Monday's 406, that brings the 7-day average down to around 891 a day, a drop of 22.4% in the last week.

perhaps 'the situation continues to improve' - the news is still bloody awful.

 

[elbows]

Just a reminder, press conference at 5pm today with Hancock joined by Jonathan Van-Tam and Dr Kinni Kanani, the Medical Director of Primary Care for NHS England.

Judging by the following smirk that briefly crossed his face, it was not lost on Hancock that it being 2 months to the day since the first patient was vaccinated means its 2 months since Hancocks 'crying' performance that actually looked more like an attempt to hide laughter behind a fake cry.

I always watch out for these things since the time he could not surpress a smile when talking about the polices usual, consent-based approach in a pandemic press conference long ago.

 

[agricola]

I didnt like the 12 weeks decision because it wasnt based on data, wasnt bassed on the way things were done in trials, and also because escape mutants are very much a focus of attention these days. As data comes in that demonstrates effectiveness with longer gaps, I can at least relax more about one side of that picture. The strains and mutations side of things is more complicated and will give me reasons to fret for probably a long time to come.

Indeed. The way that was apparently decided - in effect a massive u-turn whilst we were three weeks into the vaccination rollout - was emphatically not how it should be done. As a precedent its appalling.

 

[elbows]

Indeed. The way that was apparently decided - in effect a massive u-turn whilst we were three weeks into the vaccination rollout - was emphatically not how it should be done. As a precedent its appalling.

It resembled a gamble that they only felt the need to take because they failed to keep numbers down enough in the wave and were faced with extreme pressures of all sorts as a result. Under those conditions I do understand the rationale behind the gamble, but it goes without saying that doing the right things in August, September, October, November and December would have been a much better approach with reduced risks of various sorts.

JVT was the right man for the job tonight, in terms of how to frame the vaccine-South Africa variant scary headlines in a way that was somewhat reassuring, didnt lead to people making the wrong choices in the short-term, but that did not completely insult my intelligence when it came to the medium and long term picture.

One of the reasons I find his words easier to tollerate is that he tends to make clear when something is well supported by evidence, and when it is just a hunch of his. Some reading between the lines, joining of dots and filling in the gaps is still required, but the way he does it almost invites that approach rather than being too suspiciously guarded and dismissive of uncomfortable questions.

So for example today he spoke of various things he still expected that vaccine to be good for, and of how he didnt expect the South African strain to become dominant in the UK in the next few months. But rather than get bogged down in too many unknowns or blunder into too many possibly unsustainable positions, he acknowledged the idea of booster vaccines targeting such strains in the autumn. It seemed like a fairly reasonable attempt to get people not to change their approach to getting vaccinated at the moment, without making too many claims about the longer future that may be unsafe or lead to incorrect expectations.

Quite how far to go with filling in the blanks is debatable, since there are many unknowns and I dont claim to have a crystal ball. He said they dont think the South African strain has a transmission advantage over the current dominant UK strain. A full discussion on such themes would then need to involve the topic of vaccine-related selection advantage, eg whether in future when the strains of virus keep bumping into vaccinated people, whether a strain that vaccines works less well against will then have an advantage that will cause it to become the dominant strain.

 

[platinumsage]

More on T-cell responses to the South African strain:

 

[SpookyFrank]

The UK govt are the covidiots of Europe. Hoarding a vaccine that may very soon be useless.

It's very unlikely to be useless. Nor are they hoarding it. Other than that, spot on.