UKH

Friday Night Covid Plotting #38

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 wintertree 07 Aug 2021

Another week, another update.

First, my take on where things are now... 

My best take on the data is that both nations had a big collapse in both cases/day and the exponential growth rates following the end of the football - timed differently due to Scotland’s earlier defeat, and that with the contribution to R from the football removed, we’re about at the turning point where we've run out of enough adults susceptible to symptomatic infection to sustain rapid exponential growth, so case rates are hovering around mild decay, and subject to all the short-term (timescale of ~1 week) variations we see in the historic data currently putting them on the edge of growth.  Weather is the obvious factor for a lot of these variations; in the analysis I've been doing temperature is perhaps ~60% of the variation in the rate constant on the timescale of a week or so.

Some crude estimates I made at the end of the last thread suggest it would be ~50 days at current infection and vaccination rates to bring antibodies to the ~8% of English adults without them; so we’re looking to see a gradual then increasing fall in cases/day over the next 50 days as that susceptible reservoir decreases by vaccine or by infection, but...

  • Super-imposed on that are the weather fluctuations which I think are part of what’s taking us in to mild growth now,  and the downstream consequences of the freedom day unlocking; although these should be already fully embodied in the R number by now.
  • Soon to be super-imposed on this are the effects of increased transmissive links between households when schools return in a few weeks.   That’s in 3 weeks time in my part of England, by which point somewhere perhaps between half a million and a million more unvaccinated people could have been infected.  I think that leaves things close enough to the wire that it’s very hard to say if cases will end up growing or decaying for a while after schools go back.  Hopefully have a better idea by the time it happens; hopefully the powers that be are putting thought in to how to manage the return of schools if cases/day remain high in three weeks time, so as not to risk a big rise in cases.

From UK news reports its clear most people going to hospital are the unvaccinated, and I found an article in the San Diego Union-Tribute with a plot of case rates by vaccine status for San Diego county [1] which is quite clear…

So, in a simple model, we’d be looking for the daily case number to start dropping more and more as the susceptible pool runs out as there is enough immunity to suppress transmission of symptomatic infection.  But… in the real world, we have both gradually fading immunity against symptomatic infection and the wildcard of new variants to look forwards do.

  •  In terms of how fading immunity comes in to this; in a really simple model we end up with a steady state where the number of people loosing immunity against infection per day is matched with the number of people being infected as a feedback loop between fading immunity and re-infection naturally forms.  The lower the rate at which people loose immunity, the lower the steady state cases/day is.
    • In the real world, all sorts of things complicate this, like the possibility of asymptomatic infection refreshing immunity and not triggering criteria to go for PCR testing, seasonality bunching re-infections up in to the winter period, and 101 other things I’ve not even thought about.
    • Hopefully re-infection when it does start occurring in large numbers is less serious in terms of symptoms and hospitalisations... That's the core gamble behind what I presume the policy is.  It seems like a reasonable one, but still we'll only know when if get there.

This is the brave new world of living with the virus, and the public dashboard data as it current is will not be half as useful to understand this future as it has been to date, because it does not categorise any of the measures (cases, hospitalisations, deaths) by either vaccination status or past infection status.  Ideally there would be a release that gives each measure split by each permutation of vaccinated [yes/no] and symptomatic infection detected in the last year [yes/no].  

Link to previous thread: https://www.ukhillwalking.com/forums/off_belay/friday_night_night_covid_plotting+orchid_appreciation_37-737623

The vaccine plot shows the first doses/day continuing to decrease and the notional lag between doses going up slightly. 

[1] https://www.sandiegouniontribune.com/news/health/story/2021-07-25/with-coronavirus-increasing-rapidly-will-it-soon-be-masks-up-in-san-diego


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 wintertree 07 Aug 2021
In reply to wintertree:

The England plots.

I think the growth in cases looks bigger than it really is (e.g. see week-on-week plot above) because of some big weekend effect dips which aren’t fully resolved by my deweekending code when at the leading edge...  This bit of the plot will be clearer by next week.

The levelling off of decay in cases looks to be translating through to hospital admissions; there’s no similar day-of-week effect in tat data here so it’ll probably be a smoother plateau.  This is clear confirmation that the rapid fall in cases was real however; the peak / valley looks like it might not end up so large in admissions as cases but that’s pretty typical as the distribution of times from cases to admissions “blurs out” sharp features like a tall peak from cases into wider, shallower peaks.

Both hospital occupancy and deaths look to be slightly in decay; with another weeks data it may resolve in to a plateau as cases plateau.

The axis crossing times from growth to decay of the various measures on plot 9e look pretty standard and don't suggest anything odd in the data to my eye - said with the various good points people raised about the behaviour of cases data over past weeks in mind.


1
 wintertree 07 Aug 2021
In reply to wintertree:

As with the week-on-week plot, the decay in cases has stalled; the past decay continues to feed through to hospital admissions which are down 3x from their last peak, and occupancy continues to decrease.    Deaths could be falling but is down in the noise.  The rate constants all cross the axis in the expected sort of timing and sequence.  


1
 wintertree 07 Aug 2021
In reply to wintertree:

England, Scotland and NI are all showing a stalling of decay / return to rising in cases and the rate constant is also getting less negative in Wales.

The synchronicity of this - coming it seems too late after July 21st to be directly ascribable to that and extending to the other nations - has very much the feel of the temperature anti-correlation me; it’s the same sort of relative change in rate constant as we’ve seen for much of the year, it’s just unusually taking us over the boundary from decay to growth making the effect much more prominent - normally it only shows up really clearly in the week-on-week rate method constants plots for cases.  As I said of cases last week: They might even pogo around growth and decay for a while as changes in the weather shift the rate constants about

Could always be other factors at work as well or instead off; this is just my take on it as ever.


1
 wintertree 07 Aug 2021
In reply to wintertree:

Plot D1.c makes it clear that "freedom day" has not landed homogeneously across the demographic in England. 

  • Most ages have remained in decay perhaps until the most recent couple of days of data - but that analysis is provisional pending another week of data
  • Growth returned first in the age bands 15-30
    • Unlike the main turn to growth around May where the rate constants shifted in all bands pretty simultaneously, this time there does look to be an outwards flow up the ages, as if cases are spreading out over the demographic-time diagram (at whatever it's equivalent to the speed of light is).
    • This plot doesn't prove it's a causal flow, it just doesn't rule out the possibility with the same clarity it did the last time around
    • Hopefully the announced vaccine requirement for night clubs is going to start to limit this in a couple of ways...?
  • The age band 90+ has mostly remained in growth, and the previous turn to decay in the oldest ages is a diagonal line on the rate constants plot; it suggests to me that it's still proving difficult to fully shield the most vulnerable.

Plot P1.e shows the probability distribution of cases, and you can see a demographic shift towards younger adults returning; this means that even if cases/day are levelling off, the hospitalisations/day locked in should be decreasing a bit - perhaps not enough to see clearly in the data we get from the dashboard given the lack of corresponding demographic bins there... 

Two plots looking at the gender imbalance in cases; one is the absolute imbalance and the other is the ratio of the imbalance to total cases.  Red means more male, blue means more female.  Historically the imbalance has always been towards females (contrary to the worse health outcomes for males, impossible to say from the data if this imbalance is reflective of infections, symptomatic infections or engagement with testing).  The normalised plot is really interesting although dominated by noise when absolute cases are low.  Lots going on in there...  It's clear that the current rising cases in young adults are nothing like as imbalanced as those from the football period.

Post edited at 20:44

1
 minimike 07 Aug 2021
In reply to wintertree:

Um.. very nice, but.. where’s the waterfall?

 wintertree 07 Aug 2021
In reply to wintertree:

The regional plots show similar trends in all regions although absolute differences in the rate constants meaning some have gone in to growth a bit this last week (provisionally) and others haven't.  Almost enough data to measure rate constants for deaths in most regions this last week, the signal looks to be generally decaying.

The UTLA plot is back with the highest peaking English UTLAs; this is cases/100k (currently still using the 2019 MYE population estimate despite the update being out), a couple of the early rising regions are shown in black for comparison.  The early starter "B" regions had a lot more targeted boots-on-the-ground local health intervention early on which helped stop them from peaking so high.  From looking at the curves it sure seems like they want to have the same area under them even if they were prevented from peaking hard early on.


1
 wintertree 07 Aug 2021
In reply to wintertree:

Pretty brief set of plots and interpretations this week as the situation isn't materially changed from last week.  An obvious question is "Why Britain" when it comes to apparently starting to hit herd immunity thresholds for life with minimal restrictions.  I ran some very rough and ready numbers on this towards the end of the last thread; without good comparable antibody surveys across other nations it's all I've got.   It suggests some comparator nations will hit this point soon, first Spain, then Italy, then France and then Germany.  Germany has quite a long way to go compared to the others.  Take it with a pinch of salt.  

Still no more orchids, and after minimike rather shocked me with his beach ID skills, this week it's "Where's that waterfall".  I think this will prove altogether more challenging.  It's in the North East of England, and as you can tell from the quantity of peat being washed away in the water, it's in grouse moor.

In reply to minimike:

> Um.. very nice, but.. where’s the waterfall?

For a minute I thought you meant the waterfall plot I've done to look at the Fourier spectrum of the data.  Not a useful plot - unsurprisingly.  Anyhow, it's your job to tell me where the waterfall is...


1
In reply to wintertree:

Thank you again. I think we have to hope for a really lovely warm sunny September don't we.

In reply to BusyLizzie:

Tricky one, that. It's really hard to say where we are. Could well be fair to say that the better September is, the worse December will be. 

 minimike 07 Aug 2021
In reply to wintertree:

> Still no more orchids, and after minimike rather shocked me with his beach ID skills, this week it's "Where's that waterfall".  I think this will prove altogether more challenging.  

you may be right..

> It's in the North East of England, and as you can tell from the quantity of peat being washed away in the water, it's in grouse moor.

well, that helps I guess!

> In reply to minimike:

> > Um.. very nice, but.. where’s the waterfall?

> For a minute I thought you meant the waterfall plot I've done to look at the Fourier spectrum of the data.  Not a useful plot - unsurprisingly.  Anyhow, it's your job to tell me where the waterfall is...

Davidson’s Linn? I don’t think so, but it’s superficially similar at least

Edit: linhope spout it ain’t. 

Post edited at 22:07
 wintertree 07 Aug 2021
In reply to BusyLizzie:

I’ve been really savouring the return of dark nights and the hints of autumn in the air, I think the coming of autumn is my favourite part of the cycle.

The weather is full of cycles, perhaps a loss now is a gain later or vice versa. My field maples and my cherries have really come of age this year, so I’m hoping for a long dry spell in autumn to really set the foliage on fire.  

In reply to Longsufferingropeholder:

Que sera, sera, and we know what to do if things take a turn for the worst in mid-winter.  But given how high R0 is estimated to be for the new variant (very high), what this means for herd immunity thresholds now (very high) and what the latest and already out-of-date antibody survey says (very high), perhaps counter intuitively the scope for winter changes to R is decreasing - because it’s got almost nowhere left to go with the susceptible pool having been squeezed - and about to be squeezed a lot more “thanks” to delta.  The only real bad news scenario I can think of is if immunity from an early historical wave is about to fall off a cliff but people aren’t they synchronous…

We’ve known for a long time what to do - I’ll re post Si dH’s link to the RAEng report from the end of the last thread.

https://www.raeng.org.uk/news/news-releases/2021/july/improved-ventilation-essential-to-safe-use-of-buil

It’s notable that when chest freezers sold out everywhere in early 2020, portable HEPA units didn’t…

Post edited at 22:11
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 wintertree 07 Aug 2021
In reply to minimike:

Bit harder now I’ve taken the tracking device of the car, ey?

> Davidson’s Linn? I don’t think so, but it’s superficially similar at least

The water fragments into falling droplets in a very similar way.

Your answer is both closer and further than I’d expected.  

One hint - I think my post doubled the number of photographs of the fall on the internet (vs that indexed by google images), as hard as that is to imagine.

In reply to wintertree:

I'm hopeful that we will get there definitively by winter, but we'll need immunisation by the two mechanisms combined to keep up some pace in order to do so. If the sum drops off, I'll be looking for that brown bulb again.

Post edited at 22:13
 mondite 07 Aug 2021
In reply to minimike:

> Um.. very nice, but.. where’s the waterfall?

This thread is now agile.

Sad programmers "joke".

1
 minimike 07 Aug 2021
In reply to wintertree:

You didn’t get there by car.. you used your time machine! It IS linhope spout isn’t it? In the early Triassic..

 minimike 07 Aug 2021
In reply to mondite:

I crown you the PRINCE of UKC

edit: I’m a PRINCE2

Post edited at 22:21
In reply to wintertree:

”Name the waterfall”

OK I will.  I name that waterfall: “Wintertree Force.”  There you go. 

In reply to wintertree:

Thanks as ever WT.  I almost had a moment last night when I locked myself out of UKC and couldn't search for your update, shows how much of a routine it has become for me to try and use your tea leaves to predict our COVID-future.

I'm utterly delighted that the flash-point of this post is not what is going on in some obscure ULTA of whether the fuzzy leading edge indicates a turn to decay but where that beautiful waterfall is.

Like you too I am relishing the prospect of the change of seasons, always one of my favourite ones too.  It does mean I'm going to be back at university, very possibly in person with hundreds of those 15-30...uh-oh...post back on topic...

 wintertree 08 Aug 2021
In reply to mondite:

> This thread is now agile.

I’m afraid referring to my crack US Department of Defence training, we are not agile.

https://media.defense.gov/2018/Oct/09/2002049591/-1/-1/0/DIB_DETECTING_AGILE_BS_2018.10.05.PDF

1
 Misha 08 Aug 2021
In reply to wintertree:

In summary, it’s Paugust. 

In reply to wintertree:

The usual thanks for the plots and thoughts, etc.

You mention return to school as one of the future factors to keep an eye on. Noting the significant effects of the Euros (presumably stadium crowds + pub watching) what about the return of the English football leagues from yesterday (and probably to a lesser extent the other home nations)?

Post edited at 13:46
 RobAJones 08 Aug 2021
In reply to Michael Hood:

>Noting the significant effects of the Euros (presumably stadium crowds + pub watching) what about the return of the English football leagues from yesterday (and probably to a lesser extent the other home nations)?

Not sure, but nearly 30m watched the England games. The aggregate attendence for an entire season (top 4 leagues in England) is about that. About 2m watch a live game on sky? Not sure of the pub/home ratio. Seems significant, but small compared to schools going back. 

 Lankyman 08 Aug 2021
In reply to wintertree:

Black Force, Great Eggleshope Beck

 wintertree 08 Aug 2021
In reply to Bobling:

> Like you too I am relishing the prospect of the change of seasons, always one of my favourite ones too.  It does mean I'm going to be back at university, very possibly in person with hundreds of those 15-30...uh-oh...post back on topic...

The turn to autumn always reminds me of my first days as a fresher back in the last millennium.  It turns out there is life beyond the university system however, took me quarter of a century to make the jump and I'm not looking back. To continue a recent trend of musical illustration of the posts... [1].  I hope that the return of your term goes well and with good institutional support for ventilation.  

In reply to Lankyman:

> Black Force, Great Eggleshope Beck

Not a bad guess, but the wrong river system.  

[1]  youtube.com/watch?v=1sCo5GaDq7k&

1
In reply to wintertree:

> The turn to autumn always reminds me of my first days as a fresher back in the last millennium.  It turns out there is life beyond the university system however, took me quarter of a century to make the jump and I'm not looking back.

Me too - having a great time.  Enjoyed academia but 25 years is enough.  Other things to do too!

1
 wintertree 10 Aug 2021
In reply to thread:

Midweek update on the 7-day method rate constant plots.

Very slow growth (exponentially) speaking in both nations, no sign of the exponential growth rate increases; continues to look to my eye like the typical bobbing about with 7-14 day periodicity that's at least part weather related.

A shame they didn't go in to more solid decay to reset absolute numbers before schools turn on, would have been nice to have a few more headroom for a couple more "worst case" doubling times, but there we are.


 wintertree 10 Aug 2021
In reply to thread:

I see someone has carefully disliked every single post from me.  Is that you, Rom?  Remember not to get your two accounts in a muddle if you decide to start posting.

 elsewhere 10 Aug 2021
In reply to wintertree:

https://www.theguardian.com/world/2021/aug/10/delta-variant-renders-herd-immunity-from-covid-mythical

Delta variant renders herd immunity from Covid ‘mythical’

Head of Oxford Vaccine group rules out overall immunity, but also questions need for booster jabs

 wintertree 10 Aug 2021
In reply to elsewhere:

> Delta variant renders herd immunity from Covid ‘mythical’

Yup; those recent R0 estimates have spoken volumes.

> Head of Oxford Vaccine group rules out overall immunity, but also questions need for booster jabs

I'm waiting to see a good demographic analysis of "double vaccinated then caught Delta"; I'm also interested in the Valneva vaccine not so much as a "booster" but because it provides T-cell response against multiple different viral proteins which sets it strongly apart from the other vaccines, and because the other proteins have not - as I understand it - undergone as much variation as the spike protein.  Whilst it may come to be presented as a "Booster", perhaps part of it is "boosting" the AZ and Pfizer responses, but other parts of it are generating entirely new, broad spectrum immunity which more closely resembles that following a life infection, and which has less genetic distance between it and the new variants than the spike component.  

 oureed 10 Aug 2021
In reply to elsewhere:

> Delta variant renders herd immunity from Covid ‘mythical’

No mention in the article of whether naturally-acquired immunity is more effective against variants than vaccination. Anyone got any data on this? Wintertree surely?!

5
 HardenClimber 10 Aug 2021
In reply to wintertree:

Perhaps this is all good news.... If  transmission occurs despite vaccination (but with less disease) then this would reduce the selective pressure for emergence of mutants resistant to the vaccine....  (back to the basics... virulence - as opposed to infectivity - isn't usually a useful characteristic for most pathogens unless it enhances transmission).

Perhaps that is why we seem to have had a slow down in emergence of mutants, rather than ideas about virus having reached it optimal state.... finally something might be sustainably going right.

 elsewhere 10 Aug 2021
 wintertree 10 Aug 2021
In reply to HardenClimber:

Really good to get your view on this in particular; I've been seeking a few opinions out from offline associates, yours is up there with theirs.

> Perhaps this is all good news.... 

Indeed; if Delta had landed 9 months before it would have been an unmitigated disaster, now it's looking it might be part of the solution - escape from vaccine induced neutralising immunity but not escape from vaccine induced immunity from serious harm.  Valneva in particular could bridge the different sides of this equation for the more vulnerable?

>  transmission occurs despite vaccination (but with less disease) then this would reduce the selective pressure for emergence of mutants resistant to the vaccine....  (back to the basics... virulence - as opposed to infectivity - isn't usually a useful characteristic for most pathogens unless it enhances transmission).

Agreed.

As well as that, infection by Delta for some with vaccine induced protection from serious disease should also invoke immune responses against other viral proteins than the spike (the only part used by currently authorised vaccines).  Most of these responses will not be neutralising in the way the vaccines were against spikes with the early RBD motifs, but they should moderate the level of future infections by firing responses up before the dysregulation stage...?  Further, these other proteins don't seem to be subject to the same rapid host adaption process as the RBD so the immune response to them will be less variant sensitive.

To me, this all feels like part of normalising the virus in to the naturally circulating, nuisance level human virome.

But if I've learnt anything about immunology in the last year, it's that it's complicated, non-linear and to be taken cautiously.

What I said to a pop-up poster advocating against any dropping of restrictions back in June:

For sure, the data in the UK is as complex confusing as ever, but there is change in the air and perhaps we are threading a needle towards the way out.  A time for caution, but not necessarily for keeping R<1 - that can always change with the data.

So far, I'm keeping the faith...

 oureed 10 Aug 2021
In reply to elsewhere:

Yes I've read this and other articles suggesting that naturally-acquired immunity will be broader because the body's immune system will be able to recognise a greater range of viral proteins. There must be some data by now on which of these theories is correct. 

5
 elsewhere 10 Aug 2021
In reply to oureed:

> Yes I've read this and other articles suggesting that naturally-acquired immunity will be broader because the body's immune system will be able to recognise a greater range of viral proteins. There must be some data by now on which of these theories is correct. 

The link suggests the opposite to what you say it suggests. The link suggests vaccines produce broader immune response.

"The new evidence shows that protective antibodies generated in response to an mRNA vaccine will target a broader range of SARS-CoV-2 variants"

In reply to oureed:

On the other hand, naturally-acquired immunity has a risk of death of about 1 in 100. And a risk of long covid of about 1 in 10.

Whereas the fatality rate of the vaccines is, well, what, 1 in 1000000?

 girlymonkey 11 Aug 2021
In reply to oureed:

There's also the issue of the longevity of any protection. Naturally acquired antibodies don't last very long (5 months for my friend who is on a study). I believe the vaccine acquired ones are looking better.

 Si dH 11 Aug 2021
In reply to wintertree:

>  Valneva in particular....

Has anyone seen any published info recently on progress towards approval for, or plans for, any vaccines apart from Moderna, Pfizer and AZ? There was great hoohaa made about every option last year but more recently it's gone completely quiet and the only stuff I see is about either booster programmes or vaccinating teenagers, in either case on the assumption that it's primarily using the 60m extra Pfizer doses we have ordered.

To thread on vaccine Vs natural infection induced immunity: I have no technical expertise to add on this but thought it worth pointing out the conclusion that can easily be drawn from one of the studies reported in the last PHE variant report (see my post at the end of last week's thread): you get much better protection from infection with some new variants if you have both been vaccinated *and* been infected with Delta than if you have only had one or the other. So in terms of building up a strong immune response they must be complementary to some degree. As to which is better on their own, there was a guy on Indie Sage recently saying that the vaccine caused a stronger immune response because the live virus does some things that confuse and weaken our T-cell response (beyond my understanding after that.) Plus, the points others have made above.

Post edited at 07:46
In reply to Si dH:

> >  Valneva in particular....

> Has anyone seen any published info recently on progress towards approval for, or plans for, any vaccines apart from Moderna, Pfizer and AZ? 

I've been searching every few days. Tumbleweed. Same goes for all the promising therapeutics. Would be reassuring to know there were a few more horses still in the race.

 wintertree 11 Aug 2021
In reply to Si dH:

Janssen was approved at the end of May; single dose and so seemingly a good way of speeding up vaccination, and a way of getting young people not yet engaged with vaccination back in to nightclubs in time for the September vaccination/club deadline.  Nothing in the media since about it.  Most bizarre.  https://www.ft.com/content/c86af449-9ed7-4358-a17e-04aeb13e1859

Valneva are in to phase 3.  Build out of the manufacturing plant is Scotland continues at pace.

Novovax are the odd one - phase 3 results long ago, apparently they’re having problems around the QC documentation trail which is delaying their seeking of approval in the US; no idea if this affects the UK or not as we have a plant here in the UK - https://www.ft.com/content/c86af449-9ed7-4358-a17e-04aeb13e1859

Re: full vaccination then delta infection - you’re not the only person to have drawn that sort of tentative conclusion.  With all this I think it’s always rather speculative until there’s data, and with the way the UK there’s a lot of data to be collected…

 oureed 11 Aug 2021
In reply to elsewhere:

> The link suggests the opposite to what you say it suggests. The link suggests vaccines produce broader immune response.

Indeed, and I went on to say I'd read "other articles" that suggest the opposite. I have no idea which one is true and it seems that noone has any data to help me out. 

6
 oureed 11 Aug 2021
In reply to girlymonkey:

> There's also the issue of the longevity of any protection. Naturally acquired antibodies don't last very long (5 months for my friend who is on a study). I believe the vaccine acquired ones are looking better.

Let's hope so but research shows a rapid decline in vaccine-induced antibodies too. 

6
In reply to oureed:

> Let's hope so but research shows a rapid decline in vaccine-induced antibodies too. 

No it doesn't.

 oureed 11 Aug 2021
In reply to HardenClimber:

> If  transmission occurs despite vaccination (but with less disease) then this would reduce the selective pressure for emergence of mutants resistant to the vaccine.... 

I've been pondering this too. Thing is current vaccines do seem to lower transmissibility in the dominant Delta strain by anything between 60 and 78%. This would still provide potential for vaccine-resistant variants to do considerably better and become dominant themselves. Delta was successful because its transmission rate was greater than other strains but we've now made it considerably less competitive. Who knows, we may even have created the worst of both worlds by allowing the variant to circulate widely but rendering it potentially less competitive than emerging strains which may also prove more virulent. It seems that viral population dynamics are very difficult to model accurately. Nobody seems to know what will happen in the coming months.

4
 wintertree 11 Aug 2021
In reply to Longsufferingropeholder:

I feel like we’ve been here before.

Information theory is the lens I like to look at it with here with the immune stuff being very computational, and the *information* on fighting the virus persists, but it gets shunted (on the B-cell side of responses) from antibodies to memory B cells after some time.  These can’t confer the same neutralising immunity that high antibody prevalence matched to the RBD can, but there is far more to the response than just that.

https://en.m.wikipedia.org/wiki/Memory_B_cell

Now, if antibody levels didn’t start fading some time after infection, that would be weird and concerning.  Likewise if memory B cell formation wasn’t happening, that would be concerning.

The papers coming out help out those concerns to one side, eg:

https://www.nature.com/articles/s41586-021-03647-4

In reply to wintertree:

yep. Antibodies don't hang around forever. The recipe for them kinda does.
It was the "rapid" that I'm calling bollocks though. It's not rapid on the timescales of the pandemic phase.

 oureed 11 Aug 2021
In reply to Longsufferingropeholder:

> No it doesn't.

India Today:

"A study published in The Lancet journal has found that the total antibody levels start to become weaker six weeks after completing immunisation with Pfizer and AstraZeneca vaccines. The antibody levels may also be reduced by more than 50 per cent over 10 weeks or 2-3 months."

The Guardian:

"...blood tests on hundreds of people revealed that protective antibodies can wane substantially within weeks of second vaccine shots being given.

The UCL Virus Watch study found that antibodies generated by two doses of the Oxford/AstraZeneca and Pfizer/BioNTech vaccines started to wane as early as six weeks after the second shot, in some cases falling more than 50% over 10 weeks."

4
 wintertree 11 Aug 2021
In reply to Longsufferingropeholder:

> It was the "rapid" that I'm calling bollocks though. It's not rapid on the timescales of the pandemic phase.

At least they’ve stopped calling it a “rapid decrease in immunity” so perhaps they’re listening to you.

Next, you could move on to helping them understand that the concentration of antibodies is a poor measure, and that what matters is the fall in their efficacy not their concentration, rumour has it these aren’t linearly related, and it’s just possible the levels close to an active infection or jab are much higher than those that remain going forwards in anticipation of future re infection…. 

Post edited at 09:37
 oureed 11 Aug 2021
In reply to wintertree:

> rumour has it these aren’t linearly related, and it’s just possible the levels close to an active infection or jab are much higher than those that remain going forwards in anticipation of future re infection…. 

So you have no idea either then!

5
 oureed 11 Aug 2021
In reply to captain paranoia:

> On the other hand, naturally-acquired immunity has a risk of death of about 1 in 100.

Perhaps over the entire population, but this is very heavily skewed towards old and/or vulnerable people as I'm sure you know. A young, healthy individual has a much better chance of surviving Covid than 1/100, which is why we're not injecting them with AZ.

4
 wintertree 11 Aug 2021
In reply to oureed:

> So you have no idea either then!

I just had the idea that you've rather misread the tone of my post...

 wintertree 11 Aug 2021
In reply to Si dH:

Having a slow day, posted the wrong link for Janssen approval…

https://www.gov.uk/government/publications/regulatory-approval-of-covid-19-vaccine-janssen

 elsewhere 11 Aug 2021
In reply to oureed:

> Indeed, and I went on to say I'd read "other articles" that suggest the opposite. I have no idea which one is true and it seems that noone has any data to help me out. 

The above is inaccurate or dishonest. 

When you wrote "this and other articles suggesting that naturally-acquired immunity will be broader" you inaccurately or dishonestly said the this link https://directorsblog.nih.gov/2021/06/22/how-immunity-generated-from-covid-19-vaccines-differs-from-an-infection/ suggested that naturally-acquired immunity will be broader.

The link suggested mRNA vaccination immunity will be broader.

Data - see reference at end of https://directorsblog.nih.gov/2021/06/22/how-immunity-generated-from-covid-19-vaccines-differs-from-an-infection/

Post edited at 10:12
 oureed 11 Aug 2021
In reply to elsewhere:

> The above is inaccurate or dishonest. 

Neither actually, but my sentence might have been clearer with a comma.

"Yes I've read this[,] and other articles suggesting that naturally-acquired immunity will be broader because the body's immune system will be able to recognise a greater range of viral proteins."

However my next sentence made it clear I was talking about 2 competing theories.

"There must be some data by now on which of these theories is correct."

6
 elsewhere 11 Aug 2021
In reply to wintertree:

Janssen availability - it's very vague and from a while back (25/6/21).

"The Johnson and Johnson (Janssen) single-shot vaccine has now been authorised in the UK but supplies won’t be available for several more months." 

https://healthmedia.blog.gov.uk/2021/06/25/covid-19-vaccines-frequently-asked-questions/#:~:text=The%20Johnson%20and%20Johnson%20(Janssen)%20single-shot%20vaccine%20has%20now%20been%20authorised%20in%20the%20UK%20but%20supplies%20won%E2%80%99t%20be%20available%20for%20several%20more%20months.

 Misha 11 Aug 2021
In reply to oureed:

It’s a good question but it’s impossible to answer. You’d have to look at people getting Covid and ask (1) have they been vaccinated and (2) have they previously had Covid. (1) is known. (2) is known for those who’ve have a positive test but that misses out almost everyone from the first wave, almost everyone who was asympotomatic and those who had symptoms but didn’t get a test. So you’d be comparing apples and oranges. 

 oureed 12 Aug 2021
In reply to Misha:

> You’d have to look at people getting Covid [...]

Or you could start by looking at people who have (1) been vaccinated, (2) tested positive and (3) been vaccinated and tested positive, and then investigate which ones subsequently catch Covid.  I've seen data showing that (3) is better than (2), but nothing telling me how (1) and (2) compare...

The data must exist though, it's so obviously critical for determining future strategy.

1
 wintertree 12 Aug 2021
In reply to oureed:

You have seen the critical data.

You have seen data on how much more likely someone is to die or to suffer long term health consequences from (2) than from (1).

That rather pre-empts where your train of thought appears to be going.

Regardless of how many times one is going to catch this virus as it hopefully moves in to the background of nuisance level viruses plaguing us, it's better to receive a vaccine before catching it for the first time.  

You're talking about differences in the probability that someone will be (re-)infected after different permutations of getting their first compliment of immune responses, with the implication that said probability of (re)infection depends on the route.  

  • With the latest R value it seems likely that the probability by all routes is going to be 1 for most people.  
  • So, I wouldn't expect to find a difference in the saturated probability....  
  • This leaves the key question being about which route to (re)infection mitigates the health damage as much as possible.  The evidence on that is astoundingly clear.
 oureed 12 Aug 2021
In reply to wintertree:

> That rather pre-empts where your train of thought appears to be going.

I wouldn't have mentioned it if I thought it might 'pre-empt where my train of thought appears to be going.' Some of us prefer to look at data and draw conclusions rather than find data to defend our train of thought.

It may be that becoming infected after vaccination provides better protection than vaccination alone. This certainly seems to be the strategy pursued at the moment by the government, resulting no doubt from the surprise discovery that vaccines prevent serious disease much better than transmission.

Establishing the level of immunity that can be expected from vaccination vs purely natural infection is also critical in developing future strategy. Rich countries are buying up available vaccine stocks for booster doses and vaccination is simply not an option for everyone.

We have secured access to over half a billion doses since they have been made available. Some of these are apparently for booster shots in autumn 2022! But if we don't know the level of immunity in different sectors of the population within and outside the UK, it's impossible to have a coherent strategy with regards to what we should do with all this vaccine, even on a purely selfish national level.

5
In reply to oureed:

> I've been pondering this too. Thing is current vaccines do seem to lower transmissibility in the dominant Delta strain by anything between 60 and 78%. This would still provide potential for vaccine-resistant variants to do considerably better and become dominant themselves.

Yes, which was why France was on the red list - they didn't want the Beta variant (known to be vaccine resistant) coming in.

> Delta was successful because its transmission rate was greater than other strains but we've now made it considerably less competitive. Who knows, we may even have created the worst of both worlds by allowing the variant to circulate widely but rendering it potentially less competitive than emerging strains which may also prove more virulent. It seems that viral population dynamics are very difficult to model accurately.

It's highly likely that the vaccines will also reduce the effect of other variants in a similar way, thus preserving Delta's competitiveness. It's in everyone's interests to reduce the prevalence of any variant as it makes everything easier to deal with.

> Nobody seems to know what will happen in the coming months.

This we can be sure of!

If you've not seen it, have a look at https://covariants.org/per-country

 wintertree 12 Aug 2021
In reply to oureed:

I'm sorry, your point remains as utterly opaque to me as ever.

> It may be that becoming infected after vaccination provides better protection than vaccination alone.

Well, that isn't exactly going to send shockwaves through the immunological world.  I expect Valneva will perhaps have a different infection risk profile going forwards than the others vaccines in the short to medium term.

> resulting no doubt from the surprise discovery that vaccines prevent serious disease much better than transmission.

I'm sorry, are you being serious or ironic?  Either way....

> Establishing the level of immunity that can be expected from vaccination vs purely natural infection is also critical in developing future strategy.

Well, not really for us, because most people have been vaccinated, and many of those that aren't are going to get antibodies the natural way very soon, if they haven't already.  There's no "strategy" to be decided there, things are set in motion with a lot of momentum.

What's critical is establishing that vaccination moderates severe health damage; everything else flows from that.

The first main question IMO - as I've said before - for us is going to be about the differences in the rates at which different types of immunity fade, along the "protection from catching it" vs "protection from getting ill after catching it" lines.  This is going to be different for different vaccines and for different permutations of vaccines before even throwing different permutations of those and live infection in to the mix.

The second main question is about how best to prepare for the inevitability of a vaccine escape variant.  Both Valneva-style vaccines and infection post vaccination seem like parts of that picture.  Delta is close enough to being an escape variant that things seem to be already set in motion.

>  it's impossible to have a coherent strategy with regards to what we should do with all this vaccine

My understanding is that having placed the contracts to enable various manufacturing plants to be built before we knew which would succeed through trials, licensing and mass manufacture, we're likely to give a lot of it away as we've ended up backing (creating) a lot of winners. 

Post edited at 11:41
 oureed 12 Aug 2021
In reply to wintertree:

> Well, that isn't exactly going to send shockwaves through the immunological world.  

Of course not, but it would still be nice to see some data rather than just make assumptions. Bizarely, nobody seems to know of any.

> are you being serious or ironic?  

Sorry, I must have missed all the articles from last year predicting that vaccines would be excellent at preventing serious illness but fairly crap at preventing spread. Maybe you mentioned it in a post.

> What's critical is establishing that vaccination moderates severe health damage; everything else flows from that.

I really do remember everyone banging on about how it would prevent spread!

> The first main question IMO  is going to be about the differences in the rates at which different types of immunity fade

Indeed, one of my persistent concerns. 

> The second main question is about how best to prepare for the inevitability of a vaccine escape variant.  

Another of my persistent concerns. We may be starting to fuse!

> we're likely to give a lot of [the vaccine] away 

Well I certainly hope so, but that is just a tiny part of the equation. How much do we keep/give away? Who to? In what proportions? Selfishly or with an ethical bent? I do hope young, healthy UKCers will be willing to forgo theirs for someone more vulnerable. 

7
 wintertree 12 Aug 2021
In reply to oureed:

> I really do remember everyone banging on about how it would prevent spread!

It did.  That wasn't unexpected.  That contribution is fading with variants, that's not unexpected.  The importance of preventing spread is now much less than it was when we were on the verge of healthcare collapse in January due to both very high prevalence of the virus and very low prevalence of antibodies.  

> Sorry, I must have missed all the articles from last year predicting that vaccines would be excellent at preventing serious illness but fairly crap at preventing spread. Maybe you mentioned it in a post.

The concept that vaccines are more effective against serious illness than infection - especially as the vaccine remains genetically fixed against the drifting virus - sort of falls in to the box labelled "really obvious" for a lot of life scientists I think.  You seem to think the vaccines were presented as a miraculous elimination tool?  My read of pretty much everything has been that they were presented as a tool to massively blunt the healthcare consequences of the virus.  The media haven't given so much focus to what comes next, but nor I have seen that misrepresented as using the vaccines to eliminate the virus.

It's certainly come up on here many times, e.g.

Dec 31st, December 2021 -https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_5-729286?v=1#x9365988

Mutations tend to gradually accumulate, and each one at worst usually just weakens immunity but doesn’t break it. It seems likely this new variant broke one particular epitope or “attack location” for neutralising antibodies but leaves many more intact.  So I hope we have - worst case - a gradual failure of immunity.  This means people gradually get re-infected and there isn’t a repeat of the problem where everyone is susceptible and so it spreads like wildefire.  I’m more worried about mutations that make it more transmissible or more lethal.

The "neutralising antibodies" I referred to were the ones binding to the spike protein's "RBD".  The "RBD" is the part of the spike that tangles with a human cell and initiates the infection process.  Some of the antibodies from the vaccines bound with a high affinity to pre-Kent RBDs, which would precent them from being able to start the infection process - therefore giving high efficacy against infection and transmission following vaccination.  But neutralising or sterilising immunity is just the first line of defence, other B-cell and T-cell responses still work to provide protection against the virus after it breaches the neutralising immunity, moderating the severity of illness.  So, as the neutralising immunity is lost due to either genetic change between the vaccine and the circulating virus, or to antibodies being removed and their memory living on for future use, the defence against transmission falters but the defence against severe illness does not. 

The concept has come up on here many times - not just on the "plotting" threads and I think pre-dating that easy to find example by many months.  

I think it's falling in the box labeled "obvious" for quite a few people following as much as they can. 

Ever since the Kent variant it's seemed to me that any residual hope of elimination is gone, even with the help of the vaccines.  This was what I said back in December:

  • I doubt it can be eliminated globally now so we’ll just have to learn to live with it.

Learning to live with it is about reducing the health impact of infection and subsequent reinfection, and it's clear that the vaccines are an astoundingly powerful tool for doing that for people previously lacking in any antibodies against any component of the virus.  

Post edited at 13:01
 oureed 12 Aug 2021
In reply to wintertree:

> Mutations tend to gradually accumulate, and each one at worst usually just weakens immunity

This is the misconception that almost everyone has about evolution; that it is a slow, gradual process. Now if the environment changes slowly, then we can imagine a slow evolutionary process, however, from the virus's point of view, vaccination is pretty much like a major meteoroid strike. When a meteoroid strikes, those individuals which are susceptible to the cold will die off and those that are resistant will thrive in the absence of competition. Muscle-bound surfing dudes will suddenly be out-competed in the reproductive arena by chubby mountaineers, and subsequent generations will have a tendency to pack a bit of lard. Note that surfers didn't evolve to become more like mountaineers; the mountaineers were already there just not getting much of the reproductive action. But throw in a never-ending winter and boy will they have a good time!

After a mass vaccination campaign, those existing strains of chubby, resistant virus will likewise thrive due to the lack of competition. Their offspring will also be chubbier and more resistant and very soon the chubby virus strain will become the dominant one. As viruses replicate at time-warp speed, the selective process happens super fast.

Hope that helps!

NB: as it happens the mass vaccination program hasn't proved as much a catastrophic event for the Delta virus as everyone hoped and its capacity to spread has only been severely dented. To what extent this will affect the evolutionary process is anyone's guess. Selective pressure won't be as great as for a more effective vaccine, but as the virus continues to circulate, it also has more opportunity to mutate/recombine. So actually your example might be closer to what is happening at the moment than mine, but I'm still gonna post coz I've spent some time writing this and I quite like my chubby virus story!

2
 wintertree 12 Aug 2021
In reply to oureed:

> This is the misconception that almost everyone has about evolution; that it is a slow, gradual process. 

I wasn't talking about evolution, I was talking about the process by which the virus drifts genetically away from the template used for the vaccine.  They're related but not equivalent topics.  Evolution is a filter that can reject or amplify the genetic drift.  We've had other amplifying processes as well; hammering cases down then having large growth puts a bit of a lottery on what survives.

I don't think there's a widespread misconception about evolution either; it's clear that it's both an ongoing gradual process and one that occasionally gets a very concentrated helping hand from external factors, but anyhow that's beside the point...

> As viruses replicate at time-warp speed, the selective process happens super fast.

Yes, I think that was already obvious to all and sundry who understand the mechanic at work or who have studied the excellent visualisations of the rapid rise to prominence of both the Kent and then Indian strains.  

> Hope that helps!

Not really, I think we were there already...  It's astoundingly clear that the presence of neutralising immunity provides a selective pressure for variants that escape neutralising immunity, and that a  population endowed with neutralising immunity provides an obvious chance to amplify such a variant when it happens to be in the right place at the right time.  There've been shades of this happening for 9 months now, and it's going to continue.  Although it's tied up with the rapid host adaption going on at the RBD providing another mechanism to amplify variants that coincidentally leads to evasion of the neutralising antibodies.    

> NB: as it happens the mass vaccination program hasn't proved as much a catastrophic event for the Delta virus as everyone hoped 

I'm not sure who this "everyone" you keep referring to is?  Clear from my post from last December that I didn't think we were going to put a "catastrophic event" on the virus, nor is it clear that we should.  The main reason it seems so lethal is that (other than some SARS and MERS survivors), nobody on the planet had any immune knowledge of any part of it, leading to or compounding the immune dysregulation lethality mechanism.  

> Selective pressure won't be as great as for a more effective vaccine, but as the virus continues to circulate, it also has more opportunity to mutate/recombine

Well that's the choice.  Do we...

  • ... eliminate it (except for unknown reservoirs) and allow the induced immunity to fade with lack of use (and with increasing genetic distance from the unknown reservoirs) until we're back at square one when it breaks out of a reservoir
  • ... work on getting a broad immune response in to the population with as little harm as possible?  

The former seems both utterly unachievable and likely unwise if it were possible, and the later is what we appear to be doing.  

  • Critical point: Once again, there's really no room for doubt about how much worse this process would be without the vaccines to bootstrap it.

What lies ahead now is tapering down the dependance on vaccines  and allowing the natural processes to take over as far as is possible (as with flu, "not entirely" is probably the answer); with immunity against illness fading more slowly than immunity against reinfection, this feels achievable.  The variant/recombinant bogeymen strains always remain a threat, but that's the case for every other widely circulating member of the human virome, and we live with those.    Vigilance levels in monitoring will need to stay high for years as the experts get a handle on it all, at least the pandemic leaves us with the laboratories, staff and global political attention to this area...

Edit: A future chock full of unknowns, but with the vaccines we've got to this point with perhaps half a million less dead than the alternative, and hopefully the worst is behind us...

Post edited at 14:22
1
 wintertree 12 Aug 2021
In reply to thread:

Temperatures are rising, rate constants for cases are falling.

Schools start returning north of the border in about a weeks time I think...

The data is going to be pretty stripped of value soon if it's not categorised by vaccination status.

Michael Hood noted this on a thread in the pub:

FYI: I noticed this evening on Israel's official COVID dashboard that you can see the vaccination status over time (both, single or not) for illness, severe illness (presumably hospitalisation) and deaths. You can also select all, up to 60, or over 60. Would be nice if the UK dashboard had this.

Hopefully our data will soon be so categorised too...


 Wicamoi 12 Aug 2021
In reply to wintertree:

Thanks again wintertree.

On Scotland... that's now 8 days in a row of rising cases by specimen date (with respect to value 7 days previously). This has coincided nicely, if that's the right word, with cooler, wetter weather - at least in the central belt. The forecast I'm seeing is for the weather to start warming and drying a little here from Saturday onwards. And as you say, most schools return next week. Meanwhile 16-17 year olds have been offered jags starting 10th Aug. I'm not going to brave making any predictions!

You might perhaps want to add the 9th Aug date to the Scotland graph as a change in restrictions event - most of the remaining restrictions were lifted then, including nightclubs re-opening. Along with the previous level 0 loosening I suppose this equates roughly to a two stage version of England's freedom day, although with the requirement for masks in public indoor spaces and on public transport retained.

In reply to oureed:

> Sorry, I must have missed all the articles from last year predicting that vaccines would be excellent at preventing serious illness but fairly crap at preventing spread.

Worth remembering here that they're way, way better at both than anyone expected a year ago. All the agencies were ready to approve anything that hit 50%. So they're not fairly crap at anything. They're bloody brilliant at preventing spread and awesome at preventing deaths.

 oureed 12 Aug 2021
In reply to Longsufferingropeholder:

> Worth remembering here that they're way, way better at both than anyone expected a year ago. All the agencies were ready to approve anything that hit 50%.

Back last autumn Pfizer was claiming 95% efficacy.

5
In reply to oureed:

Firstly, efficacy for… what? Was that in regard to transmission? (Edit: I’ve just checked and as far as I can see it was not. I seem to remember at that time the effect on transmission being a big unknown and not really researched since the priority was just keeping people out of hospital.)

Secondly, efficacy and effectiveness are not the same. Real world effectiveness would be expected to be lower than efficacy. That’s just the difference between what happens in the real world vs tightly controlled trials. It sounds like you might be comparing very different analyses without realising it.

Thirdly, ‘it’s less than 95% effective’ is a pretty bizarre threshold for “fairly crap”

Post edited at 23:40
In reply to Stuart Williams:

> Thirdly, ‘it’s less than 95% effective’ is a pretty bizarre threshold for “fairly crap”

Depends on the message you're trying to push...

 Misha 13 Aug 2021
In reply to oureed:

You can look at reinfections for those who have previously tested positive vs infections for those vaccinated. However my point is testing positive isn’t the same as having had Covid. It probably means the person had symptomatic Covid after around May of last year and was able and willing to get a test. It will tell you very little about those who had Covid but were asymptomatic or those who weren’t able or willing to get a test. So the data would be problematic.

Anyway, as others have pointed out, this is rather academic. Why run the gauntlet of real infection (even if you’re relatively young and healthy) when you can get a vaccine?

 Misha 13 Aug 2021
In reply to oureed:

> It may be that becoming infected after vaccination provides better protection than vaccination alone.

Against what? Some unspecified potential future variant? How would you know, given that variant doesn’t (widely) exist yet? Or against a second infection with the same variant - but I’d rather not have it at all than have it once and be better protected against having it again. So I’m not sure what your point is here. 

 Misha 13 Aug 2021
In reply to oureed:

Out of interest, have you had the jab?

In reply to wintertree:

There's one thing i still really don't understand in all of this.... It's been 18 months now, and I'm still seeing "face shield" everywhere. Did only one company in the world start making them? Even if yes it's still the biggest missed marketing/branding opportunity the world has ever seen. I'm not saying they should have a sponsor's ad there, but at least put a company name or logo or something on them. I can see that it's a face shield.

 Si dH 13 Aug 2021
In reply to Misha and others:

I'm not going to get involved directly in the oureed discussion as it seems his motivations are suspect but there are some questions in there that deserve to be asked. The question about whether vaccine immunity is better than having caught infection, and whether having had both is better again (which certainly seems very true from lab studies) is important. It doesn't change vaccine policy but it would give us a better understanding of who is likely to have a strong immune response and in future that could potentially inform what risk mitigation measures are recommended for different groups of people.

The stuff he says about vaccine efficacy is also partially true I think. The efficacy originally reported for Pfizer was around 90% against infection; it is nowhere near that now with the delta variant and I would refute what Stuart Williams said above about efficacy vs real world effectiveness; the approval data was from mass trials in the real world. The efficacy of these vaccines has definitely dropped. As LSRH says they are still good, but they have been significantly affected by the variants that have come along and, further, there is clear incentive to try to improve them if we can. Acceptance of this is obviously important for policy making.

I suppose my big bugbear here is that I dislike it when I see people who are intelligent and understand all sides of the argument fighting misinformation and one-sided arguments with their own half truths and one-sided arguments. It is more about taking sides than trying to influence anyone to think differently and just leads to more division. I think there is quite a bit of it in this thread and similar ones. It's better to fight misinformation by presenting a balanced argument - which in this case is still clearly in favour of vaccinating people.

 wintertree 13 Aug 2021
In reply to Si dH:

> The efficacy of these vaccines has definitely dropped.

Its very easy for wires to get crossed when talking about “efficacy” given that there’s multiple different sorts of efficacy.

Efficacy of the vaccines against infection with delta is being measured as significantly lower than their efficacy against infection of early variants.  Efficacy against severe disease looks to have had no change discernible within the statistical bounds.  Efficacy against transmission is presumably reduced and lands somewhere between the other two.

(edit: I tend to use “significantly” in the sense that the difference is larger than the error bounds or CIs on the input measurements - so it doesn’t imply a large difference nor rule out a small difference - it means that one can say the difference is real with a high degree of statistical certainty; for efficacy against infection with delta the difference is significant in this sense; it’s not massive for double doses but it’s measurable).

Almost every time “efficacy” is mentioned wires start getting crossed.

> The efficacy of these vaccines has definitely dropped.

Depends on which efficacy.

> As LSRH says they are still good, but they have been significantly affected by the variants that have come along and, further, there is clear incentive to try to improve them if we can. Acceptance of this is obviously important for policy making.

A reduced efficacy against transmission may turn out to be a critical part of the long term solution; it would have been bad news in January, but now we have widespread immune responses in those otherwise vulnerable to disease by immune dysregulation, allowing spread without severe symptoms as a means of refreshing immunity and updating it to track the ongoing changes of the virus - that’s how many other intrinsically mild viruses co exist mostly peaceably with humans.  Can we bootstrap immune systems population wide to the point this happens for covid?  Double vaccination then delta infection is the first big test of that…

Updating the vaccines to track the variant means re-matching the genetic code, that probably restores neutralising immunity and restores efficacy against infection, breaking the move to a “normalised natural circulation” model. Far from clear to me we want to do that except perhaps for the most vulnerable.  T-cell immunity against more than just the spike is a big differentiator between vaccine induced immunity and infection induced immunity; hence Valneva being so interesting as that vaccine is show to induce growth T-cell responses against multiple viral proteins…

The best strategy behind all this is way complex, and I’m always a bit uneasy at the relative prevalence of input from modellers vs immunologists into SAGE.  To understand if we are achieving a “normalised natural circulation” model, it’s really critical to get the data categorised by vaccination status; our dashboard really needs that….  There is going to be some cost to this model, we’re increasing the pantheon of circulating viruses.

In terms of worrying about a massive escape variant (something oureed rises in vague terms apparently against vaccination) - we have to move forwards from where we are.  If such a variant emerges, it’s a new pandemic, and we face that then.

Re: your big bear, when one is replying to a one sided take, it’s easy to get drawn in to the matched answers which are one sided; I try and expand beyond that and just end up with mammoth wordy posts…. 

Post edited at 08:59
In reply to Si dH:

> ... there is clear incentive to try to improve them if we can. 

This bit... Until recently I thought yeah, obviously. But then, turns out there might be more to it. Immunology is weird. There's a possibility that a booster of the same again could be more effective than a tweaked vaccine. Don't ask me to elaborate because it didn't make sense to me either, but the intuitive conclusion that we should update the target proteins isn't necessarily correct. Way out of my depth here. Just repeating a thing some qualified person said on a podcast. Also links to wintertree's point though about moving to a world where it's a naturally circulating, immune updating nuisance that needs to get to a steady state somehow. 

> I suppose my big bugbear here is that I dislike it when I see people who are intelligent and understand all sides of the argument fighting misinformation and one-sided arguments with their own half truths and one-sided arguments.

This is the internet. It always starts off well but once we're 100 posts in, whaddya expect?

 wintertree 13 Aug 2021
In reply to Longsufferingropeholder:

> Immunology is weird. 

I'd argue it's not weird, it's strongly computational and we just haven't reverse engineered all of its algorithms yet...

It's got to decide which parts of its response to a disease to keep in active circulation, which to keep in storage and which to jettison, for every disease it ever sees.  Every disease and vaccine dose it sees presents inputs to this process in various ways.  

Sometimes it makes what seem to us like counter-intuitive decisions - given the success of the system at keeping complex mammals alive (statistically speaking) for 60 million years, this probably means we're missing some key insights evolution has experienced when forming our intuition... 

For now, taking your recollection of the podcast as fact and going down the Dunning Kruger rabbit hole...: What's interesting is to think about why presenting the same, outdates spike protein might elicit a better response against variants - at least in terms of efficacy from severe disease - than an updated vaccine.    Efficacy from severe disease involves a lot of T-cell stuff which - by coding against short protein segments - is pretty robust against the variations on the spike.  But it seems like somehow the whole spike must be being recognised as a monolithic object that triggers a "We have seen this before, re-double our defences" response which cascades down to the T-cells, where-as presenting a new spike has a more lack lustre "well, this is new, let's start some defences and see what happens" command.  But, AFAIK there is no obvious mechanism for the immune system to recognise a whole protein as large as the spike, so this suggests that some template matching is performed against the results of the sub-unit sampling mechanisms, combining perhaps 10 to 100 sub-units in to the match.  No mean feat, even before you have to implement it down at the molecular level operating in thermal chaos.  Or, it could be something totally different:

Edit: Or the podcast came to you in a dream and suggests it's time to either lay off the cheese or the Covid thinking.

Post edited at 09:57
 wintertree 13 Aug 2021

In reply to Jack Kim:

Interesting how an obvious commercial spam bot has this “content appears by immediate edit” appearance.  I seem to recall that being a characteristic of the pop up poster most resembling a chat bot last autumn.

 Lankyman 13 Aug 2021

In reply to Jack Kim:

> The weather has become so worst

You mean it's turned into a sausage?

 wintertree 13 Aug 2021

 oureed 13 Aug 2021
In reply to Misha:

> Out of interest, have you had the jab?

As my concerns about the vaccine are not about individual safety, loss of freedom or medical effectiveness, but rather the detrimental effect of a mass vaccination campaign on the evolutionary dynamics of the virus (over which I have no control), I'd have to be an ideologically-motivated idiot not to get it. That said, I do recycle my waste so I pretty much cover that base anyway.

However, in the coming months I hope to see healthy people lobbying for a fairer global share of vaccine supplies rather than enthusiastically laying claim to their booster jab.

Post edited at 16:10
5
 oureed 13 Aug 2021
In reply to wintertree:

> In terms of worrying about a massive escape variant [...] If such a variant emerges, it’s a new pandemic, and we face that then.

You seem remarkably unbothered about such a possibility! If it does happen, let's hope it's not any more virulent than the one we have now and that it doesn't affect younger age groups. Let's also hope that we will have learned about how not to facilitate the process.

1
 wintertree 13 Aug 2021
In reply to oureed:

> You seem remarkably unbothered about such a possibility!

We have no control over much of the world, and it could come from anywhere.

We have control over vaccination within our borders and had a situation that was going to need endless restrictions to draw out the process of killing half a million of our people without collapsing healthcare, creating millions of serious illness in the process, making us  a big variant factory.

There's a phrase - "live to fight another day".

> but rather the detrimental effect of a mass vaccination campaign on the evolutionary dynamics of the virus 

If we hadn't had a mass vaccination campaign, we'd have had a mass infection campaign, and we know that produces significant immunity too, so it's not clear to me why you think mass vaccination is going to generate your bogeyman variant and not mass infection.   Rather the opposite given what's thought to be the link between chronic infection and variant generation.

> healthy people

It's clear that for adults of all ages, healthy or not healthy, their odds in facing infection with the virus are greatly improved by having been vaccinated.  

We await clinical trial results on the new, inactivated virus vaccine as a booster.  That in particular I think has a lot to offer in terms of protection against future variants.

>  Let's also hope that we will have learned about how not to facilitate the process.

I don't buy your argument that you, and another former pop-up poster (one from a few months ago with a very similar style of circling round the issue on an evolutionary biology basis and a new account) are making.

The selective pressure from immunity is coming like a freight train to whole populations; the question is do they want to face it with a head start from vaccination, or not?

Even your call back to healthy young people is misleading - the data is clear that a fraction of those will be going to hospital, and without vaccination and without lots of control measures, that alone could be enough to quake healthcare, especially with where we are on estimates of R0 now.  

Frankly between your comments here and on other threads (blah blah genetically engineered chimp virus blah blah) I have little doubt that you are here in bad faith, just using a slightly more credible argument than we've seen from others.

Post edited at 16:21
In reply to oureed:

> You seem remarkably unbothered about such a possibility! If it does happen, let's hope it's not any more virulent than the one we have now and that it doesn't affect younger age groups. Let's also hope that we will have learned about how not to facilitate the process.

Not really seeing how you think not vaccinating would make our position better.

In reply to wintertree:

You're right; as usual, it's intuition that's weird. That's more accurate.

 wintertree 13 Aug 2021
In reply to Longsufferingropeholder:

> Not really seeing how you think not vaccinating would make our position better.

You should read the thoughtful comments from a totally different poster called "mcdif" we had a couple of months ago.   Perhaps they'll prove illuminating to that question.

https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_30-735836?v=1#x9477191

Although they do share the same odd views over basic evolutionary biology, vaccination as a means of forcing variant generations (whilst not considering the alternative scenarios), and even implying racism against the analysis/discussion.

Lots more from "mcdif" and their next account "Tru Dat" here.

https://www.ukhillwalking.com/forums/off_belay/covid_-_your_response_to_another_wave-736356?v=1

I still harbour my suspicions - with reasons - they are the former poster known as  "Big Bruva".  I'm reasonably sure this is a separate person to to the plethora of Rom accounts although you never can tell.

In reply to wintertree:

Oh yeah, interesting. They say vaccination is a poor strategy for dealing with covid and propose as an alternative not dealing with it. Inspirational stuff. Never would have thought of that.

Edit: pretty clear that mcdif is alyson30 is leahgoodall is oureed.
If I'm wrong about it it makes no difference. We can only possibly offend one person by assuming they're all the same and I wouldn't count that as a great loss.

Post edited at 17:30
 elsewhere 13 Aug 2021
In reply to wintertree:

First jabs for ages 16-17 up to 38% in Scotland. Small age range and population compared to 18-29 etc. so hopefully pretty quick.

 Misha 13 Aug 2021
In reply to wintertree:

On refreshing immunity - this would be ok if it wasn’t for long covid. That is my biggest concern personally and why I have no desire whatsoever to get covid. 

 Misha 13 Aug 2021
In reply to oureed:

Ok so you’ve had it but are concerned about the impact on future evolution of the virus? All I can say is if we don’t have mass vaccination we’ll just have mass infection and that would advantage new immunity resistant variants anyway. Might as well get there via vaccination which doesn’t involve lots of people in hospital or dead.

I agree re booster jabs but surely vaccinating more people would make a vaccine escape variant even more likely? I struggle with your logic. 

 wintertree 13 Aug 2021
In reply to Misha:

> On refreshing immunity - this would be ok if it wasn’t for long covid. That is my biggest concern personally and why I have no desire whatsoever to get covid. 

That depends very much on how much long covid is:

  1. An intrinsic result of infection from the virus
  2. A result of severe immune dysregulation that occurs (in an age  dependent way) when someone with zero immunity against covid catches it.

Evidence is starting to stack up that “autoantibodies” - antibodies targeting host (human) stuff - are associated with long covid.  There’s presumably two ways these could be generated by infection - if parts of the virus are similar enough to parts of humans, and as a result of immune sampling and training going bonkers during severe immune dysregulation and training against human stuff.  The lack of long covid like symptoms arising in the trials of the inactivated virus candidate vaccine from Valneva (which elicits response against many viral proteins) is a bit of a steer that it’s a result of dysregulation not shared human/viral epitopes.  If all that is on point, then the vaccines are going to prevent severe infection - aka immune dysregulation - and remove the long covid risk from infection.

That’s my best understanding of this but it’s seriously limited.  I can read papers and talk with immunologists but I don’t know where the critical gaps in my knowledge are. 

Edit: again, it comes back to wanting the data categorised by immune status - what’s the demographically adjusted prevalence of long covid in symptomatic infections for vaccinated vs unvaccinated?

The data on long covid has never been very tight, and when it comes to long covid and breakthrough infections we haven’t really had enough time come to pass yet to have a chance of quantifying it well.  There’s the dilemma - the longer a person isolates themselves after vaccination whilst awaiting more data on long covid risk from post vaccine infection, the more they risk their vaccine granted immunity becoming further removed (genetically speaking) from the live infections that are circulating,  it’s a decision weighing intangibles on both sides with poor quality data informing it.   Still, I consider myself lucky to be facing that set of options compared to those available to many other people out there.

Post edited at 00:06
 oureed 14 Aug 2021
In reply to Misha:

> All I can say is if we don’t have mass vaccination we’ll just have mass infection and that would advantage new immunity resistant variants anyway.

Vaccination was a great solution for saving the lives of the old and vulnerable, but we were blessed by the fact that Covid-19 was relatively low-risk for young, healthy people. The natural tendency for coronaviruses is to become more transmissible but less virulent and we could have limited ourselves to controlling its spread with various combinations of regular testing, local restrictions and face-masks as well as increasing healthcare capacity to care for the sick. 

As it is, almost everyone is vaccinated and we are waiting for the "inevitable" "escape variant" to arrive and hoping it won't turn out to be too nasty.

8
 Jon Read 14 Aug 2021
In reply to oureed:

> The natural tendency for coronaviruses is to become more transmissible but less virulent

You state this as if it is a fact; can you point to *any* scientific evidence to support this? I'm not aware of any.

There is undoubtedly uninformed opinion, often by professional scientists/clinicians, who trot this dogma out in the media but, as I say, I've not seen anything to back it up. Happy to be proved wrong....

In reply to oureed:

But if we did what you're suggesting, the "inevitable" "escape variant", that nobody had vaccine derived immunity to, would just be "the virus". There's no situation where we're any worse off for having vaccinated. 

 wintertree 14 Aug 2021
In reply to oureed:

> Vaccination was a great solution for saving the lives of the old and vulnerable, but we were blessed by the fact that Covid-19 was relatively low-risk for young, healthy people.    

Bullshit alert.  Lots of younger people have been going to hospital and even dying.  What’s healthiness got to do with this, are you a back door eugenics fan?  Doesn’t matter if the less healthy working aged adults with a decade or three ahead of them die?

Beyond that, enough healthy young people are susceptible to break healthcare.

> The natural tendency for coronaviruses is to become more transmissible but less virulent

Total bullshit alert.  So far the virus has become more lethal and more transmissive and I doubt it’s finished changing.

The reason the others in circulation are less lethal is perhaps because they’re not unknown to the immune system of adults, because they’ve been in endemic circulation for millennia and children are routinely exposed.

So yes, hopefully this one will become less lethal - *after* we bootstrap the immune process.

> and we could have limited ourselves to controlling its spread with various combinations of regular testing, local restrictions and face-masks as well as increasing healthcare capacity to care for the sick. 

So, immunity by infection with more illness and death and longer restrictions?  As well as my “back door eugenics” comment, there’s another problem with this…

> As it is, almost everyone is vaccinated and we are waiting for the "inevitable" "escape variant" to arrive and hoping it won't turn out to be too nasty.

Your immunity through infection route also poses the risk of an escape variant.  It just does it with more economic harm through more restrictions, more illness and a bit of backdoor eugenics.

Given they you’ve been on here through other accounts pushing bullshit that changes with our situation but always pushes against vaccination, I have to ask - are you genuinely believing this or are you trying to spread harm?  Either way, I have a very low opinion of you and your drivel.

 oureed 14 Aug 2021
In reply to Jon Read:

>> The natural tendency for coronaviruses is to become more transmissible but less virulent

> You state this as if it is a fact; can you point to *any* scientific evidence to support this? 

SARS Covid-2 has evolved to become almost twice as transmissible as the original virus. 

The virulence of the virus is possibly not great enough for that to constitute a significant selective pressure in itself but we certainly want to avoid creating conditions where we might facilitate the competitive advantage of a more virulent strain.

But, as I've stated above, now we have chosen mass vaccination as a one-size fits all strategy it is in everyone's interest to get vaccinated. 

Hopefully we will soon have data which will allow us to compare the efficacy, breadth and duration of the immune response in vaccinated/naturally infected people within the UK and around the world and so will be better able to formulate a global strategy for the future.

6
 oureed 14 Aug 2021
In reply to Misha:

> I agree re booster jabs but surely vaccinating more people would make a vaccine escape variant even more likely? I struggle with your logic. 

What I meant by a fairer distribution of jabs was giving them to vulnerable people in poorer countries rather than young, healthy people here. Given that booster jabs are being approved by an increasing number of rich countries, I doubt there'll be supplies available for mass vaccination campaigns in the poorest countries for quite some time. Pfizer have just put their prices up!

6
 wintertree 14 Aug 2021
In reply to mcdif/true that/oureed:

It's clear your'e not going to answer any of the points put to you by multiple posters and it seems to me like you have an ever evolving argument against vaccination in the UK.

Still, that's Jon taught over viruses (...), wot wot.

Away with you.

 oureed 14 Aug 2021
In reply to wintertree:

My argument evolves pretty much like the virus does, depending upon prevalent conditions! Over the past few months:

  • We have had a mass vaccination campaign (there is now no reason not to get jabbed)
  • A more transmissible variant has become dominant and others are now widely considered "inevitable"
  • Vaccine efficacy has proved to be less than initially claimed (see above)
  • Protection against serious disease has proved good up until now
  • Waning immunity in some people and/or appearance of variants is requiring the use of booster doses after 6 months
  • A serious side effect in one of the cheaper and more easily distributed vaccines precludes its use for young people

So basically my main concern has materialised and some more shit has been added to the mix!

Meanwhile, many of the world's most vulnerable people remain unvaccinated and susceptible to serious disease or death. I think they should be next in line for the jab. Do you agree?

7
 wintertree 14 Aug 2021
In reply to mcdif/true that/oureed:

> A more transmissible variant has become dominant and others are now widely considered "inevitable"

In terms of your use of "now" - that's rather obviously been on the cards from the beginning.   Like I said to Coel back in March 2020 [1], "This virus could be a relatively benign precursor for something worse.  The fewer people it infects, the lower the probability of that mutation occurring.".  Well, back in March 2020 we screwed the pooch royally on keeping that probability low...

As for your other points, once again it's all rather opaque but you seem to be hinting that we're more doomed than we would have been without mass vaccination.  You've more or less said as much upstream.

I'm afraid this makes me think you're either a fool or a manipulator.   Shouldn't jump to conclusions, could be both.

You also keep implying that the vaccination is driving the variants, but that seems pretty loose of the mark, given what we've actually seen.  Like I've said before, the rapid host adaption phase is exploring changes in the part that the neutralising antibodies bind too...

Several posters have asked you why you think getting here via mass infection would have posed a materially lower risk of forcing a worse variant on us than a campaign of mass vaccination.  You continue to ignore that question - help me out here, is it because you don't understand the question (casting the validity of the rest of your train of thought in to doubt) or because you understand how it undermines your position (your silence casting your motives here in to doubt) or some other reason (it is an overly simplistic question in the face of complex stuff after all).

[1] https://www.ukhillwalking.com/forums/off_belay/is_it_worth_it-717284?v=1#x9154383 

 oureed 15 Aug 2021
In reply to wintertree:

> In terms of your use of "now" - that's rather obviously been on the cards from the beginning.   

I've had plenty of flak for suggesting it in the past! Nice to see it is now widely accepted.

> You also keep implying that the vaccination is driving the variants

Not sure what you mean by 'drive'. Vaccines with a high efficacy can abruptly remove all competition allowing resistant variants to thrive and their population levels to explode. Now that efficacy has been revised downwards from 95% (Pfizer last November) to 39% (latest Israeli study), this potential is much less concerning (although as the virus continues to circulates it also continues to mutate/recombine).

> Several posters have asked you why you think getting here via mass infection would have posed a materially lower risk of forcing a worse variant on us than a campaign of mass vaccination.  

Yoy seem to think only in binary terms. We don't have to choose between mass vaccination or mass infection. A multi-pronged approach involving vaccinations for the vulnerable, more investment in medication to treat the sick, regular testing and localised restrictions to slow transmission may yet prove to be the only workable long-term global solution. A UK-centered strategy is not sustainable. 

Natural immunity, which recognises the whole virus, may turn out to be more effective with regards to variants than current vaccine-induced immunity, which only recognises a spike protein. Rather surprisingly I can't source any reliable data for this (not even on UKC!), although the information I have seen suggests that confirmed cases of re-infection are extremely rare. This could be considered a moot point in the UK because the efficacy of the vaccines is much lower than originally claimed and so many vaccinated people are catching Covid anyway and ending up with both types of protection. (We can be thankful that vaccines are at least proving effective against serious disease.) On a global scale, however, mass vaccination is an increasingly unrealistic strategy because the need for booster jabs after 6 months means there simply won't be enough vaccine available to go around for a long time. 

6
 wintertree 15 Aug 2021
In reply to oureed:

> I've had plenty of flak for suggesting it in the past! Nice to see it is now widely accepted.

You'l see I suggested it in March 2020.  It's not a new concept, unlike your presence here (registered 03/Jul/21) or do you want to list your previous accounts so we know what you've said before?

What you've been getting flack for is pushing the change in the virus as a reason against immunisation.

>>  Several posters have asked you why you think getting here via mass infection would have posed a materially lower risk of forcing a worse variant on us than a campaign of mass vaccination.  

> You seem to think only in binary terms.

If you read what I've written you'll see that's false.   

> Natural immunity, which recognises the whole virus, may turn out to be more effective with regards to variants than current vaccine-induced immunity, which only recognises a spike protein. Rather surprisingly I can't source any reliable data for this (not even on UKC!), 

  • It has been discussed multiple times on UKC over the last six months including on several threads that you have replied too.   
  • Some of the past discussion including comment form me have been about the desirability of broader spectrum vaccines to guard against escape mutations
  • Dave Garnett has shared papers on the T-cell response to multiple viral proteins, a discussion we had perhaps 6 months ago.
  • It's come up endlessly since, and it's come up on this very thread - https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_38-737862?v=1#x9503814

If you're not going to read what anyone else is writing there's very little point in engaging with you.  

I still think your argument is fundamentally broken however.

  •  "Better" or not, naturally acquired immunity carries significantly more risk to health for all ages of adults than vaccine induced immunity.  
    • Vaccine induced immunity still provides excellent health protection against variants, and will continue to do so against mutations on the spike portent (T-cell response); the only real threat is probably a recombinant spike swap... 
  •  It looks like this virus is not going away, ever, and so eventual re-infection becomes a near certainty.  
    • The only real question is "do you want to get your first dose of immunity from the vaccine or from live infection" and the data is clear on that.

If I'm gong to be (re)infected due to genetic change in the virus or due to fading immunity, I would far rather this happens to me after I've had immunity from a vaccine than after I've had immunity form live infection.

Beyond that, the data is out on Valneva - something you seem to have a blind spot on when it comes to the discussion, perhaps because it doesn't fit the point you are pushing - and this has been shown to elicit a broad T-cell response against multiple viral proteins.  That seems to be the only specific point you've actually found for why we should go for a "managed mass infection / backdoor eugenics" approach to immunity in adults.

In reply to oureed:

You've also completely declined to account for any long-covid effects, which would result in the oureed manifesto permanently banjaxing anything up to 10% of the workforce.

 Stichtplate 15 Aug 2021
In reply to oureed:

> So basically my main concern has materialised and some more shit has been added to the mix!

You always reckon you're possessed of God like prescience Rom but your posting history doesn't quite back that up does it?

-Troops will likely have to man UK borders (didn't happen).

- UK is now a Failed State (errr???).

- UK will definitely have to increase border controls (a week later HMRC announced they'd be relaxed).

- UKIP is now the most powerful political party in the UK (they won zero seats in elections a couple of months later).

- Nigel Farrage has a good chance of becoming the next PM (LOL!).

-The UK is likely to become a dictatorship in the very near future (Jesus).

- Brexit will cause widespread food shortages (Nope).

- Brexit will cause widespread pharmaceutical shortages (also Nope).

- I'm leaving the UK and taking my tax money with me and I'm never coming back (you're back in the UK cos it was too difficult to work in Cyprus, Apparently despite all of the above  ).

- I'm leaving UKC for ever! Multiple overwrought declarations, multiple time, from multiple different profiles, but you're still bloody well here aren't you

There comes a point Rom when even you have to admit you talk a right load of old pony.

2
 Duncan Bourne 15 Aug 2021
In reply to oureed:

> Not sure what you mean by 'drive'. Vaccines with a high efficacy can abruptly remove all competition allowing resistant variants to thrive and their population levels to explode. Now that efficacy has been revised downwards from 95% (Pfizer last November) to 39% (latest Israeli study), this potential is much less concerning (although as the virus continues to circulates it also continues to mutate/recombine).<

I feel that is somewhat disingenuous. Not withsatnding that the Delta variant came from a country with a poor vaccination record.

Here is the study not a NYT headline.

https://pubmed.ncbi.nlm.nih.gov/34289274/

Results: Effectiveness after one dose of vaccine (BNT162b2 or ChAdOx1 nCoV-19) was notably lower among persons with the delta variant (30.7%; 95% confidence interval [CI], 25.2 to 35.7) than among those with the alpha variant (48.7%; 95% CI, 45.5 to 51.7); the results were similar for both vaccines. With the BNT162b2 vaccine, the effectiveness of two doses was 93.7% (95% CI, 91.6 to 95.3) among persons with the alpha variant and 88.0% (95% CI, 85.3 to 90.1) among those with the delta variant. With the ChAdOx1 nCoV-19 vaccine, the effectiveness of two doses was 74.5% (95% CI, 68.4 to 79.4) among persons with the alpha variant and 67.0% (95% CI, 61.3 to 71.8) among those with the delta variant.

Conclusions: Only modest differences in vaccine effectiveness were noted with the delta variant as compared with the alpha variant after the receipt of two vaccine doses. Absolute differences in vaccine effectiveness were more marked after the receipt of the first dose. This finding would support efforts to maximize vaccine uptake with two doses among vulnerable populations.

also from the bmj

https://www.bmj.com/content/372/bmj.n217

Concerns have been raised over how much protection a single dose of the Pfizer BioNTech covid-19 vaccine provides, following reports from Israel that it is much lower than expected.

Israel, which, like the UK, is currently in its third national lockdown, has so far vaccinated more than 75% of its older people with at least one dose. Early reports from the vaccine rollout have suggested that the first dose led to a 33% reduction in cases of coronavirus1 compared with efficacy of at least 52% reported in clinical trials.2

A preliminary report from the Clalit Research Institute compared the infection data of 200 000 people aged 60 and over who were not vaccinated with the infection data of 200 000 people of the same age group who received one vaccine dose and were monitored for at least 11 days from the date of vaccination. On day 14 there was a “significant decrease of about 33% in the rate of positive tests for the coronavirus” among those who had been vaccinated. This decrease remained the same between days 15 and 17.

The report has raised concerns, as published results have suggested that the efficacy of the Pfizer vaccine was 52.4% between the first and second dose (spaced 21 days apart), and data assessed by Public Health England indicated it could be as much as 89% protective from day 15 to 21.

The Clalit Research Institute stressed, however, that its results included only people aged 60 and over—whereas Pfizer trials also included younger people—and that the findings have not yet been peer reviewed. Additionally, the Clalit study identified those infected according to laboratory tests of those who chose to be tested, while Pfizer’s studies only referred to the appearance of symptomatic disease.

In other words a reduction in effectiveness of a single dose, not a double dose, and that is from 52% for a single dose to 33% for a single dose. So yes it is concerning but not the drop from 95% to 39% that you are suggesting. Unless you have a study which shows otherwise.

Post edited at 14:30
 wintertree 15 Aug 2021
In reply to Duncan Bourne:

> I feel that is somewhat disingenuous. [...] So yes it is concerning but not the drop from 95% to 39% that you are suggesting

I missed that part.  I think they are deliberately and wilfully misrepresenting the fall in efficacy by conflating first and second dose numbers as you have taken the time to outline.

It's probably time for them to bugger off TBH.   Perhaps we can cut to the frothing angry part as seen with previous incarnations.

Their entire contribution appears to boil down to calling for young adults to be deliberately infected with Covid (with orders of magnitude higher risks of death and risk of long covid vs vaccination) because it might given them better resistance against future variants.  Any merit  this idea has is demolished I think by the T-cell at a on the Valneva vaccine candidate.

 oureed 15 Aug 2021
In reply to Duncan Bourne:

> In other words a reduction in effectiveness of a single dose, not a double dose

You got me a bit worried there, thought I was going senile. But I checked the data from the Israeli study I cited and the numbers were correct. And yes, I am talking about protection against transmission, not serious disease which is still good. That should have been clear from the context.

Here's the original report published by the Israeli government. It's in Hebrew but the data I quoted is on page 7 in English:

https://www.gov.il/BlobFolder/reports/vaccine-efficacy-safety-follow-up-committee/he/files_publications_corona_two-dose-vaccination-data.pdf

And here's a report in English on the study:

https://www.infectioncontroltoday.com/view/latest-data-point-to-a-need-for-covid-19-booster-shots

6
 Duncan Bourne 15 Aug 2021
In reply to oureed:

Thank you that was interesting.

The passages I took away were:

“The findings, which are preliminary and based on a small sample, suggest that after two shots the vaccine was 39% effective at reducing the risk of infection and 40% effective at reducing the risk of symptomatic disease during a period when the Delta variant dominated cases in Israel, according to the country’s Health Ministry,”

Which confirms that we are talking about two shots and:

"The Israeli data appear to be in marked contrast to that from England, which was recently reported by Bernal, et al. They concluded that the Pfizer and BioNTech vaccine was 88% effective in the prevention of symptomatic disease from the Delta variant. Thus, the Israeli data and this analysis needs to be confirmed. A good first step would be for the Centers for Disease Control and Prevention to release its data on reinfections so all can evaluate it."

I would say based on that it is something to be concerned about. I will be looking to see if it is confirmed by larger studies.

 Misha 16 Aug 2021
In reply to oureed:

> What I meant by a fairer distribution of jabs was giving them to vulnerable people in poorer countries rather than young, healthy people here.

Yes I know what you meant. However your main point seems to be that mass vaccination is bad because it’s more likely to result in an immunity resistant variant. So it seems inconsistent for you to then argue in favour of using doses to vaccinate people in poorer countries rather than for boosters. I agree that donating the doses would make sense (perhaps limiting boosters for the most vulnerable here), just pointing out that you’re contradicting your own logic. Anyway, the whole booster strategy hasn’t been confirmed yet.

Your various points have been refuted by others above and generally don’t stand up to scrutiny. You are either confused or  deliberately obtuse. 

 Misha 16 Aug 2021
In reply to oureed:

Just to add, your idea of a third way between immunity through infection due to a fully blown epidemic and immunity through vaccination is either naive or dishonest. The last 18 months have shown that it’s impossible to contain the virus without vaccination unless you have a lockdown. Clearly perpetual lockdown is not an option, so  vaccination is the only sensible way without breaking the NHS and killing a load of people.

Also, suppose vaccination leads to an immunity evading variant? That would be bad news but at least we will have more or less contained Delta (cases, hospitalisations and deaths are all demonstrably lower than they would have been without the vaccines). We’ll deal with immunity resistant variants as and when they pop up. Hopefully existing immunity would offer at least some protection. A combination of some restrictions and existing vaccines being tweaked would see us through Whereas your idea of immunity through infection would still drive variants, except each time the Grim Reaper will get his share. 

 Misha 16 Aug 2021
In reply to Duncan Bourne:

I would not be too concerned about preliminary findings based on a small  sample…

 Offwidth 16 Aug 2021
In reply to Misha:

'Slabs' recently posted this link on the other channel which has useful warnings about some anti-vax association (especially for HART) and so much black humour value I thought it well worth copying here.

https://mobile.twitter.com/_johnbye/status/1424060886956843016

 oureed 16 Aug 2021
In reply to Misha:

> We’ll deal with immunity resistant variants as and when they pop up. 

Sounds wonderful, but we're not actually doing great on that front. Delta 'popped up' last December.

> I agree that donating the doses would make sense (perhaps limiting boosters for the most vulnerable here), just pointing out that you’re contradicting your own logic

My logic has always been that vaccines should be used to protect vulnerable people. This seems to be their greatest benefit. Hopefully rich countries will do the decent thing.

4
 Misha 16 Aug 2021
In reply to oureed:

Alpha turned up before vaccination started and Delta originated in India as far as we know, where hardly anyone had been vaccinated. Same for the SA and Brazil variants. Just goes to show that vaccination isn’t the issue. Now imagine where we would be without mass vaccination, in view of Delta.

On the second point, you’re in favour of vaccinating ‘the vulnerable’ but not in favour of mass vaccination for fear of generating vaccine resistant variants? How do you define ‘the vulnerable’ and what about the fact that in an uncontrolled epidemic there will be enough ‘non-vulnerable’ going into hospital to break healthcare anyway? As I said earlier, I don’t disagree about prioritising vaccination overseas instead of boosters but your overall logic makes little sense. Unless, that is, you have some kind of anti-vac agenda. 

In reply to oureed:

> My logic has always been that vaccines should be used to protect vulnerable people.

That's exactly what's happening. You vaccinate the vulnerable first, then vaccinate everyone else to get the number of cases down so that hospitals don't overflow with the 5% of everyone else and the vulnerable can still get treated for whatever makes them vulnerable, and so that there isn't so much virus in circulation that the vulnerable are constantly exposed to it. Rich countries will do the decent thing. They're doing more for the health of other nations than they ever have before.
I don't hear you campaigning for us to send any other pharmaceuticals to poorer countries rather than using them to help younger people here.

 oureed 16 Aug 2021
3
 wintertree 16 Aug 2021
In reply to mfdif/true that/oureed:

Hmm, let me engage what's left of my brain:

  • The crux of your argument lately has been that in going for widespread vaccination in the UK, we raise the risk of a bad variant emerging.
  • Now you're posting an article whose crux is that, by keeping doses in the developed world for a 3rd "booster" jab, we raise the risk of a bad variant emerging in the developing world, by denying them access to widespread vaccination.

You seem confused.  Is there someone else we can speak with?

It starts to look like your argument is just whatever you think you can get away with to argue against vaccination...  Fancy that.

In terms of doing the right thing, the doses the UK could export are a small fraction of the ~100 million doses a month the SII in India are gearing up to, using IP developed within the UK and transferred to India on a non-profit basis.   Nevertheless, I hope we will be exporting a lot of doses soon, as we've funded the construction of multiple different production sites for multiple different candidate vaccines, all of which are turning out to have high efficacy and are working their way through approvals.   I also note that one of them - Valneva - addresses one of your points yet you consistently failed to acknowledge that when mentioned.

 oureed 16 Aug 2021
In reply to wintertree:

> by keeping doses in the developed world for a 3rd "booster" jab, we raise the risk of a bad variant emerging in the developing world, by denying them access to widespread vaccination.

I have no idea what you are talking about. 

4
 wintertree 16 Aug 2021
In reply to oureed:

> I have no idea what you are talking about. 

Do you not read the links you post?  The link you posted has this quote:

[Dr. Dorit Nitzan, WHO Europe’s coordinator for health emergencies]  stressed that the question isn’t only a moral one, because vaccinating the rest of the world also contributes to Israelis’ safety. As she explained last month, unvaccinated countries “are a hothouse for the development of new strains of the virus,” and therefore, until the global vaccination rate reaches 60 percent, it won’t be possible to protect the whole population long-term.

The expert commentary in the link you give to support your case for not vaccinating here - a case you’ve repeatedly said hinges on mass vaccination driving variant risk - has expert commenters starting that *not* having global (mass) vaccination drives variant risk.

You seem a little slow, is there someone else we can talk to?

In reply to oureed:

> What I meant by a fairer distribution of jabs was giving them to vulnerable people in poorer countries rather than young, healthy people here. 

Government's duty is to its citizens and taxpayers first.  Young people are citizens and many of them are taxpayers.  What right do older people who have already been jagged have to decide its 'fairer' that the young don't get a jag and need to catch Covid without any protection.

If we've got excess vaccine, donate it, but make sure all our own population is vaccinated as effectively as possible first.  That includes booster doses if useful and vaccination of younger people.

In reply to tom_in_edinburgh:

I agree. Although there may be a moral issue, it's very unlikely that any elected government anywhere will put others before their own citizens.

Apart from any electoral consequences, governments have a duty of care for their people.

1
 Ian W 17 Aug 2021
In reply to oureed:

> I have no idea what you are talking about. 


Having read through your contributions to this and other threads, i reckon this short contribution explains more about you than any other.

 oureed 17 Aug 2021
In reply to wintertree:

You don't seem to realise that forum debates involve an opinion expressed and then a response. That's why there's a reply function and option to quote the relevant part of the original comment! The opinion expressed was that rich countries would 'do the decent thing' and share vaccines with poorer countries rather than undertake mass booster programs. My response was an article showing that Israel was not doing the decent thing despite pleas from the WHO. That doesn't mean I support every sentence in every article I post a link to! 

I personally don't think everyone in the world can be vaccinated and those vaccinations updated to ensure variants and waning immunity are regularly compensated for in the near future. I also have grave doubts about the long-term efficacy of mass vaccination programs against Covid-19. These doubts are regularly demonstrated to be well-founded.

I think vaccines are a good solution for protecting vulnerable people and I think the priority in the future should go to vulnerable people around the world.

What's your view on this?

6
 wintertree 17 Aug 2021
In reply to oureed:

> My response was an article showing that Israel was not doing the decent thing despite pleas from the WHO. That doesn't mean I support every sentence in every article I post a link to! 

But one of the key reasons the WHO are making that plea directly undermines the evidence free opinion you have lately been putting forwards a lot.

This is what we call "cherry picking".  

Or very confused.

> What's your view on this?

Charitably, that you are rather slow and confused.  

However, I'm all out of charity and honestly I think you're here with hidden and unpleasant motivations.  

You are prone to making confident sounding but utterly evidence free statements about the virus in support of your stance people should not get immunised, and when called out in it by other posters (plural), you don't answer - e.g. [1].  Your previous incarnations "mcdif" and "True dat" conducted themselves in a similar way.  I can't immediately recall if I reared to one of them as a shitty weasel or a slippery weasel, but that seems prescient.

[1] https://www.ukhillwalking.com/forums/off_belay/friday_night_covid_plotting_38-737862?v=1#x9505207

In reply to wintertree:

> is there someone else we can talk to?

I'm sure there are plenty of other profile incarnations.

In reply to oureed:

>  The opinion expressed was that rich countries would 'do the decent thing' and share vaccines with poorer countries rather than undertake mass booster programs. 

You've misrepresented that, too. That's an implication that we're all agreed on exactly what 'the decent thing' is, which we clearly aren't.

 Stichtplate 17 Aug 2021
In reply to oureed:

> The opinion expressed was that rich countries would 'do the decent thing' and share vaccines with poorer countries rather than undertake mass booster programs. 

You do make me laugh with this latest incarnation where you posture as occupying The Moral High Ground on pandemic response.

You're the same bloke that told us you'd made a nice profit out of covid (crass beyond belief) and also told us you'd visited nine countries on four different continents during the pandemic (irresponsible much?). Same bloke who's introduced us to a whole new level of lies, scams, deceit and misrepresentation in the manner in which you've chosen to engage on here?

If I ever find myself occupying the same Moral High Ground as yourself, rest assured I'll be checking the soles of my boots as I exit.

>You don't seem to realise that forum debates involve an opinion expressed and then a response.

I'm waiting with bated breath.

Post edited at 14:34
 oureed 17 Aug 2021
In reply to Stichtplate:

> >You don't seem to realise that forum debates involve an opinion expressed and then a response.

> I'm waiting with bated breath.

😘

4
 Misha 17 Aug 2021
In reply to oureed:

> I personally don't think everyone in the world can be vaccinated and those vaccinations updated to ensure variants and waning immunity are regularly compensated for in the near future. I also have grave doubts about the long-term efficacy of mass vaccination programs against Covid-19. These doubts are regularly demonstrated to be well-founded.

Not everyone as some people don’t want it but a significant majority can be. Updating the vaccines for new variants is technically possible and already happens for flu.

Why do you have grave doubts and what evidence suggests they are well-founded? The evidence is plain to see here in the UK - hospitalisations, ICU admissions and deaths are all a fraction of what they would be without mass vaccination, given the level of cases this summer. I know you say long term efficacy but not sure what you mean by that. If it’s long term as in future efficacy, that can’t be demonstrated as obviously we aren’t in the future yet.

 Misha 17 Aug 2021
In reply to Stichtplate:

> You're the same bloke that told us you'd made a nice profit out of covid (crass beyond belief) and also told us you'd visited nine countries on four different continents during the pandemic (irresponsible much?).

Missed that but it’s hard to keep up with all the bullshit post(ers). Of course none of this might be true… On another thread, alyson30 was busy persuading people that she (?) knew all about the banking system because she was some kind of financial services consultant and was convinced that banks can create and lend money out of thin air while most of their staff could be sacked with no impact on anything. Completely off topic but I mention that because it’s another example of self-confident bullshit to pursue an agenda, with potentially a completely made up backstory.

 jkarran 17 Aug 2021
In reply to oureed:

> I personally don't think everyone in the world can be vaccinated and those vaccinations updated to ensure variants and waning immunity are regularly compensated for in the near future.

Why not?

> I also have grave doubts about the long-term efficacy of mass vaccination programs against Covid-19. These doubts are regularly demonstrated to be well-founded.

They are?

jk


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