UKC

Friday Night Covid Plotting #23

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 wintertree 24 Apr 2021

Another short update as there’s not that much to discuss, definitely falls under “little news is good news”.  There’s been a general trend of decay in all measures, although Northern Ireland is wobbling around, and we’re seeing a return to growth in some places; in England at least we know this is down to the asymptomatic LFD testing that ramps up with the return of schools after Easter;  the PCR data alone is remaining in decay.

There's a new plot below.  This is the exponential rate constant for English PCR-only data.  This is measured using my new approach of measuring the ratio (cases on day x+7)/(cases on day x) and casting it as an exponential rate constant.  This avoids almost all of the gunk introduced in to analysis by the day-of-week or weekend effects in the cases data; when cases aren't changing much, that starts to dominate the analysis.  Previously - and in all my other plots still - I try and patch it up with reassignment of cases based on the pattern (deweekending) and some filtering.  I prefer this approach as much less invasive and closer to the data.  Wish I'd thought of it 6 months ago...

The more negative the exponential rate constant, the faster cases are halving.   We see that there's only been two days in 2021 where the PCR cases have been rising by this measure.  These are caused by the easter bank holiday.  We know that fewer samples are taken on bank holidays.  When that date lands on the top of the ratio, the under sampling causes a false decay signal.  7 days later it lands on the bottom of the ratio, and it causes a false rise in the signal.   The blue annotations link the two points in the data affected by each bank holiday, and we see they are indeed outlier lows and then highs.  I'm confident that "real PCR cases" - as elusive a concept as that is - have remained in decay for all of 2021 to date.

I'm more or less convinced that the weather is responsible for most - not all - of the changing rate in this plot and I'll get in to that later on.

Bit of a diversion to go through this first, but it makes the point that in England - where we have the data broken down by test type, symptomatic PCR cases are still falling, even if headline cases are starting to rise associated with the return to schools.  Perhaps that explanation proxies over to what we're seeing in the other home nations.

Link to previous thread: https://www.ukclimbing.com/forums/off_belay/friday_night_covid_plotting_22-733665


 wintertree 24 Apr 2021
In reply to wintertree:

Squint and you might think there's an up-tick in cases everywhere except Wales.  It's hard to say now on a weekly basis as the numbers are low and there's a lot of noise.  The rise seen in NI last week has not been sustained but nor is it decaying much.  

If you compare Wales and Scotland, which had roughly similar peaks, the consistently slower halving times for Scotland have really added up and it's got quite a stuck high baseline compared to Wales which is close to elimination.  

The characteristic time for cases in the provisional zone (far right of plot 9x) for England is about to hit growth; I'm pretty sure that's the schools associated LFD data switching on again and so doesn't indicate growth in infections.   The demographic plots later illustrate this.


 wintertree 24 Apr 2021
In reply to wintertree:

In relative terms, deaths in England have decayed a lot more than admissions.  I've commented on this before in terms of a faster halving time for deaths; this has now clearly developed in to the numbers with deaths having fallen most of the way back to the axis and admissions stuck some way off.  Likely a sign that the vaccines are moderating effects for the most vulnerable but not entirely preventing hospitalisations.  That's a point to keep in mind when considering reduced immunity from emerging variants.

Last week I noted that we had some growth in cases in older demographics and perhaps a reduced decay in hospitalisations.  That's not been sustained as we'll see in the demographic post, but there are bumps in the hospitalisations and deaths curves in the yellow "Stay Local" period of plot 9.  This shows that the decay backed off significantly for a week or so.  Perhaps this was a couple of care home outbreaks or perhaps an effect of the weather.  A warning sign I think that as phenomenally well as the vaccination program is working, it is not a magic solution. 


 wintertree 24 Apr 2021
In reply to wintertree:

The English demographic plots.

As always, the right edge of D1.c is provisional.  The growth in over 60s seen last week returned to decay, but there is a small island of orange indicating growth still present that made it out of the provisional window.  I've encircled it in red on the annotated plot.  The return to growth in younger adults did not persist.  We now see a big orange growth spike in the bottom right which is I am certain mostly the additional LFD data associated with schools.  Remember that  PCR cases are still in decay. 

There's perhaps a smidge of orange indicating growth in D1.d for ages around 90; there's not much in the way of absolute numbers though so it could be noise.  Other than that, deaths are all still in pretty definite decay.  I don't tend to look at the absolute numbers so much as the rates, as it's the trends I'm trying to understand.  I've put an absolute numbers plot in for deaths (D5).  It's really reassuring to see where we are now.


 Yanis Nayu 24 Apr 2021
In reply to wintertree:

Especially given the risk that mutations like the E484K one evade the vaccine. That is establishing itself in the UK now and there is concern that it can evade the vaccine and antibodies. The Indian variant will be getting a foothold here too because the measures to prevent it have been shite. Indian hospitals are full of people under 40. 

 wintertree 24 Apr 2021
In reply to wintertree:

A grab bag of plots.

The vaccine plot now shows a simple estimate of the lag from first to second dose - the method is covered in the previous thread.  We continue with a clear focus on second doses and the lag between doses looks to be very slowly increasing and still around 11 weeks.

Te variants plot:

  • Data sourced from here - https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data - with time series pieced together from the Wayback machine copies of the page
  • The SA variant continues to follow a roughly exponential rise.  As previously discussed this plot is total number of cases detected, but if its rising exponentially so is the rate of new cases.  Very odd that we had the big news about 10 days ago about a large number (large in terms of being a significant fraction of the numbers on this plot) community outbreak detected in parts of London as there's still no corresponding spike on this plot; that rather suggests to me that quite a lot of this data is actually related to community transmission and not border detection - as it's unlikely in the extreme that border detection would plummet at just the right moment to compensate for a spike in community cases.  All just inference without full information on my behalf though - I really would like more transparency and clarity in the variant reporting.    
  • The red curve is a variant under investigation - not of concern - that stood out in absolute numbers so I've been plotting it.  We never really know what the numbers mean with variants as we don't know how much is surge sampling vs random etc, or how much is local vs border.  The numbers look to be dropping below a fixed rate exponential fit indicating a slow down.  Provisionally good.
  • I've added a curve for the P.1 Manaus variant.  Odds are this one is Bad News.  There's a couple of others rising in number that could be worrying - but we know so little about where these cases come from it's borderline pointless thinking about it.

Comparing the nations - this normalises the filtered case rate curves for all nations to peak at the same value.   It drives home how the weaker exponential decay rates for Scotland have compounded over time.

Post edited at 21:52

 wintertree 24 Apr 2021
In reply to wintertree:

Finally, these were on the previous thread but a forum glitch that seems to be going around took the images off.

I think a lot of the answers to covid transmission are literally blowing in the wind - indoor ventilation and indoors/outdoors.

Figure 1 - the exponential rate constant for England (black) and the Central England Temperature (hadCET [1], red).  When the temperature is up, the rate constant is more negative indicating faster decay.  The blue line shows when schools are open.  The rate constant data is plotted on the date of the first day the 7-day period it's measured over; as it covers an average of that whole period it should perhaps be plotted at +3.5 days to the right, but as it happens that matches the lag from cause to effect from weather to rate constants, so I left it where it is.  

Figure 2 - derivatives of the rate constant and the CET, both done with an 11-point 1st order polynomial filter.   I've flipped the d/dt temperature y-axis to drive the point home.  When the temperature gets better (red line goes down), Covid transmission gets better (black line goes down) and vice versa.  This doesn't hold with the opening of schools.  I think the differentiation works as a high pass filter rejecting baseline drift in the Covid rates from non-weather factors, and the school change on rates is sudden and so not rejected.  

Figure 3 - scatter plot of the two gradients.  The linear fit to the non-school black data points has a correlation coefficient or R value with a magnitude of about 0.8 which is no mean feat.  

Ventilate even when it's cold. 

[1] https://www.metoffice.gov.uk/hadobs/hadcet/

Post edited at 21:59

 wintertree 24 Apr 2021
In reply to Yanis Nayu:

> The Indian variant will be getting a foothold here too because the measures to prevent it have been shite.

We've certainly had the borders a lot more open than I would have liked, with quarantine a lot softer than I would have liked. 

> Indian hospitals are full of people under 40. 

Indeed.  Partly they have a lot fewer really old people, which means the proportion of the victims who are younger will be larger.  It's an awful situation and it's going to get quite a bit worse yet I fear.  55 new cases of the Indian variant detected in the UK this week.  I haven't seen a qualified estimate of what fraction of infections will make it through the border undetected but the answer I suspect is Too Many.  This variant is popping up in other locations that are doing a lot of sequencing, so it'll be coming in from non red-list countries soon enough.

 Si dH 24 Apr 2021
In reply to wintertree:

Thanks again.

I confess I'm really surprised how PCR cases are continuing to decline and there has been no increase in positivity numbers since 12/04. I think we'd have seen something by now if the changes had made a significant impact. Of course the weather has been amenable to sitting outside. I definitely called this wrong - I was expecting rising cases in all under 50s by now. Really good news (in the UK.)

 Yanis Nayu 24 Apr 2021
In reply to wintertree:

What happens is this - person A comes homes from India to their family of 8 people. They isolate but their family don’t (as they don’t have to). On day 2, Person A has a bad headache and does his covid test. The results take 4 or 5 days to come through. His wife and kids carry on going to work and school; some of them notice they’ve got a headache too and feel out of sorts. Person A gets his result - it’s positive. There is a delay in getting that result on CTAS because it comes from a private lab, so no contact tracing is done. Other family members go for tests and 4 of them are positive with numerous close contacts. Only at this stage is contact tracing carried-out. Person A and his family have followed all the rules and spread the mutation very effectively. 

 Yanis Nayu 24 Apr 2021
In reply to wintertree:

Just FYI, nearly all positive PCRs are being genome sequenced now. 

 girlymonkey 24 Apr 2021
In reply to Yanis Nayu:

In terms of the variants. There was talk a while ago about vaccines being tweaked to deal with the variants and giving boosters of these in the autumn. Has anyone got any reliable information as so whether this is in progress and if it is likely to keep up with the new variants?

 mik82 24 Apr 2021
In reply to wintertree:

The Indian variant has probably been thoroughly seeded throughout the UK already given the amount of travel, and the high positivity rates in India. As we're now starting to open up I really don't want this to be a real-world test against a population partially vaccinated against an older variant. 

I would hope that the scenes in India are really due to the huge number of cases and that proportionately younger people are not more affected.

In reply to Si dH:

I think we need to see another week’s data before we can ‘call it’ that we seem to be getting away with the reopening. The reason is that most of the social mixing didn’t take place until Thursday 15th onwards. Add 5 days on average for symptoms to show and another day or two for people to get tested, then the processing and reporting lag. It’s good that it’s not showing in the numbers yet but I’d want another week’s data as it’s pretty provisional at the moment.

I may be being simplistic but PCR cases seem to have stopped dropping from Tuesday 20th. Week on week numbers have been +/- 100 since then.

The real issue is going to be the 17 May relaxations. Letter from Heneghan & co demanding the end of all restrictions and face mask wearing from June 21st. Oh dear...

 Si dH 25 Apr 2021
In reply to Misha:

> I think we need to see another week’s data before we can ‘call it’ that we seem to be getting away with the reopening. The reason is that most of the social mixing didn’t take place until Thursday 15th onwards. Add 5 days on average for symptoms to show and another day or two for people to get tested, then the processing and reporting lag. It’s good that it’s not showing in the numbers yet but I’d want another week’s data as it’s pretty provisional at the moment.

To be definitive I agree. But there's no sign at all yet, which I think is a very strong indicator. To be even more confident I'd want to do a full survey of UTLAs and see if any had recorded small spikes over more than a couple of days, then monitor them. I don't have the time though.

> I may be being simplistic but PCR cases seem to have stopped dropping from Tuesday 20th. Week on week numbers have been +/- 100 since then.

Definitely still dropping in England where we have the data split by test type - see graph below that I just pulled off the dashboard. (Data is fairly final for all but the last two days now) as well as WT's first post. It's interesting how the rate of PCR case reduction has been fairly smooth through all this period with the up/down mostly coming from variation in LFTs.

> The real issue is going to be the 17 May relaxations. Letter from Heneghan & co demanding the end of all restrictions and face mask wearing from June 21st. Oh dear...

Agree re: 17th. Re: the rest; fu*king numpties.

Post edited at 05:51

 Si dH 25 Apr 2021
In reply to Si dH:

On a separate topic I'm how surprised how many people that graph suggests are still not bothering to get confirmatory PCRs. I thought they were recommended for people doing school related testing now. It really makes no sense not to get one, does it?

In reply to Si dH:

We're at the point now where a positive LFD has about a 50% chance of being correct. Someone I work with made a comment that because of this fact, if he was +ve on LFD, rather than go for a PCR he'd first do another LFD. Another distant colleague agreed.

I work exclusively with people who have at least one science or engineering degree. I dread to think what that could mean for population level behaviour.

In reply to wintertree:

> Ventilate even when it's cold. 

Just listened to a really good Science Unscripted that cited (and interviewed the lead author) of an open letter written by German aerosol experts to the government. Trying to find the papers now.  I heard it on the weekly roundup but there's an episode entitled "99.9% of COVID-19 infections happen indoors" which must be more of the same. You'll like it.

Science unscripted: Weekly roundup — The (not-so) great indoors https://radiodownloaddw-a.akamaihd.net/Events/podcasts/en/31485_podcast_spectrum/7542DE38_2-podcast-31485-57277782.mp3

Science unscripted: 99.9% of COVID-19 infections happen indoors https://radiodownloaddw-a.akamaihd.net/Events/podcasts/en/31485_podcast_spectrum/330C8479_2-podcast-31485-57230418.mp3

Post edited at 06:21
 Si dH 25 Apr 2021
In reply to Longsufferingropeholder:

> We're at the point now where a positive LFD has about a 50% chance of being correct. Someone I work with made a comment that because of this fact, if he was +ve on LFD, rather than go for a PCR he'd first do another LFD. Another distant colleague agreed.

> I work exclusively with people who have at least one science or engineering degree. I dread to think what that could mean for population level behaviour.

Don't you get T&T calling you though, if you register the positive result? At which point, if you don't isolate or get a negative PCR, you're breaking the law. A subsequent negative LFT isn't enough. And if you were going to break the law, well then you just wouldn't register the positive LFT in the first place...

 wintertree 25 Apr 2021
In reply to Si dH:

>  I was expecting rising cases in all under 50s by now. Really good news (in the UK.)

Yes, I was expecting a rise by now so I'm very glad to have been wrong.  Accounting for LFDs the demographics suggest the fall is still happening in all age range, so we don't even have rising younger cases masked by falling older ones, but a genuine fall.  This is great news for us, as it means that by the next unlocking, cases should be so low that if we do return to signifiant spread, there's still a lot of time to understand and act on that before the absolute numbers become worryingly high.

In reply to Yanis Nayu:

> Just FYI, nearly all positive PCRs are being genome sequenced now. 

Interesting.  The COG-UK coverage maps are almost all saturated at 20% now; it sounds like they need to adjust their colour map...

In reply to mik82:

> The Indian variant has probably been thoroughly seeded throughout the UK already given the amount of travel, and the high positivity rates in India

There were similar thoughts over the SA variant a couple of months ago, and that's remained surprisingly low, especially if we're now sequencing most cases.  Perhaps the enhanced contact tracing and surge testing has been enough to keep a lid on it; let's hope so.

In reply to Misha:

> The real issue is going to be the 17 May relaxations. Letter from Heneghan & co demanding the end of all restrictions and face mask wearing from June 21st. Oh dear...

How the hell Heneghan continues to hold a chair at Oxford University I'll never know.  

In reply to girlymonkey:

I've not seen definitive information on variant adapted "boosters".  Given that the same mutations are cropping up over and over again, it doesn't feel like a lost cause.  But at some point do we have to face up to accepting widespread infection by new variants, moderated in their effects by existing vaccines and improved therapeutics so that we end up with true herd immunity?  I don't think that time comes for another year as a lot of hopefully very useful immunomodulatory stuff is still in the clinical trials pipeline.  

> Just listened to a really good Science Unscripted that cited (and interviewed the lead author) of an open letter written by German aerosol experts to the government. Trying to find the papers now.  I heard it on the weekly roundup but there's an episode entitled "99.9% of COVID-19 infections happen indoors" which must be more of the same. You'll like it.

Thanks for the links.  Back in early 2020 when chest freezers sold out everywhere, I had no trouble getting a couple of HEPA filters for home (in case one of us got it) and for my office/workshop (assuming opening windows isn't enough on a breeze-free day).  There's been 14 months now to fit air filtration and ventilation to workplaces and schools.  

In reply to Si dH:

Well that's what I thought. Also thought educated people would have the sense not to think a do over would be any use. I honestly don't know what he was thinking. Like, what path was he going to take after the second one, whichever the outcome?

 Yanis Nayu 25 Apr 2021
In reply to Si dH:

> Don't you get T&T calling you though, if you register the positive result? At which point, if you don't isolate or get a negative PCR, you're breaking the law. A subsequent negative LFT isn't enough. And if you were going to break the law, well then you just wouldn't register the positive LFT in the first place...

I don’t think you are breaking the law by failing to self-isolate after a positive home LFD. Everything kicks-in with the PCR result. You’re just being a tw*t. 

In reply to wintertree:

An observation on regional dynamics. Very high level as I’m just going off changes in the dashboard map over the last couple of weeks and clicking on a few areas to see if they’re up or down.

The pockets of relatively high infection rates (dark green) have been diminishing. In most of these areas the rates are still falling, so it’s possible that in about a week there will be very few dark green areas (as long as we don’t get a general rise in rates as a result of the 12th catching up with us).

At the same time, some areas are going up. Very few areas have turned dark green - Cambridge is one of the main exceptions. Presumably a local outbreak.

Most areas are more or less steady. There’s been a gentle uptick in previously yellow areas, presumably due to LFDs. In that context, the continued reduction in the previously stubborn dark green areas is even more impressive. Presumably they’re also seeing an uptick due to LFDs and yet something else is forcing their rates down. Could this be due to higher temperatures and better ventilation? Or are there more local factors? Who knows...

 Si dH 26 Apr 2021
In reply to Yanis Nayu:

The breaking the law bit is if you get called by T&T, and don't isolate when told to do so. Do you not get a call if it's a positive LFT? I had assumed you did - seems a bit of a gap in policy otherwise.

Post edited at 17:26
In reply to wintertree:

Just a thought, if it's easy, could the vaccines plot have "2nd dose debt" plotted on there? So we can more easily make guesses about when and how quickly the age range will open up? Or is that a bit of a nonsense? It would possibly require some circular logic but I don't see that being a deal-breaker.

 elsewhere 26 Apr 2021
In reply to Longsufferingropeholder:

In ten weeks time the demand for second doses will plummet matching how the number of first doses plummeted a couple of weeks ago.

Hence in about 10 weeks time we should have a surge in first vaccinations again hopefully rattling through the rest of the adult population in a month.

20 or 25 million adults with no first jab at the moment.

7 million first vaccinations in 10 weeks at 100,000 per day whilst we are doing mostly 2nd jabs like now followed by 14 million first jabs in 4 weeks. That would do most of the unvaccinated adult population. Then 20 million 2nd jabs completed 6 weeks after that - 20 weeks from now.

Might be a bit quicker and give or take weeks if vaccine supply fluctuates.

Moderna will be purely first jabs for a while which could really speed things up if there is a good supply.

Post edited at 20:04
In reply to Si dH:

My understanding: if you have a LFT at a test centre then you must legally self isolate. If it’s a home LFT, the ‘stay at home’ is not legally enforceable. I think. 

 jonny taylor 26 Apr 2021
In reply to elsewhere:

If it takes another ten weeks before first doses ramp up, then Johnson, Hancock, sturgeon and others have been straight out lying about how long the current slowdown is expected to last...

(which is certainly a possibility)

 elsewhere 26 Apr 2021
In reply to jonny taylor:

Keep an eye on daily total jabs - if it exceeds 500,000 per day it will be quicker.

At the current rate they should meet the target of all adults offered a first jab by end of July which is 14 weeks from now.

 wintertree 26 Apr 2021
In reply to jonny taylor:

> If it takes another ten weeks before first doses ramp up, then Johnson, Hancock, sturgeon and others have been straight out lying about how long the current slowdown is expected to last...

> (which is certainly a possibility)

It’s hard to see them ramping up much before then given the various news stories over production delays (Elsewhere: I was going to post that on your comment re: Moderna but I ended up posting it on the other thread fired up tonight on vaccines) and the extra demand locked in by the first dose high rates at the end of March(*).   I’m not sure it’s out and out lies so much as running with the more optimistic side of projections.  I doubt very much we’ll be getting our delivery from SII in India - nor I think should we, nor any more for some time.  Various other production/scale issues.

I’m not sure how fast novovax can come online; I think that should be quite amenable to scale compared to many.  It must be very close to approval (or rejection as a very low probability?) by now.

(*) given the astounding effects of the first doses on our situation, using everything we can get and not stockpiling for second doses seems, like the move to a 12 week gap, bold but now proven worthwhile.  With the summer in our favour and cases low and deaths nearly eliminated we have a grace period ahead to enjoy the summer and defang the coming winter.

 Offwidth 27 Apr 2021
In reply to wintertree:

I wouldn't normally link this on a covid data thread but the headlines today are pretty extraordinary. It seems very likely Boris was of the mind to 'let it rip' in September and regretted the first lockdown. It seems we dodged a large bomb because enough of the rest of the cabinet actually did follow the science.

https://www.bbc.co.uk/news/blogs-the-papers-56896604

In reply to Offwidth:

who’d have thought lying repeatedly about everything for years would have any consequences when you need people to take you at your word?

literally no-one (called Boris) could have seen this coming....

Along with the poll mentioned showing 50% vs 11% in whether people think the government is mired in sleaze or not, and the tabloids treating him as a joke as well as a liar, and this is starting to look like his shelf life is coming to an end 

And when even minor league ministers are backing away as fast as they can, you wonder how much longer this can go on

Asked about the funding, Work and Pensions Secretary Therese Coffey told BBC Breakfast: "The only thing I do know is the prime minister has said that he paid for the expenses of redecoration."
 

Cabinet to meet as pressure builds on Boris Johnson amid leaks https://www.bbc.co.uk/news/uk-politics-56897213

Post edited at 08:44
 Offwidth 27 Apr 2021
In reply to no_more_scotch_eggs:

Maybe leave the party politics to another thread. I posted the link to flag the story that Boris was a 'let it rip' supporter in September

 wintertree 27 Apr 2021
In reply to no_more_scotch_eggs & Offwidth:

We’ll see what else is released to the press as part of this.  It’s hard to know how much - if any - of these “leaks” to trust when it’s all part of a power play.  One thing I am really bad is is predicting matters political. 

Might be time for a thread in the new Politics forum...

 bruxist 27 Apr 2021
In reply to Offwidth:

We knew there was a cabinet rift in September, with Johnson and Sunak wanting a no-lockdown approach, and Gove and Hancock arguing against.

I suspect we can pin that former view on the meeting with Heneghan, Gupta, and Tegnell on the 21 Sep. Johnson and Sunak merely sought some alternative scientific view to follow instead of that of SAGE: https://bylinetimes.com/2021/02/11/records-confirm-turning-point-boris-johnson-meeting-with-lockdown-sceptics/

 wintertree 27 Apr 2021
In reply to Longsufferingropeholder:

> Just a thought, if it's easy, could the vaccines plot have "2nd dose debt" plotted on there? So we can more easily make guesses about when and how quickly the age range will open up? Or is that a bit of a nonsense? It would possibly require some circular logic but I don't see that being a deal-breaker.

Possibly; I seem to be having a slow week so you'll have to spell the concept out a bit more.  I've thought about forecasting 2nd dose demand from the first and second doses to date; this could be overlaid a notional forecast availably (e.g. derived from the most recent weeks)  with any deficit from the running total hi-lighted.   I don't think there's anything circular in that.   

I did wonder if we're going to see the gaps between doses pulled down to about 10.5 weeks in advance of the second doses for the first doses given in the exceptional peak in the W/C 2021-03-15, to broaden the peak of second doses by raising the gap to 11.5 weeks during the corresponding second peak.

 wintertree 27 Apr 2021
In reply to bruxist:

> I suspect we can pin that former view on the meeting with Heneghan, Gupta, and Tegnell on the 21 Sep. Johnson and Sunak merely sought some alternative scientific view to follow instead of that of SAGE:

Given Gupta's overt association with a foreign lobbying organisation, and given that she has made no COI declarations this meeting should be a matter for the security services IMO.  I'd note that Gupta has also had a meeting with Trump's White House.

The BBC were reporting on H and co the other day.  A letter signed by about 20 scientists (*).  They didn't report on the other tens of thousands of scientists who hadn't signed it...

(*) Well, not all were actually scientists...

In reply to wintertree:

This kind of thing, yeah. It sort of already exists on that paulmainwood thing from the twitters that someone posted somewhere, so maybe don't worry. He seems to factor in a load of info that would be a faff to gather.

 neilh 27 Apr 2021
In reply to wintertree:

The meeting was set up by Vallence so that Johnson and others could listen to alternative view points.I understood that it was at Vallences suggestion.

Post edited at 11:55
 wintertree 27 Apr 2021
In reply to neilh:

> The meeting was set up by Vallence so that Johnson and others could listen to alternative view points.I understood that it was at Vallences suggestion.

Gupta and Heneghan in particular have no credibility as an alternative view point IMO because the science they claim to be experts in, and which they present, has been consistently and fundamentally flawed.  They have alternative views on how we should handle the crisis, but those views are rooted in nonsense.  Good reading on how consistently wrong they have been here - https://www.covidfaq.co

 jkarran 27 Apr 2021
In reply to Yanis Nayu:

> The Indian variant will be getting a foothold here too because the measures to prevent it have been shite. Indian hospitals are full of people under 40. 

I wonder if that's a change in the behaviour of the virus or a symptom of extreme health inequalities, young rich urbanites having access to hospitals to the exclusion of those dying at home? Or both.

jk

 wintertree 27 Apr 2021
In reply to jkarran:

> I wonder if that's a change in the behaviour of the virus or a symptom of extreme health inequalities

I think partly that there are fewer older people, which shifts the barycentre of age in those being hospitalised, and partly the inequalities affecting who gets to go to hospital.  If you ration access to hospitals based on medical ethics and not cash, you're going to see the older people being turned away in general.  The inequality angle  is part of why I think there is significant under-reporting of deaths going on.. It could be related to the variants as well, but I've not seen any solid support for that. 

 jkarran 27 Apr 2021
In reply to Si dH:

> On a separate topic I'm how surprised how many people that graph suggests are still not bothering to get confirmatory PCRs.

I don't think that's quite what the graph shows, it shows how many positive LFT were subsequently confirmed by PCR, not many. It could be most didn't bother with subsequent PCR testing or it could be they did and we're mostly seeing the false positive LFTs. Bit of both I guess.

jk

In reply to wintertree:

And remember all those studies we had from multiple Western countries that suggested worse outcomes in certain ethnicities. It seems to be a lot of not greats adding up to a pretty terrible.

 neilh 27 Apr 2021
In reply to wintertree:

Agreed. My understanding is that Vallence considered it was important that Johnson and others in making political decisions heard those views as a counter view point. I am confident that Vallence did not support them- as I am sure you are..

 Si dH 27 Apr 2021
In reply to jkarran:

> I don't think that's quite what the graph shows, it shows how many positive LFT were subsequently confirmed by PCR, not many. It could be most didn't bother with subsequent PCR testing or it could be they did and we're mostly seeing the false positive LFTs. Bit of both I guess.

> jk

From the dashboard: "A positive case is defined as as an individual with at least one confirmed positive test from a polymerase chain reaction (PCR), rapid lateral flow tests or loop-mediated isothermal amplification (LAMP) test. Positive rapid lateral flow test results can be confirmed with PCR tests taken within 72 hours. If the PCR test results are negative, these are not reported as cases."

So it's not about false positives because those confirmed negative by PCR are removed from the numbers. The only logical explanation I can see, having thought through this some more, is one whereby longsufferingropeholder's mates get a positive LFT result, take another of the LFTs in their pack to see if it confirms it, and then if they get a second positive, they don't bother with a confirmatory PCR because they assume the likelihood of it coming back negative is so low that it isn't worth their time to go for test. That would make some sense.

The alternative explanation of course being that lots of people don't understand that they should get the result confirmed before isolating for the full ten days.

It doesn't really matter much, I just find the numbers surprising.

Post edited at 12:45
 wintertree 27 Apr 2021
In reply to neilh:

> Agreed. My understanding is that Vallence considered it was important that Johnson and others in making political decisions heard those views as a counter view point. I am confident that Vallence did not support them- as I am sure you are..

I understand the importance of considering different views. 

Where I struggle -severely - is understand the rational to present those whose alternative views are built on a tower of lies and falsehoods.  

There are people out there who have different views on how this should be handled, who recognise what this would involve and who accept that.  I disagree strongly with them based on my morals and my ethics and what kind of world I want my children to grow up in, but they present an honest case.  G & H present a fantasy built on falsehoods.  It's not an alternative view, it's a fiction.

In reply to wintertree:

> Where I struggle -severely - is understand the rational to present those whose alternative views are built on a tower of lies and falsehoods.

I wonder if Johnson et al had been banging on about having heard stuff about H, G et al, Vallence said "okay, let's get them in to present their case", in the hope that they could then put their claims firmly to bed. Just to shut Johnson up on the H & G argument.

 wintertree 27 Apr 2021
In reply to captain paranoia:

Makes sense.  I can't see me lasting the first day if I had Vallence's job.  

In reply to Si dH:

> longsufferingropeholder's mates

Point of order; "Colleague".

In reply to wintertree:

> I can't see me lasting the first day if I had Vallence's job.  

These cows are very small. Those are far away.

Small. Far away...

 Si dH 27 Apr 2021
In reply to captain paranoia:

> I wonder if Johnson et al had been banging on about having heard stuff about H, G et al, Vallence said "okay, let's get them in to present their case", in the hope that they could then put their claims firmly to bed. Just to shut Johnson up on the H & G argument.

I think this is a good logic and I'm glad Vallance sees it as part of the job - it's impossible to stop all sorts of guff being reported in the media so rather than just present his own (Sage's) viewpoint to ministers, if he is confident the guff doesn't stand up to scrutiny then why not bring the protagonists in and have them present it themselves and be interrogated.

 wintertree 27 Apr 2021
In reply to Si dH, captain paranoia, neilh:

Before we get too far in to theorising what Vallance was doing, I note that the byline times article suggests Sunak organised the meeting, not Vallance.   Byline aren't forthcoming with their source for that - neilh, do you have a solid source for your counter-claim?

Reports of this meeting at the time mentioned Sunak and not Vallance, and suggested it contributed to the PM going counter to his scientific advisors on a "circuit breaker"

The Byline Times article also suggests meetings were held on the same day between the PM and various right wing media leaders.  Including the editor of the Spectator.  

I don't exactly look forwards to the next round of orchestrated leaks in the power play that's going on around the leadership, but I dare say it could be illuminating.

> I think this is a good logic and I'm glad Vallance sees it as part of the job - it's impossible to stop all sorts of guff being reported in the media so rather than just present his own (Sage's) viewpoint to ministers, if he is confident the guff doesn't stand up to scrutiny then why not bring the protagonists in and have them present it themselves and be interrogated.

I disagree.  There are thousands of people out their with utter guff.  Should we parade them all in front of the PM for his scientific advisors to question?  This is not effective nor efficient. At a time we were loosing control of cases, the PM was spending his limited time with a group of people who have consistently lobbied against the public interest on both sides of the Atlantic.  He either trusts his scientific advisors or he needs to replace them - parading select guff for the PM to watch Vallance question them and wasting everyone's time would IMO be a recognition of a failure of the systems.

Somewhat academic if this was actually arranged by Sunak to bring pressure to bear on the PM to go counter to his own scientific advisors.

Oh to have been a fly on the wall.

 wintertree 27 Apr 2021
In reply to wintertree:

Gone down a rabbit hole now on BTs excellent dissection of the people involved in the latest open letter [1].  Links to Russian backed misinformation over Syria that I wasn't previously aware off.

The article links to a peer review of a recent paper submitted by Henhegan and others [2]. I'm loving the peer review as well - the reviewer is a legend and I am gong to send them an email thanking them for their efforts.  Two choice quotes below but for anyone who has been on either end of peer review, I highly recommend reading it in full.  It's gold.  I wonder what the hell the postdoctoral staff at CEBM think about all this?  I don't know if they've been chosen for political alignment to their leadership or if they're worried about the immolating reputation attached to their current employer.

  • Clearly, this is fantasy, since it also [logically] implies that SARS-CoV-2 is sentient and is aware of the current WHO convention for dichotomising respiratory particle size.
  • Finally, I do not think it would be appropriate – and I don’t want to risk wasting your time in reading yet further comments – for me to undertake any further point-by-point discussion/review of the conclusions which you have drawn from your chosen methods, since it is my contention that your chosen methods are so importantly flawed that the present manuscript should be completely re-written using methods with greater scientific validity, and including the whole range of available data towards SARS-CoV-2 transmission, as described. I hope this seems reasonable.

[1] https://bylinetimes.com/2021/04/27/mendacious-approaches-great-barrington-group-letter-co-signed-by-government-advisors/

[2] https://f1000research.com/articles/10-232/v1#referee-response-82591

Post edited at 18:10
 bruxist 27 Apr 2021
In reply to wintertree:

That peer review is supremely disdainful. The point about implied sentience is devastating. I think Heneghan's just going to jump ship, like Niall Ferguson before him, to a post at a U.S. uni paying a U.S. salary.

 wintertree 27 Apr 2021
In reply to bruxist:

I think the point on their methods as applied to measles was more blunt in some ways.  I also appreciated the reviewer hi-lighting the direct contradiction between different papers from co-author Jefferson. 

>  I think Heneghan's just going to jump ship, like Niall Ferguson before him, to a post at a U.S. uni paying a U.S. salary.

Indeed.  I'd not really been aware of the CEBM before Covid came on the scene.  It's enough to make a curios person wonder about some of their previous outputs, especially where there is obvious overlap with certain US interests.

In reply to wintertree:

From the peer review:

No evidence is presented for this hypothesis, and on the basis of universally applicable physical laws, it is impossible.

ouch.

Post edited at 21:29
 wintertree 27 Apr 2021
In reply to wintertree:

Going back to this temperature post, having established a linear relationship between the rate of change of temperature and the rate of change of the exponential rate constant, the gradient of the linear fit between them translates directly to the datasets before differentiation.  This can be used to convert temperature in to a "temperature dependant component of the rate constant", which can be subtracted from the measured rate constants to reveal the baseline rate constant before the effects of temperature.  A constant of integration is lost in this process, so the resultant curve is not anchored on the Y-axis.   The plot below shows the actual rate constant after some filtering (black), and the result of subtracting the temperature dependant part using the model linear fit calibrated in the period before schools opened (green.  The vertical position of the green line is arbitrary due to the missing constant of integration, so it only really tells us about stability or change in the temperature independent baseline of the exponential rate constant.    This is by no means a robustly justified approach, but it's illustrative and it suggests to me that there's been a gradual weakening of the baseline decay since Jan 1st - which tallies with e.g. traffic and public transport data discussed many threads ago.  It's hard to understand what's happening when schools opened.  Hopefully the HadCET data will appear soon for April and I can update all this, and I'm still hoping to look at late last summer and throw a simple pre-print together on it.

Post edited at 21:51

In reply to wintertree:

Something I’ve been wondering. How much difference would a circuit breaker have made? Especially if we assume that Kent would  have popped up anyway (of course that’s the bit we don’t know). Certainly would have made some difference but don’t think it would have avoided subsequent lockdowns. Perhaps a series of 2-4 week firebreaks at best.

Retrospectively, what would have made a difference? No overseas leisure travel last summer, no indoor hospitality, better T&T with proper financial support for those unable to work due to self isolating, tougher and faster tiering in hotspots, a more considered approach to the return of schools and universities. Probably a few other things.

Lockdowns are just tactics to deal with effects. There was never a strategy to address the causes. That’s the real issue - it was ‘back to normal by Xmas’. I fear it will happen again, despite the vaccination drive...

Post edited at 02:29
In reply to Misha:

It will happen again, but we have tons of PCR machines, vastly scaled up vaccine production infrastructure, a public that will accept not going out, all things we didn't have a year ago. We can do pandemic now. Still done cock all to prepare for giant fire breathing lizards though. It's like we've learned nothing.

 wintertree 28 Apr 2021
In reply to Misha:

> Something I’ve been wondering. How much difference would a circuit breaker have made?  [...] Certainly would have made some difference but don’t think it would have avoided subsequent lockdowns

Impossible to say without access to alternative timelines, as the emergence of variants and all political decision points would differ along that road not taken.

My noddy first order view on your question is that if we'd had two weeks of decay instead of growth (due to the firebreak) and then we went back to the exponential growth rates as before, we'd have been about three weeks(*) further ahead with the vaccination program when the big peak followed by lockdown came.  This would have made a material difference, but then again so would locking down two weeks sooner around New Year.  

> Retrospectively, what would have made a difference? 

I think there's been a significant shift in messaging towards ventilation in recent months.  If I had a time machine, I'd go back to March 2020 and I'd institute the "Window Police" and unleash them on workplaces and public transport.  

(* assuming cases fell with a halving time twice the duration of the doubling times bracketing the firebreak, adjusted for cause/effect/detection lag times).

In reply to Longsufferingropeholder:

I think we now have a public which sees sense in a short(ish), hard(ish) lockdown early on. Not sure everyone in government would agree though. 

In reply to wintertree:

I was going to say, we could look to Wales as they had a firebreak. However in reality they just had a slightly earlier and shorter second lockdown and then went into the third lockdown slightly earlier as well (which England should have done as well). So not surprising that their experience has been similar.

 Si dH 29 Apr 2021
In reply to Misha:

My view of Wales' policy at the time was that it went very badly. The problem was that after only 2 weeks in lockdown it was impossible to see how much rates had really fallen, and with hindsight it was possible to see that rates in some areas, mostly the old mining areas in the south, were still high. They unlocked anyway because that had been the plan the leadership had said out beforehand rather than because the data suggested it was sensible, and did it too fast. As a result the rates immediately rocketed and parts of South Wales were at rates of 1000/100k per week very soon after the end of lockdown.

This says nothing about whether a firebreak could theoretically help, but it does present some practicable challenges: (1) the need to understand the impact of the changes more quickly than we are usually able in order to take action in an informed way and (2) a firebreak that ends too suddenly and results in a major change in behaviour at once will backfire.

I personally think what we needed was the lockdown and release strategy taken in England, but implemented a bit earlier at the time a firebreak was discussed. Problem is compliance would have been por because Govt messaging last summer had been all about opening up and not about the reasons for caution. And then more importantly of course, a willingness to react faster and change plans after that when we realised rates hadn't dropped in the south east.

Post edited at 07:08
In reply to Longsufferingropeholder:

> It will happen again, but we have tons of PCR machines, vastly scaled up vaccine production infrastructure, a public that will accept not going out, all things we didn't have a year ago. We can do pandemic now.

We also have a population that think they're invulnerable because they've had a jab, want to do fun stuff they've not been able to for a year or so, and have used up all their savings.  It will be very difficult for them to accept they're back to square 1, and we still don't have financial & policing mechanisms for making people actually stay at home.

In reply to wintertree:

> Ventilate even when it's cold.

I've been struggling all week and still can't get my head around why the fit is so good with the differential of temperature. Less transmission when it's getting warmer doesn't sit right.
What else changes when it's getting warmer and has notably been up and down a ton in recent weeks?......???....?
Humidity data seem to be available in the same place but looks like more of a faff to extract, and it's a bloody tenuous thought at best so I'd recommend not looking too hard before dismissing.

Edit: Found this: https://idpjournal.biomedcentral.com/articles/10.1186/s40249-020-00708-0
Edit again: And this: https://www.tandfonline.com/doi/full/10.1080/02786826.2020.1829536

Sunlight. There's sunlight when it's getting warmer. That's a much more sensible thing to blame. "Sunshine duration" is an available dataset too.... :-/

Post edited at 18:05
 wintertree 29 Apr 2021
In reply to Longsufferingropeholder:

This is speculation on my behalf not evidenced.

I don’t think it’s the rate of change that’s the causal factor.  I just think that the differentiation is a high pass filter that rejects baseline drift in the exponential rate constant unrelated to the temperature.  Then, we’ve had quite cyclical weather patterns so things aren’t as independent as the could be.

In reply to wintertree:

To look at your idea more broadly, could you look at regional temperature records and case data? 
at various times different bits of the U.K. have been slightly out of step in terms of the case growth picture - does regional weather explain part of this?

 wintertree 29 Apr 2021
In reply to Dr.S at work:

> To look at your idea more broadly, could you look at regional temperature records and case data? 

> at various times different bits of the U.K. have been slightly out of step in terms of the case growth picture - does regional weather explain part of this?

It’s a good suggestion.  Funnily enough I started trying to write this up formally last night and began with the “limitations” list; one of which is regional data.  There’s no public access to PCR only data at the regional level AFAIK and I’m wary of the confounding effects of LFD data at the regional level.  

I think my limited time is probably better spent trying to put a clear, coherent pre-print out drawing attention of this to the right people than in doing increasingly detailed analysis of the confounded public data.   I mean, the rabbit hole is open and beckoning but still, I feel the analysis is worth doing properly and I am not positioned to do that.  Sticking to the England PCR only level I can make a clear, concise and I believe credible case that this warrants more investigation. 

In reply to wintertree:

I did a bit of a delve into the literature and didn't find anything with a different message than those papers above. I.e. either in vitro or 'we think there's something there but it depends how you squint at the data'.

It needs some proper analysis, real world, up to date, knowing what we didn't know 6 months ago. That is what doesn't seem to exist.

 wintertree 29 Apr 2021
In reply to Longsufferingropeholder:

Well I’m not much of an epidemiologist but perhaps I can show them how to squint at the data.

The behavioural aspect is very interesting - and complicated - given the way people track the seasons and respond to a day that is exceptional for the season if not the year.

In reply to Si dH:

That is a very good point about unlocking before understanding the impact (or lack thereof). Which rather suggests that a 'firebreak' needs to be longer than a couple of weeks - more like 4 weeks. Which is what England had in November and perhaps it would have kind of worked if it wasn't for Kent (plus it was implemented too late as you pointed out). Realistically, we would have needed a series of firebreaks but 4 weeks on, 4 weeks off (say) is better than 4 months on...  Also, a firebreak implemented early on need not have been as drastic as the lockdown we actually had (in particular, schools and a few other things may have been able to stay open, perhaps).

It just goes to show that even with hindsight it's difficult to say what would have 'worked'. I think the reality is that due to unrealistic expectations, the lack of a strategy, the poor contract tracing and lack of support for self isolating, the holiday travel last summer and umpteen other reasons, anything done in the autumn would have been insufficient anyway (and even then they didn't take the necessary measures until too late, which just made a bad situation even worse).

I fear there will be a repeat of this in the coming months. It's not just the government, it's generally sensible people who seem to have decided (just like they did last summer) that Covid is 'over'. Witness people already returning to their offices, for example.

In reply to Toerag:

> We also have a population that think they're invulnerable because they've had a jab, want to do fun stuff they've not been able to for a year or so, and have used up all their savings.

It's an unequal pandemic. Some have used up their meager savings and therefore have not choice but to go back to work, unless they happen to be on furlough. Others have saved up a fair bit of money because there wasn't anything to spend it on and are now eager to spend it on going out etc, which is good in some ways but is going to be an issue in other ways, especially once indoor hospitality opens up.

In reply to wintertree:

Apologies if I missed this but do your graphs adjust out the delay between date of infection and specimen date? This is probably around a week. I believe it's 5 days on average to showing symptoms, though that's a number I picked up way back last year so there may be more accurate information available now but at any rate it's going to be a few days. Plus a day or two before people get round to getting a test.

Sunlight isn't going to impact on indoor environments very much so I'd be surprised if that's a significant factor.

In reply to wintertree:

Going off topic here but Macron announcing relaxations in the coming weeks and ending all restrictions other than nightclubs, while average daily cases are over 20k... Increasingly, I think it's not just the Trumps, Bolsonaros and BoJos of this world, it's most politicians (outside SE Asia, Oz and NZ ). They just can't deal with the fact that Covid isn't going to magically go away. Oh well, wasn't planning any overseas holidays this year anyway...

 Si dH 30 Apr 2021
In reply to Misha:

> Going off topic here but Macron announcing relaxations in the coming weeks and ending all restrictions other than nightclubs, while average daily cases are over 20k... Increasingly, I think it's not just the Trumps, Bolsonaros and BoJos of this world, it's most politicians (outside SE Asia, Oz and NZ ). They just can't deal with the fact that Covid isn't going to magically go away. Oh well, wasn't planning any overseas holidays this year anyway...

The mainland European approach is going to be an interesting test of the benefits of partial vaccination and summer weather over the next few months in the face of relaxations while case loads are still very high. Draghi has even publicly admitted he is taking a gamble but many countries incl France are doing similar. They should have vaccinated the most at-risk groups because the EU vaccination rate has been improving so presumably they think it's worth the risk of higher cases to relax restrictions and are hopeful deaths will stay low.

 wintertree 30 Apr 2021
In reply to Misha:

> Another one to add to your variants graph? 

Two more "India" variants appeared yesterday on the webpage [1].  I've added the larger valued one to the plot.

I know you know this, but I like to repeat it on all the variants plots - they're not one we can interpret very well as they involve surge testing and testing on arrivals, so continued exponential growth in numbers on here against a backdrop of consistently falling PCR cases in pillar 1 and pillar 2 doesn't necessarily mean that infections of variants are growing exponentially.  As I've said before, if they're not growing then there's only so much growth in data surge testing can generate before the infection is chased down.  

Perhaps that's what's happening with VUI-21FEB-03 (red), a variant first sequenced in the UK I believe that is now levelling off suggesting perhaps that it's been run to ground.   Perhaps the same is happening with the SA strain (black).  As well as the obvious tupping over in the curves, the measured doubling times have increased since last Saturday's update - although it's not really that sensible to measure a doubling time from these curves it still tells us they're backing off.

The Manaus curve (Blue) is showing slightly faster exponential growth than last Saturday, but again that could mean anything across the gamut from "bad: spreading against a background of decay" to "good: enhanced contact tracing and surge testing is mopping it up".  Without a lot more context, who knows...    Perhaps we can infer from the red and black curves that sustained exponential growth for more than 40 days is when it would tip over in to definitely bad, but even that's a bit close to phenomenology for my liking. 

Doubling time of 11.1 days on the first India variant.  There's one point in each of the red and black curves where the gradient on the log plot (same gradient => same doubling time) was that fast, perhaps related to surge testing.    It's also worth keeping in mind that India only went on the red list for travel 7 days ago ( 6 days before the date of the latest data on the plot).  The absolute numbers are low - ~200 cases total (this is a cumulative plot, not daily rate).

It's really hard to interpret this data without knowing a lot more about it; I'm happy to see the red curve apparently tipping over.

[1] https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data


 Si dH 30 Apr 2021
In reply to wintertree:

Thanks for the update. I guess we might expect the Indian variant count from travel to grow much faster than the equivalent growth of south African or Brazilian variants due to the greater links between the countries, and more so to date because of India only just going on the red list. I agree it's impossible to interpret usefully for that variant without knowing how much community growth is contributing to each. Will still be useful to monitor it, hopefully it will turn over like the red one has.

I just did a bit more background reading into those new ones that have been added. Ironically more cases of b.1.617.2 have seemingly already been sequenced in the UK than in India...

Post edited at 18:03
 wintertree 30 Apr 2021
In reply to Si dH:

Partly in response to your post on the other thread, it would be interesting to see a breakdown of strains sequenced from inbound travellers from India and neighbouring countries from the period leading up to India's red listing.


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