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The Coronavirus Discussion Thread.

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Very and Effective are fairly vague… my shower cubicle isn’t very well sealed for example (its got a good 15cm gap at the top) … if I take a shower with the room closed then the mirror a meter away might get slightly damp after a while from the steam.(looks good enough to shave).. but as soon as I open the shower door all the steam spills out everywhere. It doesn’t seem like an effective barrier but it actually does a fair job.

Perhaps you could do with some ventilation? 🤔🤭

Thanks for the set up 🙃

I need to go read the guidance in more detail and check out the source studies referenced. But I’d need to switch on the work computer for that and I’m deliberately distancing myself from ‘work’ today...

This isn’t the only way people have died from the virus though is it?

Aren’t they linking a case of Kawasaki Syndrome to it as well?


 
Posted : 16/05/2020 7:39 pm
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we needed a bit of extra freedom to combat the unintended consequences of full lockdown

Well if an 'unintended consequence' is holding up wave 2 too long then you might have a point.

There will always be some idiots but that will have been taken into account in the planning.

To reverse the Darth Vader quote:

"I find your surfeit of faith disturbing".


 
Posted : 16/05/2020 8:05 pm
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There will always be some idiots but that will have been taken into account in the planning.

It's the idiots in the planning that worries me


 
Posted : 16/05/2020 8:20 pm
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Well if an ‘unintended consequence’ is holding up wave 2 too long then you might have a point.

https://www.theguardian.com/society/2020/apr/29/extra-18000-cancer-patients-in-england-could-die-in-next-year-study

Among others.

I’m not claiming one is worse than the other. I don’t have the information to know.

Anecdotally, SWMBOs Uncle is now more or less paralysed (some sort of growth in the neck) and is unlikely to get any treatment for some time. Lost her Grandad to CV19 the same week, so shit all round.


 
Posted : 16/05/2020 8:31 pm
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It seems like today’s daily briefing hit a staggering new low in ministerial barrel-scraping.

Having watched Gavin Williamson/Frank Spencer... he is actually the education minister? Seriously?

The man can barely string a coherent sentence together


 
Posted : 16/05/2020 9:07 pm
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TiRed

You are correct. But people are presenting late with pneumonia, coagulopathy, and so on after they’ve already seen some hypoxia. We are looking at treatments at each end of the spectrum, but I’m sure early is likely to be more successful. Maybe early oxygen reduces the inflammatory cascade in the lungs?

I'm all for early though that does seem to be an achillees heel for the UK. (You mentioned as much earlier)
I'd seen some (speculative) observations of the hypoxia being more like altitude sickness than pneumonia with the same physician speculating higher pressure forced ventilation was possibly/partly responsible for the damage and low pressure oxygen being preferable. (At a time Boris was in on oxygen)

We do know that mopping up some inflammatory signals works when patients are severe. Two antibodies are approved for arthritis and neutralise IL-6 signalling. One (sarilumab) showed a positive response in a small trial against placebo with a severity endpoint at the highest dose tested. That’s encouraging.

There is a lot encouraging ... it seems to me not so much actual understanding that enables pre-emptive identification of specific risks and action.

For example if someone is on immuno-suppressants (either explicitly or as a byproduct) would changing their medication type/dose etc. help? For those of us who could be on them (I have a personal interest) .. are certain haplotypes more at risk of one or the other? [is anyone even doing genetic testing against symptoms or are we cremating the evidence]?
Lots of talk of "pre-existing" conditions but what exactly does that mean in terms of early treatment or even pre-emptive?

metalheart

Aren’t they linking a case of Kawasaki Syndrome to it as well?

something "like" ... though that seems part of the immune response branch.

Perhaps you could do with some ventilation?

Well ... yep though it's really a case of fixing/replacing the fan so it doesn't wake up the OH...(Meaning I usually have to switch it off at the times I tend to shower) 😉


 
Posted : 16/05/2020 9:17 pm
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I’m not surprised AA is a little techy

FFS TJ! You’re hardly going to calm him down by referring to him as a technician when he’s a fully fledged teacher, while at the same time calling him a shortarse.


 
Posted : 16/05/2020 9:20 pm
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FFS TJ! You’re hardly going to calm him down by referring to him as a technician

I was going to correct the spelling but i r sciance teacherist and speelling isnt a strength.


 
Posted : 16/05/2020 9:31 pm
 myti
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Well if an ‘unintended consequence’ is holding up wave 2 too long then you might have a point.

Well yeah exactly we don't want wave 2 in December plus flu do we?!


 
Posted : 16/05/2020 9:51 pm
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It's all been very calm and sensible around the local honey pots. 👍

Question, are the daily reported new cases a genuine indicator of new cases?
Are these spread across a period of days dependent upon test date/return etc,
I'm looking at 'lab confirmed daily cases by specimen date in England' on the gov website and the data doesn't seem to align with any thing else reported???


 
Posted : 16/05/2020 9:56 pm
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Lolz @ thegreatspe


 
Posted : 16/05/2020 10:02 pm
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So, I note that the code that Ferguson’s team wrote which was used for the models to justify the lockdown strategy has been described as a buggy mess. No wonder he has a track record of making terrible forecasts (swine flu, BSE, etc).

Thoughts on this? (article is only on The Telegraph at the moment, but I’m sure other papers will pick it up soon).

JP


 
Posted : 16/05/2020 11:56 pm
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This is reporting a code review on Toby Young’s lockdown sceptics website. I will say that academic coding is not professional coding. And that there were plenty of analyses and models predicting the same thing, some of which were data not assumption-driven. The decision to lock-down was robust based on an expectation of overwhelming healthcare and the precedence set by Italy and Spain. The case fatality rates in that model have turned out to be reasonable, we have not seen the high prevalence the naysayers would like. We will see about 75k excess deaths WITH the lockdown just from the first wave. It’s not a hard extrapolation to several multiples of this total had we not done so.

The concentration of these deaths in the elderly and additional mortality (which I do not believe is as significant as many will make out), is the tragedy of policy choices. Drive by lack of testing capacity and limited PPE in care homes. We had an opportunity to act earlier, perhaps with a less severe lockdown. We did not.


 
Posted : 17/05/2020 1:44 am
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Completely agree with that assessment TIRED. I would be more empathetic towards the government if we hadn't been screaming at them for weeks to act before they did by which point it was far too late.


 
Posted : 17/05/2020 8:18 am
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Boris Johnson accepts 'frustration' over lockdown rules

I think that's as close as we're going to get for him saying he ****ed it up. Unfortunately hes still living in anything but the real world:

But Mr Johnson said he trusted the "good sense of the British people" to observe the new rules and thanked the public for "sticking with us" so far.

What is it now, a week or so before the second spike numbers start to roll in?


 
Posted : 17/05/2020 9:02 am
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will say that academic coding is not professional coding.

Yep think of it as a smarter fag packet 🙂

It doesn’t need to be great just work enough, if he’d have spent another two weeks polishing his code 🙁


 
Posted : 17/05/2020 9:08 am
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What is it now, a week or so before the second spike numbers start to roll in?

Will the spike show soon enough to put a halt to schools reopening on 1st June?


 
Posted : 17/05/2020 9:16 am
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Unfortunately hes still living in anything but the real world:

His real world and ours are totally different thou.


 
Posted : 17/05/2020 9:20 am
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I think the Unions will push as hard as they can to delay English schools opening long enough for the figures to start coming in, two weeks should be enough. I know my teacher friends here in Wales are glad their schools aren't opening soon.


 
Posted : 17/05/2020 9:20 am
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The gutter press ramping up the hatred for teachers in this mornings headlines (glanced over them at petrol station this morning)


 
Posted : 17/05/2020 9:24 am
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His code is literally decades old and appears to be extremely unstable and crappy (from what I saw somewhere, it's not reproducible due to parallelism, which if true is shockingly incompetent practice). He should have published it years ago. However, this is not the source of the problems in the modelling.

In the geosciences we have:

https://www.geoscientific-model-development.net/

expressly for this purpose


 
Posted : 17/05/2020 9:25 am
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How can schools be going back and yet the LDNPA and Yorkshire Dales etc are saying please dont come, makes no sense to me. Its a logic fail, had Boris said game on get back to it for all it would make sense but its a hard sell to say I can eat out in a socially distanced restaurant but schools will open, its blatant bull shitting. However the gov picked this fight because they want to distract the plebs, they could have released guidance to schools and said be ready at a weeks notice after a 3 week prep or something and avoided all this shite.


 
Posted : 17/05/2020 9:31 am
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TiRed
...We had an opportunity to act earlier, perhaps with a less severe lockdown. We did not.

We being the govt, and if they were a business then the directors and management would be all going to goal for that amount of deaths.

Which raises the question of the liability of the private care home owners.

They can't claim they didn't see this coming. We have a practise run with every year's flu epidemic. Some managed by good planning to totally avoid any CV deaths.

Can we expect some criminal proceedings against them?


 
Posted : 17/05/2020 9:33 am
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Damien Hinds on BBC news sounding like a normal human being on schools going back.


 
Posted : 17/05/2020 9:40 am
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I believe there may be action taken against the owners of Home Farm on Skye


 
Posted : 17/05/2020 9:41 am
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Care Home blame? There is plenty to go round. Case 1 in a local care home was a resident who went to hospital for IV antibiotics and was returned some days later to the home without being tested. So is that the fault of the care home for not managing the outbreak or the NHS for seeding it?


 
Posted : 17/05/2020 9:51 am
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Some might have acted negligently but my dads care home locked down on the 12th march while the goby was still claiming there was little risk to them.

Afaik they haven’t had a case yet.


 
Posted : 17/05/2020 10:00 am
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Care Home blame? There is plenty to go round. Case 1 in a local care home was a resident who went to hospital for IV antibiotics and was returned some days later to the home without being tested. So is that the fault of the care home for not managing the outbreak or the NHS for seeding it?

While people need to be held to account, I'm really worried that we will be so distracted by the blame game that blessings that need to be learnt will get lost. I'm not sure how we walk that tightrope.

Plus, do we really want the legacy of this crisis to be courts getting bogged down in litigation and (a few) lawyers getting fat.


 
Posted : 17/05/2020 10:08 am
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His code is literally decades old and appears to be extremely unstable and crappy (from what I saw somewhere

Thirteen years old and calibrated for influenza transmission against previous epidemics (including 2009 H1N1). Then applied to COVID19 based on the mixing patterns and population numbers in the model and some guesses about duration of infection and transmissibility. Those guesses were likely off by some margin from Wuhan, and refined by data from Italy.

Personally, as you have found, simpler models are equally able to be reproduce the epidemic curves right down to authority level, and are useful for near-term projection. But people confuse sophistication with precision.

When I joined Pharma I switched from C++ to coding in SAD/R/python so that the code was easily understood by others. My code gets reviewed line by line by the FDA and EMA, so it had better be reproducible!

I think arguments about the code are a bit of a distraction to be honest.

[TL:DR] Robust decisions are not sensitive to the models used for prediction. All projections by any means were bad, and lockdown a reasonable response.


 
Posted : 17/05/2020 10:28 am
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There is however a critical detail that has been missed by most, and which is being actively covered up by the modellers. They got the doubling time badly wrong, and stuck with it for far too long. That's not a problem of the model coding per se, it's the parameters they put into it. They told the govt that it had plenty of time, until suddenly they did a u-turn and said oops too late.


 
Posted : 17/05/2020 10:30 am
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Which raises the question of the liability of the private care home owners.

They can’t claim they didn’t see this coming. We have a practise run with every year’s flu epidemic. Some managed by good planning to totally avoid any CV deaths.

They may have seen it coming but then were not only given advice that "this wasn't what they had prepared for" but fed misleading information.

Even if they wanted they were forced to take infected patients whilst the government actively prevented them buying PPE.

Can we expect some criminal proceedings against them?

Well there were plenty of civil cases for the ones that locked down...
From a simple economics perspective it seems to me that they wouldn't deliberately mass kill their source of income?


 
Posted : 17/05/2020 10:35 am
 DrJ
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There is however a critical detail that has been missed by most, and which is being actively covered up by the modellers. They got the doubling time badly wrong, and stuck with it for far too long.

If you know it, they didn't do a very good job of covering it up, right?

I've published papers based on numerical models of geo-systems and I'd hate to be judged on the elegance of the code, or for real life decisions to be based on the results. I did my best, but someone using it alone without checks would be grossly negligent.


 
Posted : 17/05/2020 10:38 am
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What is it now, a week or so before the second spike numbers start to roll in?

What if there is no spike?

Care homes are all now much more clued up - and that's where a lot of the deaths were occurring.

A few clueful employers might start insisting on people staying at home if they feel rough, rather than coming in to work and "toughing it out".

General anxiety anyway.

Vitamin D levels in most people will be rising, since it's summer again. This probably helps white people more than anyone with a dark skin.


 
Posted : 17/05/2020 10:38 am
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TLDR but has anyone questioned why supermarkets are explicitly mixing the most vulnerable with the most infected?


 
Posted : 17/05/2020 10:38 am
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Blaming care home bosses for deaths due to following government advice is like blaming a first world war lieutenant for the failure of military strategy at the Somme.


 
Posted : 17/05/2020 10:39 am
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What if there is no spike?

I am certainly no expert but I dont see a new spike coming just yet, but we could well see a flattening of the rates at a higher level. The second wave will come when we return to "normal" and are starting to forget about it.


 
Posted : 17/05/2020 11:01 am
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They got the doubling time badly wrong, and stuck with it for far too long. That’s not a problem of the model coding per se, it’s the parameters they put into it.

Not a cover up. But the problem I see is that the committee was populated by groups with perhaps an over-reliance/belief on the utility of models. Were this influenza, things would have been fine, because the committee, advisors, technology etc, were all calibrated for influenza.

We have seen that early in an epidemic of a new pathogen, data is king, assumptions and parameter estimates come later (I still don’t believe R values btw). My first estimate of doubling time for the global epidemic was March 16. In truth, I may have gained an extra week if I’d started earlier. No more than that.

The epidemic was doubling every 3 days. If the infectious generation time is 7 days, then R is about R ~ 1 + 7 Ln(2)/3 = 2.6, but we don’t actually know the 7 days. We DO absolutely know the doubling time was 3 days VERY precisely.


 
Posted : 17/05/2020 11:06 am
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Having watched Gavin Williamson/Frank Spencer… he is actually the education minister? Seriously?

The man can barely string a coherent sentence together

He's far better threatening a straw man of his own making China with a non-existent navy.

That's the key problem with the current bunch of swivel-eyed loons and political opportunists who have ended up in charge via some kind of reverse meritocracy. No some real shit is happening and they look like what they are. Bullshitters and frauds.

But at least we have Trump to laugh at, I mean at least we're not the most ridiculous nation on earth, so that's something, right?


 
Posted : 17/05/2020 11:09 am
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If R is 2.6 (which is very believable given how well hidden the virus is in many people) then we are doomed to a long cycle of lockdown-release-lockdown-release.

Basically managed herd immunity.

Unless......vaccine.


 
Posted : 17/05/2020 11:12 am
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Sorry, if R = 2.6 (undiluted) then I think that means you need 60% of the population to be immune to stop overall spread.....?

So we are looking at c.350k deaths overall in the UK(?)


 
Posted : 17/05/2020 11:16 am
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Hopefully not. Given advances in therapy, management, and eventual vaccination. Otherwise, yes, but over a sustained period with a net overall reduction in life expectancy that increases again with advances in healthcare. That’s how HIV went (life expectancy for HIV patients has increased 40 years due to treatment).


 
Posted : 17/05/2020 11:32 am
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ended up in charge via some kind of reverse meritocracy.

You get good eggs and you get bad eggs; unfortunately bad eggs float.


 
Posted : 17/05/2020 11:58 am
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martinhutch
Blaming care home bosses for deaths due to following government advice is like blaming a first world war lieutenant for the failure of military strategy at the Somme.

There was plenty warning signs before the govt started bullshitting. There is plenty experience from previous flu epidemics.

The lieutenants weren't the guys responsible for the cost cutting, they were more like the staff working without PPE and not being listened to.

But your WW1 analogy is good, because what was expected of the WW1 troops was to make a suicide charge to the German lines in the hope a few would make it, and that is basically what was expected of our care givers and medical professionals.

Heads need to roll.


 
Posted : 17/05/2020 11:58 am
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What do think of the studies that have shown a correlation between low Vit D levels and the severity of covid 19 immune response?

Frontline medical opinion (the consultants and researcher I'm following on Twitter) is that it's unproven and needs further work but currently they are leaning towards unlikely.


 
Posted : 17/05/2020 12:08 pm
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Vit D

    deficiency

does appear to have an effect on likelihood to get significant chest infections - and there's supporting data for supplementation but that's in the fairly long-term.

Some tempting and unproven vaguely related factors might include:
Older people suffer more from COVID, but women do better than men - look at their osteoporosis prophylaxis (often Ca and VitD)
BAME - darker skins require more uv exposure to make same amount of VitD
Weather generally - we're coming off winter; Aus/NZ just finished summer so might have higher overall VitD
(... could bring you to lockdown and effects of only 1hr a day outside)

(At my place we're measuring VitD levels in admitted COVID pts - mostly because it's easy; not part of any formal trial - but not really sure whether we can "help" if/when we find deficiency. We do supplement cancer patients fairly routinely but again, that's preventitive. As Sandwich's comment, it's a bit of a stretch to get to "take this and you'll waltz off the ICU tomorrow" or even "take this and you'll never be admitted")


 
Posted : 17/05/2020 12:49 pm
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