Coronavirus - Modelling Aspects Only

[johnhemming]

When I have looked at the WHO reports the hotter countries don't seem to have the same issues.

[jfgw]

In any event we will need cooler weather or air conditioning for infections to grow until autumn.

Or more 5G protestors group-hugging. (Darwinism in action.)

Julian F. G. W.

[servodude]

When I have looked at the WHO reports the hotter countries don't seem to have the same issues.

Got any ideas of the ranges of temperature that make any difference to transmission?

What do you consider hot for this context?

Genuinely interested, but slightly sceptical
- seasonal variation in infections is normally attributed to behavioral modifications rather than effect of weather on a virus
-sd

[johnhemming]

There is quite a bit of research on this. It looks like things get quite a bit lower over about 23 degrees centigrade and that peak infection is about 12.

[9873210]

regarding "They estimate that 35% are infectious, but not symptomatic", I wonder how this impacts the effectiveness of the UK govts "track and trace" scheme. This relies on infected people reporting themselves i.e. "But from now on, everyone with symptoms should ask for a test online or phone to arrange a test by calling 119". But if 35% fail to report, because they don't have symptoms and an unknown proportion prefer not to for privacy or other reasons, or even do not realise that they have to report, how effective is this system likely to be?

More effective than not doing it. Measures do not have to be perfect to have a positive impact.

If we keep R below 1 the number of cases decreases and it's a manageable situation. A rational goal is to find the least costly* actions that will do this. Having a cooperative portion of the population self identify, test and quarantine is one of the easiest ways to reduce new cases. Each case avoided reduces R. It may not reduce R enough, and we have to adopt more costly measures as well, but that's no reason not to do the easy stuff.

* balancing money, effort, intrusiveness, hygge, and anything else anybody considers important.

[Mike4]

In a battle between cockup and conspiracy in government cockup normally wins hands down.#

In any event we will need cooler weather or air conditioning for infections to grow until autumn.

Surely that was debunked long ago. Or do you hold that places like Singapore and Malaysia are getting good control of it due to their hot climate? How do hot places with dreadful stats like Brasil fit in with this?

[Mike4]

regarding "They estimate that 35% are infectious, but not symptomatic", I wonder how this impacts the effectiveness of the UK govts "track and trace" scheme. This relies on infected people reporting themselves i.e. "But from now on, everyone with symptoms should ask for a test online or phone to arrange a test by calling 119". But if 35% fail to report, because they don't have symptoms and an unknown proportion prefer not to for privacy or other reasons, or even do not realise that they have to report, how effective is this system likely to be?

More effective than not doing it. Measures do not have to be perfect to have a positive impact.

If we keep R below 1 the number of cases decreases and it's a manageable situation. A rational goal is to find the least costly* actions that will do this. Having a cooperative portion of the population self identify, test and quarantine is one of the easiest ways to reduce new cases. Each case avoided reduces R. It may not reduce R enough, and we have to adopt more costly measures as well, but that's no reason not to do the easy stuff.

* balancing money, effort, intrusiveness, hygge, and anything else anybody considers important.

Totally agree with you. Masks in public are another example, but it seems to be the English way to resist taking any measure until proven perfect, in case sometimes it doesn't work. Desperately frustrating. Masks in public are cheap as chips to implement and have virtually no downside, yet there are endless arguments here resisting the use of them.

If we just took all the imperfect but obvious measures available to us immediately (stopping inbound travel, locking down hard and early, masks in public, a phone app, manual contact tracing) like the Asian countries e.g. Malaysia instead of insisting everything is gold plated first, we could have had this thing licked long ago. These measures would have looked like an overreaction taken early but our economy would have had suffered only a small fraction of the damage being done now.

[servodude]

In a battle between cockup and conspiracy in government cockup normally wins hands down.#

In any event we will need cooler weather or air conditioning for infections to grow until autumn.

Surely that was debunked long ago. Or do you hold that places like Singapore and Malaysia are getting good control of it due to their hot climate? How do hot places with dreadful stats like Brasil fit in with this?

I'm taking this with a similar does of salt

We've not had this a year yet and i think it would be too easy to look at the spread of the infection and overlay what would appear to be a natural pattern on it

The outbreaks we've seen have followed people around the globe not the seasons (well not directly - but yes you might contract it on a ski-ing holiday)

in cases where there have been super-spreader incidents the actions of the individual in question and their contacts has been what has driven the infection; these normally involve workplaces, care homes, night clubs, bars, dinner parties
- not cold places

some of what are considered "hotter" countries had exposure to SARS, MERS, Bird Flu, Swine Flu in recent times and did take quick action to isolate and and impose social distancing measures
- would it not seem reasonable to consider this action might be the moderator rather the temperature?

- sd

[servodude]

Totally agree with you. Masks in public are another example, but it seems to be the English way to resist taking any measure until proven perfect, in case sometimes it doesn't work. Desperately frustrating. Masks in public are cheap as chips to implement and have virtually no downside, yet there are endless arguments here resisting the use of them.

If we just took all the imperfect but obvious measures available to us immediately (stopping inbound travel, locking down hard and early, masks in public, a phone app, manual contact tracing) like the Asian countries e.g. Malaysia instead of insisting everything is gold plated first, we could have had this thing licked long ago. These measures would have looked like an overreaction taken early but our economy would have had suffered only a small fraction of the damage being done now.

I absolutely agree that it does not need to be perfect - every little bit helps

It's always seemed to me like it's a big messy stochastic system with two main components

They can probably be best described as:
- the probability of exposure
- the probability of transmission

Probability of exposure is simply how likely you are to encounter the disease
- it's a function of the prevalence of the disease in a population
- and the behaviour of that population (specifically the amount of interactions)

This is the part of the "system" that a "lockdown" attempts to address by reducing the number of interactions with other humans
- it has an immediate limiting effect on the spread of a disease as it cannot move beyond the confines of a home (if adhered to)
As "lockdown" regulations are relaxed this aspect of the "system" can still be addressed by continuing to limit interactions (wrt normal exposure) along with tracing and quarantine of suspect/known cases - and yes an app might help here

Probablility of transmission
This is a function of our behaviour (during interactions) and the properties of the disease

We can't affect the time the virus survives suspended in moisture droplets or how it sits on surfaces but we can modify how we act based on what we know or suspect about it
- maintaining distance during interactions, keeping them as brief as possible
- hygiene: sneezing/coughing etiquette (conscientious isolation)
- amount of air expelled from lungs (stop SHOUTING!)
- wearing masks in public
- a vaccine or having gained immunity
- etc etc

Bringing either of those probabilities down decreases the likelihood of the disease being passed on

- sd

[stockton]

If we just took all the imperfect but obvious measures available to us immediately (stopping inbound travel, ...............

Just in case anyone is in charge during the next pandemic - controlling inbound travel is sensible, stopping inboard travel is not.

[johnhemming]

Surely that was debunked long ago. Or do you hold that places like Singapore and Malaysia are getting good control of it due to their hot climate? How do hot places with dreadful stats like Brasil fit in with this?

This document from the WHO is a reasonably good indicator
https://www.who.int/docs/default-source ... 5b154880_2

Places like the USA and Brazil need detailed consideration based upon the localised climate and to what extent air conditioning is used.

[Mike4]

Totally agree with you. Masks in public are another example, but it seems to be the English way to resist taking any measure until proven perfect, in case sometimes it doesn't work. Desperately frustrating. Masks in public are cheap as chips to implement and have virtually no downside, yet there are endless arguments here resisting the use of them.

If we just took all the imperfect but obvious measures available to us immediately (stopping inbound travel, locking down hard and early, masks in public, a phone app, manual contact tracing) like the Asian countries e.g. Malaysia instead of insisting everything is gold plated first, we could have had this thing licked long ago. These measures would have looked like an overreaction taken early but our economy would have had suffered only a small fraction of the damage being done now.

I absolutely agree that it does not need to be perfect - every little bit helps

It's always seemed to me like it's a big messy stochastic system with two main components

They can probably be best described as:
- the probability of exposure
- the probability of transmission

Probability of exposure is simply how likely you are to encounter the disease
- it's a function of the prevalence of the disease in a population
- and the behaviour of that population (specifically the amount of interactions)

This is the part of the "system" that a "lockdown" attempts to address by reducing the number of interactions with other humans
- it has an immediate limiting effect on the spread of a disease as it cannot move beyond the confines of a home (if adhered to)
As "lockdown" regulations are relaxed this aspect of the "system" can still be addressed by continuing to limit interactions (wrt normal exposure) along with tracing and quarantine of suspect/known cases - and yes an app might help here

Probablility of transmission
This is a function of our behaviour (during interactions) and the properties of the disease

We can't affect the time the virus survives suspended in moisture droplets or how it sits on surfaces but we can modify how we act based on what we know or suspect about it
- maintaining distance during interactions, keeping them as brief as possible
- hygiene: sneezing/coughing etiquette (conscientious isolation)
- amount of air expelled from lungs (stop SHOUTING!)
- wearing masks in public
- a vaccine or having gained immunity
- etc etc

Bringing either of those probabilities down decreases the likelihood of the disease being passed on

- sd

There is another dimension, the development of effective treatments. As treatments get better, the fear will reduce. In the beginning doctors perceived the deaths as being caused by bi-lateral pneumonia treated with a ventilator. Nowadays they see the pneumonia as being caused by clotting of blood in the lung capillaries and the pneumonia being the body's immune response, and treatment now involves heading it off before it happens with blood thinners/anti-clotting drugs. The disputed HXQ treatment works by giving it really early in the infection cycle (ideally before the infection occurs in the first place) because it interrupts the process by which the virus enters cells to cause infection in the first place. This is why the studies of hospital patients show it not working, by the time a patient is ill enough to show up at a hospital it is WAY too late for HXQ to do it's best work.

Which leads on to the flawed Lancet HXQ study. It turns out there are major doubts over the validity of the data used. It was gathered by a company no-one has ever heard of called Surgisphere. Surgisphere won't reveal how they collected it. Hospitals supposedly supplying data have denied they supplied it as their patient confidentiality protocols prevent them releasing it. Surgisphere seem to be only two months old, and run by one of the authors of the Lancet study. The study has only four authors, none of them statisticians - how can only four people have physically collated over 90,000 patient records in such a short time? How did they persuade 600 hospitals in five continents to hand over their data so quickly, must have been in breach of confidentiality protocols given the speed they obtained it? The data used is not 'reproducable', it is 'black-boxed' and cannot be released for 'commercial reasons'.

Have a quick scan through this web page:

https://melwy.com/blog/lancet-paper-on- ... -black-box

Very worrying.

[Mike4]

Surely that was debunked long ago. Or do you hold that places like Singapore and Malaysia are getting good control of it due to their hot climate? How do hot places with dreadful stats like Brasil fit in with this?

This document from the WHO is a reasonably good indicator
https://www.who.int/docs/default-source ... 5b154880_2

Places like the USA and Brazil need detailed consideration based upon the localised climate and to what extent air conditioning is used.

Thanks. Having scanned through that document I'm finding it rather impenetrable, but can't see anything in there directly associating transmissibility to prevailing temperature. Could you point me to the parts of the document that indicate this please?

[johnhemming]

Haiti 1 174 111 33 2 Community transmission 0
Costa Rica 956 5 10 0 Clusters of cases 0
Paraguay 884 7 11 0 Community transmission 0
Uruguay 789 2 22 0 Clusters of cases 0
Nicaragua 759 480 35 18 Community transmission 0
Jamaica 564 8 9 0 Clusters of cases 0
Guyana 139 2 11 0 Clusters of cases 0
Trinidad and Tobago 116 0 8 0 Sporadic cases 30
Bahamas 100 0 11 0 Clusters of cases 3
Barbados 92 0 7 0 Clusters of cases 3
Antigua and Barbuda 25 0 3 0 Clusters of cases 24
Grenada 23 0 0 0 Clusters of cases 1
Belize 18 0 2 0 Sporadic cases 43
Saint Lucia 18 0 0 0 Sporadic cases 23
Saint Vincent and the Grenadines 18 0 0 0 Sporadic cases 7
Dominica 16 0 0 0 Clusters of cases 47
Saint Kitts and Nevis 15 0 0 0 Sporadic cases 37
Suriname 11 0 1 0 Sporadic cases

[servodude]

There is another dimension, the development of effective treatments. As treatments get better, the fear will reduce

Indeed. But I kind of see that as the perception of risk affecting behaviour which impacts both the likelihood of meeting cases and how one might act in the presence of people. The difficult thing about that aspect is that there are huge differences in how those risks are perceived within a population.

Certainly the mechanics of this disease are quite different from your normal respiratory disorder, and the apparent risk of fibrosis is probably what concerns me most personally.

-sd

[zico]

This is the graph to accompany the FT article.

[zico]

Important update to the Financial Times's deaths/million country comparison since I posted earlier.

Until Thursday, the UK had a higher rate of death than in any country for which high-quality data exist. However, Spain made a revision to its mortality estimates, adding 12,000 to its toll of excess deaths from coronavirus in a one-off adjustment to 43,000. This increased its death rate to 921 per million, compared to UK's 891 per million.

They also have a revised "lockdown time" graph, where infections/million are measured rather than total infections. This changes the picture somewhat, and gives an interesting graph. (Unfortunately you'll have to open the link to see it, because I can't copy it).
According to the graph UK locked down at a similar infections/million point to France, Switzerland, Portugal and Austria, but UK has done much worse than these countries.

Interestingly in the graph, "lockdown" is defined as "50% or less of normal transit usage" so Sweden has a data-point.
I'm a bit surprised that UK and Switzerland are shown as similar lockdown levels, because Switzerland banned mass gatherings, festivals only 3 days after discovering their first Covid-19 infection. By comparison, the first Covid-19 infection in the UK was discovered on 31st January in York, but the Cheltenham horse festival went ahead 12-14 March (well over a month later).
This may show that stopping potential "superspreader" events early on is a more effective (and less disruptive option) than general lockdown.

FT just compares 19 countries with comparable high-quality data on excess deaths. It's almost certain that Brazil will end up being the worst affected country in the world. Brazilian deaths have had a slower increase than countries such as USA, Spain, UK and Italy, but it's almost certainly due to under-reporting and under-recording. Their curve shows very few signs of tailing off and deaths are now in excess of 1,000 per day.

https://www.ft.com/content/6b4c784e-c25 ... 8ffde71bf0

[Mike4]

Frigged is a technical term in every industry I've worked in

Have some here really not not encountered the term do you think? Like you, I've been using it since I was at skool. Probably learned it from my dad.

Frigging is to fiddle and adjust things to suit your needs.

So to frig the data means to deliberately change it or leave important bits out to support your argument. Dr Didier is suggesting The Lancet set out with the preconceived notion that HXQ doesn't work, and when the data didn't support this notion, someone frigged the data until it did. What other explanations might exist for the percentage of patients with hypertension to be near identical across all five continents. Same for smoking when the percentage of smokers in the general populations varies widely.

He is suggesting the data used by Lancet 'smells' wrong. Here is the data chart he is questioning, from his Twitter post. Not that I understand most of it.

And now the big guns weigh in, questioning the integrity of that Lancet study.

"Covid-19 study on hydroxychloroquine use questioned by 120 researchers and medical professionals.

Surgisphere issues public statement defending integrity of coronavirus study published in the Lancet

More than 120 researchers and medical professionals from around the world have written an open letter to the editor of the Lancet raising serious concerns about a large and widely publicised global study that prompted the World Health Organisation to halt several Covid-19 clinical trials.

On Thursday Guardian Australia revealed that the Australian data in the study, published last week, did not reconcile with health department records or databases."

https://www.theguardian.com/world/2020/ ... are_btn_tw

[GoSeigen]

Important update to the Financial Times's deaths/million country comparison since I posted earlier.

Until Thursday, the UK had a higher rate of death than in any country for which high-quality data exist. However, Spain made a revision to its mortality estimates, adding 12,000 to its toll of excess deaths from coronavirus in a one-off adjustment to 43,000. This increased its death rate to 921 per million, compared to UK's 891 per million.

They also have a revised "lockdown time" graph, where infections/million are measured rather than total infections. This changes the picture somewhat, and gives an interesting graph. (Unfortunately you'll have to open the link to see it, because I can't copy it).
According to the graph UK locked down at a similar infections/million point to France, Switzerland, Portugal and Austria, but UK has done much worse than these countries.

Interestingly in the graph, "lockdown" is defined as "50% or less of normal transit usage" so Sweden has a data-point.
I'm a bit surprised that UK and Switzerland are shown as similar lockdown levels, because Switzerland banned mass gatherings, festivals only 3 days after discovering their first Covid-19 infection. By comparison, the first Covid-19 infection in the UK was discovered on 31st January in York, but the Cheltenham horse festival went ahead 12-14 March (well over a month later).
This may show that stopping potential "superspreader" events early on is a more effective (and less disruptive option) than general lockdown.

FT just compares 19 countries with comparable high-quality data on excess deaths. It's almost certain that Brazil will end up being the worst affected country in the world. Brazilian deaths have had a slower increase than countries such as USA, Spain, UK and Italy, but it's almost certainly due to under-reporting and under-recording. Their curve shows very few signs of tailing off and deaths are now in excess of 1,000 per day.

https://www.ft.com/content/6b4c784e-c25 ... 8ffde71bf0

Here's the image zico referred to with the full text of his post above.

[GoSeigen]

https://www.ft.com/content/6b4c784e-c259-4ca4-9a82-648ffde71bf0

The article quotes Natalie Dean, assistant professor of biostatistics at the University of Florida, saying that:

some countries such as Italy had “bad luck” as they were caught by the virus early on. This gave other countries, such as the UK, time to learn lessons, she added.

“I was very surprised by the delayed response in the UK. Given what we were observing in Italy at the time and that the UK was on the exact same trajectory, had the same very steep rise, I was surprised to see discussion about waiting. There was an immediate need to stop what was happening,” she said.


I'm sure if she contacts our own ElectronicFur he can explain to her exactly why delay was the rational response. Or rather, how there was in fact no steep rise as not observed in Italy, and how she and the whole world were duped by an incompetent computer programmer.




GS