Coronavirus - Modelling Aspects Only

[XFool]

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

Where? Also, does India not have a "hot climate"?

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

Oh "air conditioning", yes, that has been identified as a risk factor - e.g. inside restaurants. But that could imply a possibly higher risk in warmer climates, surely?

[johnhemming]

There are all sorts of difficulties with this. Firstly we should really try to distinguish excess deaths where people are infected by Covid-19 from excess deaths caused by Covid-19 where people are not infected. The latter are the cases where people have avoided the health services because of the situation. The former are people who are actually infected (some of whom did not die as a result of the infection)..

Secondly as this chart relies upon a date of "lockdown", but otherwise uses a measurement of transport it should really try using some consistent measurement such as levels of transport (which is not a bad mechanism).

However, I don't think it produces useful or reliable conclusions.

[johnhemming]

Oh "air conditioning", yes, that has been identified as a risk factor - e.g. inside restaurants. But that could imply a possibly higher risk in warmer climates, surely?

That was identified a mechanism for spreading infection. It would be quite possible that wealthier hot countries with more air conditioning and the tendency to use it have this as a risk factor.

I don't think I have enough information to look at that issue beyond it being a reasonable hypothesis.

[Alaric]

That was identified a mechanism for spreading infection. It would be quite possible that wealthier hot countries with more air conditioning and the tendency to use it have this as a risk factor.

The recent good weather in the UK may have had an effect. Those breaking or bending the rules about contact with other households have been able to do so outdoors.

The week by week statistics of UK deaths in normal times show higher rates in early January. Is this Christmas and New Year celebrations acting as super spreaders for nasties like Flu and colds?

[Mike4]

That was identified a mechanism for spreading infection. It would be quite possible that wealthier hot countries with more air conditioning and the tendency to use it have this as a risk factor.

The recent good weather in the UK may have had an effect. Those breaking or bending the rules about contact with other households have been able to do so outdoors.

The week by week statistics of UK deaths in normal times show higher rates in early January. Is this Christmas and New Year celebrations acting as super spreaders for nasties like Flu and colds?

Yes Dr John Campbell put this forward in one of his COVID-19 videos as a hypothesis the other day too.

Simply that in warm weather people spend more time outside, but in cold weather they spend more time inside leading to more opportunities for infection. So possibly not that the virus thrives in cold weather due to an inherent biological characteristic where low temperatures make it more infectious, but that its hosts' behaviour changes in cold weather in a way that assists it's spread.

[johnhemming]

There does, however, appear to be some evidence on how long the virus hangs around in different temperatures. It is in the end a coronavirus.

[Mike4]

There does, however, appear to be some evidence on how long the virus hangs around in different temperatures. It is in the end a coronavirus.

Yes good point. There was a bloke on the radio the other day saying he had done the research and 5c was the optimum temp for long life on hard surfaces. If you accept they are alive in the first place, but I think that's one for the philosophy board

[zico]

There are all sorts of difficulties with this. Firstly we should really try to distinguish excess deaths where people are infected by Covid-19 from excess deaths caused by Covid-19 where people are not infected. The latter are the cases where people have avoided the health services because of the situation. The former are people who are actually infected (some of whom did not die as a result of the infection)..

Secondly as this chart relies upon a date of "lockdown", but otherwise uses a measurement of transport it should really try using some consistent measurement such as levels of transport (which is not a bad mechanism).

However, I don't think it produces useful or reliable conclusions.

The UK government itself has accepted "excess deaths" as the most appropriate measure to use, but that's not necessarily any kind of proof! There's a better logic than that.

Firstly, on a purely statistical basis, Covid-19 is a potential major cause of death, but for many individual deaths it may not be possible to determine whether Covid-19 caused the death - often people who die have several health problems, so not clear which was the true cause of death.
However, Covid-19 is a new cause of death, and if deaths occur in sufficiently large numbers after the arrival of Covid-19, it's very clear that Covid-19 is the reason for deaths. Counting excess deaths also avoids care homes, hospitals and governments attempting to make themselves look good, and enables comparisons to be made between countries.

Secondly, there will of course be additional deaths caused in the Covid-19 epidemic because hospitals are too overloaded to treat heart attack victims, or because people decide not to attend for life-saving treatment for other diseases. However, these are still deaths caused by the pandemic, because people are changing their behaviour due to the pandemic. There will also be lives saved through declines in road traffic accidents or stress-related heart attacks at work - these will also be directly related to the pandemic. The 5-year weekly average of deaths shows us the picture without a pandemic. The current weekly average deaths show us the picture with a pandemic.

I agree some extent on your point about the "date of lockdown" because not every lockdown was the same, typically starting with partial measures before moving to more stringent lockdowns. (For example, Switzerland banned mass gatherings far more quickly than UK, but full lockdown appears to have been done at a similar stage in both countries)

[zico]

Africa is interesting. Only 4,000 confirmed deaths from Covid-19 in the whole continent, just over 50% from 3 countries - Algeria, South Africa, Egypt.

https://www.bbc.co.uk/news/resources/id ... 15079548bc

[zico]

Comparison on %age of care home deaths. Canada at 82%, UK somewhere in the middle. Even though UK has clearly made mistakes, it may well simply be that people in very high-risk categories are very difficult to keep safe, no matter what. South-East Asia countries clearly have the answer, probably from their SARS experience, though strange that Western countries haven't also learned lessons from what these countries have done for coronavirus.


https://www.rte.ie/news/coronavirus/202 ... s-ireland/

Figures contained in a Department of Health publication show Ireland with a high number of care home resident deaths, as a percentage of all Covid-19 deaths, as part of a rough comparison with 20 other countries.

It says that Canada, at 82%, has the highest number of care home resident deaths, as a percentage of all Covid-19 deaths listed.

It puts Ireland in second place, with the number of care home resident deaths, as a percentage of all deaths due to the virus, at 62%.

The report warns that international comparisons are difficult, due to different approaches to recording deaths, as well as differences in testing and policies.

The third ranked country on the list is France at 51%. Sweden is at 49%. Austria is at 41%, the US 41% and Portugal at 40%.

The UK is ranked at between 38-52% depending on various criteria applied.

Some countries such as South Korea, Hong Kong and Singapore have no deaths in care homes listed.

The report notes that some countries only record the place of death, while others also report deaths in hospital of care home residents.

[Nimrod103]

Some countries such as South Korea, Hong Kong and Singapore have no deaths in care homes listed.

It is a long time since I lived in Singapore, and things may have changed, but I am very surprised there are any care homes there. It is just not the Asian way to send elderly dependent relatives away. Filial duty is to care for them in the home.

[servodude]

Some countries such as South Korea, Hong Kong and Singapore have no deaths in care homes listed.

It is a long time since I lived in Singapore, and things may have changed, but I am very surprised there are any care homes there. It is just not the Asian way to send elderly dependent relatives away. Filial duty is to care for them in the home.

There's plenty of them and it's a growing market;
https://www.austrade.gov.au/Australian/ ... /aged-care

I think that aged care is one of those things you don't notice until you do... and then it seems like it's everywhere.

-sd

[johnhemming]

This (which I have also posted on health)
https://twitter.com/BallouxFrancois/sta ... 4143087628

Recent preprint reporting that 24/24 (100%) people form Singapore infected by SARS-1 in 2003 have pre-existing T-cell immunity against #SARSCoV2, but more surprisingly 9/18 (50%) with no exposure to SARS-1 also possess T-cells targeting #SARSCoV2.

https://www.biorxiv.org/content/10.1101 ... 1.full.pdf

Gives solid evidence that an unknown percentage of people who have had coronavirus colds have some immunity to Covid-19.

Of the 18 patients tested 50% had some immunity to Covid-19.

That gives a detailed medical explanation of why Covid-19 does not affect as many people as one would expect and does explain the low level of antibodies in London which I would think otherwise has the equivalent of herd immunity.

[Itsallaguess]

Denmark has published an in-depth analysis of its 9,519 COVID patients -

Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCRtest for SARS-CoV-2 in Denmark: A nationwide cohort -

Objective - To provide population-level knowledge on individuals at high risk of severe and fatal coronavirus disease 2019 (COVID-19) in order to inform targeted protection strategies in the general population and appropriate triage of hospital contacts.



Report PDF link - https://www.medrxiv.org/content/10.1101/2020.05.24.20111823v1.full.pdf

Cheers,

Itsallaguess

[GrahamPlatt]

Dynamic causal modelling...

https://www.theguardian.com/world/2020/ ... ark-matter

[Nimrod103]

Dynamic causal modelling...

https://www.theguardian.com/world/2020/ ... ark-matter

We’ve been comparing the UK and Germany to try to explain the comparatively low fatality rates in Germany. The answers are sometimes counterintuitive. For example, it looks as if the low German fatality rate is not due to their superior testing capacity, but rather to the fact that the average German is less likely to get infected and die than the average Brit. Why? There are various possible explanations, but one that looks increasingly likely is that Germany has more immunological “dark matter” – people who are impervious to infection, perhaps because they are geographically isolated or have some kind of natural resistance.

My gob is utterly smacked. Who would have guessed that the Germans are a superior race? - at least from the point of view of resistance to infection.

[johnhemming]

https://www.theguardian.com/world/2020/ ... e-to-light

A day before the first confirmed fatality from coronavirus outside mainland China was reported on 2 February this year, the death of the influential guitarist and musician Andy Gill was announced. The 64-year-old, who fronted the post-punk band Gang of Four, died of pneumonia after two weeks in St Thomas’ hospital in London.

[zico]

I've just done a spot of modelling for potential second waves, following easing of lockdown, using various scenarios for R-values.
For me, one key point is that when we're told R is between 0.7 and 0.9 it makes a big difference which one of those it is.
The other key point is that, even if R-values are quite high, it would take a few weeks before the death total went above 100.


My assumptions
Currently 8,000 infections daily (as stated in recent daily press conferences)
IFR = 0.63% (Cambridge modelling estimates used by SAGE)
Time from infection to death = 19 days (so any increase in infections today affect numbers of deaths in 19 days).
I used ONS data on Covid-19 deaths up until mid-May, then assumed daily deaths will steadily decrease down to 50 by mid-June (based on the current daily new infection estimate of 8,000 and the IFR of 0.63%.
2nd lockdown achieves R=0.7 from the day it's imposed.

I've used 2 scenarios, first graph has no re-imposing of lockdown. Second graph has 2nd lockdown occurring on August 1st.
I haven't modelled R=1.0 because that simply wouldn't be a major problem (though it would be around 15k deaths in a full year).





At first sight, it looks like the curves have different levels before 1st August lockdown, but they haven't - it's just a trick of the eye.

N.B. The second scenario includes a scenario of R=2. If that was the true figure, then we'd still be below 100 daily deaths until 26th June, 200 daily deaths by 6th July, but 1,000 deaths by end-July.

P.S. In this modelling, number of additional infections by end-September are as follows.
R = 1.1 New Infections = 2million
R= 1.2 Infection = 4 millions
R= 1.3 8 million
R = 1.4 15 million
R = 1.5 30 million (this is the point at which the "exponential" assumption would almost certainly break down, because the adult population is only 57 million).

[johnhemming]

Obviously I disagree on a number of factual issues. However, what is key in this situation is that the government should be aware of the numbers of people being admitted to hospital with pneumonia. Hence they should have a good warning of increases in infections (if any) well before people start dying in any numbers.

Personally I expect a smaller second wave in winter. (almost regardless of what the government does)

[zico]

Obviously I disagree on a number of factual issues.

Are you replying to my scenarios or some other topic?