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Coronavirus - modelling aspects only please

Scientific discovery and discussion
Mike4
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Re: Coronavirus - modelling aspects only please

#329955

Postby Mike4 » July 31st, 2020, 1:47 pm

servodude wrote:Has anyone found a study that can explain why white middle class middle aged men in the UK who live in single generation households and were in a position to isolate comfortably are so under represented in the death figures?

-sd

Give me £4m and I'll check it out for you.....

zico
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Re: Coronavirus - modelling aspects only please

#329965

Postby zico » July 31st, 2020, 2:40 pm

Worrying figures from the latest Coronavirus infection pilot, based on results from private households (so excluding hospitals and care homes).
Percentage of population infected increased from 0.05% to 0.07% between 1st July - 31st July, so assuming average infection time of 10 days, that gives an estimate of R=1.1 for England and Wales.
This is the best estimate of what will happen if we continue as we have in July - so even if there is no further easing of lockdown, the R-value would stay at 1.1 for the foreseeable future.

During the most recent week (20 to 26 July 2020), we estimate there were around 0.78 new COVID-19 infections for every 10,000 people in the community population in England, equating to around 4,200 new cases per day (95% credible interval: 2,200 to 8,100).

Between 26 April and 26 July, 6.2% of people tested positive for antibodies against SARS-CoV-2 on a blood test, suggesting they had the infection in the past.

Further analysis indicates that we can be confident that there was a real small increase in the most recent estimated daily infection rate when compared with the lowest daily rate from the last six weeks, which was 0.05% (95% credible interval: 0.04% to 0.07%) on 1 July 2020.



Image

https://www.ons.gov.uk/peoplepopulation ... 31july2020

zico
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Re: Coronavirus - modelling aspects only please

#329971

Postby zico » July 31st, 2020, 2:53 pm

Nimrod103 wrote:
I assume the English high excess death rate among the under 65s is due to the BAME effect, with the high immigrant numbers in the England? An early statistic I remember was that, of 36 doctors died of Covid19, 35 were BAME. I'm not sure how those numbers look now.


Yes, that may explain it in individual cities, but not so much for the country as a whole, given that 86% are White British.
For the individual UK cities in the report, London/Manchester/Cardiff had very similar excess deaths for u-65 and 65+. Birmingham/Edinburgh/Glasgow/Belfast had a significant difference between the 2 groups - with 65+ age group being worst affected.

johnhemming
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Re: Coronavirus - modelling aspects only please

#329982

Postby johnhemming » July 31st, 2020, 3:27 pm

ons wrote:The modelled estimates for the latest six-week period are based on 116,026 swab tests collected over this period. During these weeks, 59 individuals from 58 households tested positive.


I think they should reveal the model they are using. The number of positive tests is really low and it would be difficult to conclude much from this.

They really should show their working.

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Re: Coronavirus - modelling aspects only please

#329988

Postby johnhemming » July 31st, 2020, 3:46 pm

I have found the raw source figures for this:

Table 3
Overall number of COVID-19 infections by non-overlapping 14 day periods (weighted)
between 4 May to 26 July 2020
Positivity rate (weighted): Sample counts (unweighted):
% testing positive for COVID-19 95% confidence interval Individuals testing positive for COVID-19 Total individuals in sample Households testing positive for COVID-19 Total households in sample
Lower Upper
4 May to 17 May 0.35% 0.23% 0.52% 51 16,236 46 7,622 0.31% 0.60%
18 May to 31 May 0.15% 0.08% 0.25% 32 20,390 24 9,314 0.16% 0.26%
1 June to 14 June 0.07% 0.03% 0.13% 13 25,519 11 11,883 0.05% 0.09%
15 June to 28 June 0.09% 0.05% 0.16% 18 23,767 17 11,483 0.08% 0.15%
29 June to 12 July 0.05% 0.03% 0.09% 19 31,542 19 15,235 0.06% 0.12%
13 July to 26 July 0.09% 0.06% 0.14% 24 28,325 24 14,019 0.08% 0.17%


I have calculated extra columns on individuals testing positive without any weighting. We know so little about how the samples are being generated that it is difficult to say anything about this.

Mike4
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Re: Coronavirus - modelling aspects only please

#330080

Postby Mike4 » August 1st, 2020, 4:34 am

johnhemming wrote: We know so little about how the samples are being generated that it is difficult to say anything about this.

Not only details of how the samples are generated from their cohort but how their cohort itself has been selected. They say random households but if you knock on random front doors and ask to stick swabs up their noses most would say NO I reckon, unless they had a reason to want to be tested which they may not disclose so the cohort gets biased towards those who suspect they have it.

I guess if one tells them the results remains anonymous perhaps that would fix it, but that presents something of an ethical bind. Shouldn't one TELL the people in the cohort who test positive so they can self-isolate?

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Re: Coronavirus - modelling aspects only please

#330081

Postby johnhemming » August 1st, 2020, 4:41 am

One odd thing about the figures is the large number of people in multiperson households where only one tests positive for the virus. In the last two samples in all the multiperson households where someone tested positive only one person tested positive.

Mike4
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Re: Coronavirus - modelling aspects only please

#330085

Postby Mike4 » August 1st, 2020, 5:08 am

johnhemming wrote:One odd thing about the figures is the large number of people in multiperson households where only one tests positive for the virus. In the last two samples in all the multiperson households where someone tested positive only one person tested positive.

Yes I've noticed this too but more directly, i.e. in the people I know of who have had it. In every case (not that there are many) they have been the only person in their household to fall ill.

This seems similar to the way common colds circulate. I've noticed over the decades I can get a cold out of nowhere, and pass it on to no-one in the family, and equally I can spend long periods in close association with a person or people with colds and not catch one myself. COVID-19 looks the same to me. Makes me wonder if coronavirus colds can also be caught asymptomatically.

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Re: Coronavirus - modelling aspects only please

#330093

Postby Nimrod103 » August 1st, 2020, 8:27 am

Mike4 wrote:
johnhemming wrote:One odd thing about the figures is the large number of people in multiperson households where only one tests positive for the virus. In the last two samples in all the multiperson households where someone tested positive only one person tested positive.

Yes I've noticed this too but more directly, i.e. in the people I know of who have had it. In every case (not that there are many) they have been the only person in their household to fall ill.

This seems similar to the way common colds circulate. I've noticed over the decades I can get a cold out of nowhere, and pass it on to no-one in the family, and equally I can spend long periods in close association with a person or people with colds and not catch one myself. COVID-19 looks the same to me. Makes me wonder if coronavirus colds can also be caught asymptomatically.


This is something I have also observed in a dozen cases, though it is anecdotal evidence, and none of the people I know of have been tested. In only one case has the infection (if present) been passed from boyfriend to partner.

I now think it likely my wife had it back in March, she had the cough, but never a fever or other symptoms (and I still find it difficult to convince her that she might have had it). I never got it, perhaps because I never go through a normal winter without 2 or 3 colds.

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Re: Coronavirus - modelling aspects only please

#330098

Postby johnhemming » August 1st, 2020, 8:49 am

Mike4 wrote:Makes me wonder if coronavirus colds can also be caught asymptomatically.

The point about these tests is that they pick up asymptomatic cases. Hence the logical conclusion is that the other house members have resistance from having had another coronavirus (or Covid-19 previously).

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Re: Coronavirus - modelling aspects only please

#330127

Postby dealtn » August 1st, 2020, 10:58 am

Nimrod103 wrote:I now think it likely my wife had it back in March, she had the cough, but never a fever or other symptoms (and I still find it difficult to convince her that she might have had it). I never got it, perhaps because I never go through a normal winter without 2 or 3 colds.


What makes you think she had "it" rather than the dozen plus other "things" that generate a cough (and no fever ....)?

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Re: Coronavirus - modelling aspects only please

#330264

Postby Nimrod103 » August 1st, 2020, 8:22 pm

dealtn wrote:
Nimrod103 wrote:I now think it likely my wife had it back in March, she had the cough, but never a fever or other symptoms (and I still find it difficult to convince her that she might have had it). I never got it, perhaps because I never go through a normal winter without 2 or 3 colds.


What makes you think she had "it" rather than the dozen plus other "things" that generate a cough (and no fever ....)?


Fair question, to which I don't think there is an answer yet. She never had a test for the active virus. The test for the antibodies would seem to not pick up all those who had mild or no symptoms (today's DT - https://www.telegraph.co.uk/global-heal ... ronavirus/). This is potentially startling news because it may mean that all the studies which indicate only 5-10% of the population have had the disease, may just be plain wrong.

Her symptoms were a persistent dry cough for about 3 weeks, and feeling rough and lacking energy for a week. Never had anything like it before. But crucially no fever, at a time when the pictures on TV only showed guards testing for high temperatures.

We will probably never know.

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Re: Coronavirus - modelling aspects only please

#330273

Postby johnhemming » August 1st, 2020, 9:14 pm

I spent a bit of time reading some of the references in this piece (there are a lot)
https://blog.argonautcapital.co.uk/arti ... -lockdown/

It is interesting and raises the question as to what extent social distancing held back the peak infection rate in the UK or even just herd immunity held it back because social distancing was relatively late.

Obviously in some places interventions have delayed the first wave to such a point as it becomes a second or third. However, some of the links argue that the profile of infections and deaths in the UK was essentially limited by herd immunity alone. In many ways it does not matter as the outcome from now is the same.

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Re: Coronavirus - modelling aspects only please

#330321

Postby dspp » August 2nd, 2020, 11:48 am

Apologies if these have been posted before,

US GAO : Covid19, Data Quality and Considerations for Modeling and Analysis - https://www.gao.gov/assets/710/708527.pdf

UK ONS : Comparison of European excess mortality - https://www.ons.gov.uk/peoplepopulation ... tojune2020

- dspp

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Re: Coronavirus - modelling aspects only please

#330325

Postby johnhemming » August 2nd, 2020, 12:03 pm

This twitter account has a number of useful links
https://twitter.com/mlevitt_np2013?lang=en

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Re: Coronavirus - modelling aspects only please

#330492

Postby johnhemming » August 3rd, 2020, 9:32 am

https://www.cebm.net/covid-19/covid-cas ... heres-why/
COVID cases in England aren’t rising: here’s why

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Re: Coronavirus - modelling aspects only please

#330682

Postby Sorcery » August 3rd, 2020, 9:08 pm

An interview with Sunetra Gupta that I had not seen : https://reaction.life/we-may-already-ha ... tra-gupta/

And an update from Nic Lewis https://judithcurry.com/2020/07/27/why- ... more-26449 with far more comments on it than are useful and where I found the link to the Sunetra Gupta interview.

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Re: Coronavirus - modelling aspects only please

#331606

Postby johnhemming » August 7th, 2020, 6:07 pm

The ONS now say cases are not rising.

A BBC report which as usual does not give enough useful facts
https://www.bbc.com/news/health-53695477

The figures in their details report for percentages of people with Covid-19 are (these are modelled)
6 July to 12 July 0.04%
13 July to 19 July 0.05%
20 July to 26 July 0.07%
27 July to 2 August 0.05%

Table 1b.
Modelled mid-week estimates of the number of COVID-19 infections, England
25 June 2020 0.04%
02 July 2020 0.04%
09 July 2020 0.05%
16 July 2020 0.05%
23 July 2020 0.05%
30 July 2020 0.05%

Given that restrictions were kept in place because infections were rising. What is going to happen now that they are not? (which was obvious anyway)

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Re: Coronavirus - modelling aspects only please

#331659

Postby servodude » August 8th, 2020, 1:33 am

johnhemming wrote:The ONS now say cases are not rising.

A BBC report which as usual does not give enough useful facts
https://www.bbc.com/news/health-53695477

The figures in their details report for percentages of people with Covid-19 are (these are modelled)
6 July to 12 July 0.04%
13 July to 19 July 0.05%
20 July to 26 July 0.07%
27 July to 2 August 0.05%

Table 1b.
Modelled mid-week estimates of the number of COVID-19 infections, England
25 June 2020 0.04%
02 July 2020 0.04%
09 July 2020 0.05%
16 July 2020 0.05%
23 July 2020 0.05%
30 July 2020 0.05%

Given that restrictions were kept in place because infections were rising. What is going to happen now that they are not? (which was obvious anyway)


Does that not just mean that with the current restrictions the growth rate is 1?
That for every person who recovers one more becomes infected?
That the cumulative number of cases is rising at a constant rate?

-sd

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Re: Coronavirus - modelling aspects only please

#331660

Postby johnhemming » August 8th, 2020, 1:46 am

Probably


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