SARS-CoV-2 testing

Covid-19 discussion, bring your own statistics
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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sun May 17, 2020 5:14 pm

... and it's definitely true that in the England data, test results get back dated, so the past few days are always going to show very few results. So if you just use that, and you're an idiot, you'll always think that the virus has just died out. The data just haven't come in yet. The UK data doesn't seem to suffer this artefact, previous days' counts don't get updated.
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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Mon May 18, 2020 6:46 am

Oh apparently it has been accepted and you'll notice the figures are updated a bit. So their Fig. 1 runs until a later date but still suffers from the artefact of the last few days' data not having come in yet, and they still fit it with an unphysical function.
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Re: SARS-CoV-2 testing

Post by shpalman » Mon May 18, 2020 1:50 pm

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Some data on the proportion of health workers in Lombardy who have been found to be positive for antibodies, averaged over the whole region and in different health authority areas.

Como is in the Insubria area I think, Bergamo has been a well known hot spot in which the all-causes death rate seems to have been 6 times higher than normal at one point, with the official number of cases at over 12000 (population of the whole province is 1.1 million, so 1% of the population has officially been positive) and even there barely 25% of health workers have the antibodies.
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Re: SARS-CoV-2 testing

Post by shpalman » Mon May 18, 2020 5:45 pm

The entire population* of Castiglione d'Adda is going to be tested for antibodies. It's less than 5000 people but it's right in the original hot-spot.

Three other hot-spots are also going to be tested in the same way.

https://www.corriere.it/salute/malattie ... 4de9.shtml

* well those who consent of course; it's voluntary.
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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Mon May 18, 2020 5:47 pm

Thanks for these updates, shpalman.

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Re: SARS-CoV-2 testing

Post by jimbob » Tue May 19, 2020 7:00 pm

Millennie Al wrote:
Sat May 16, 2020 2:10 am
lpm wrote:
Thu May 14, 2020 1:19 pm
Mancester Uni: over 25% of UK has had it...

https://www.manchester.ac.uk/discover/n ... 9-already/
It is highly implausible that lots of people (substatially more than half of those infected) have been asymptomatic cases, regardless of any modelling or guesswork. This is based on contact tracing experiences. Let Sx represent symptomatic cases and Ax asymptomatic cases and X->Y mean that X infects Y. If we have S0->S1 then contact tracing easily explains how S1 got infected. If we have S0->A0->S1 or S0->A0->A1->S1, it's still easy - get plausible contacts for S0 and S1 and see the link that might have passed on the infection. Beyond that, things get difficult and it starts to look like S1 got infected for no reason.

If there are equal numbers of S and A, then the probability of S->S is 0.5, S->A->S is 0.25, S->A->A->S is 0.125, which means all other possibilites are 0.125. As the proportion of A rises, this value also rises, so we can estimate the ratio of A to S by the proportion of symptomatic cases which seem to have no cause, and we can get a general feel for this by reading the news to see if in some parts of the world where contact tracing is done there are lots of unexplained cases or few. Lots of unexplained cases would be very alarming to anyone trying to do contact tracing, so would be very newsworthy. Since we read of contact tracing being very successful, we can conclude that there cannot be many A for each S. This means it's hardly worth bothering to read any paper which claims there is a huge number of asymptomatic cases.

Unless, there's a bad assumption, namely that S->A is just like A->S. If instead A->S is impossible, then we could have each S infect three more S and sixty A. That would mean we would never see unexplained infections, but there are twenty times as many asymptomatic cases as symptomatic cases. The problem with this hypothesis is that it should show up during contact tracing whereby when the contacts of an infected person are found and tested, in cases where there has been excessive delay in locating the individuals, we would see many people who test positive, are asymptomatic, and have not infected anyone else. That too would be quite remarkable, so I'd expect it would be newsworthy, so the lack of stories about it suggests it doesn't occur, undermining the plausibility of this mechanism.

Another odd case that would work is that S->A is rare, but A->A is common and A->S is impossible. That would make it hard to notice the S->A infections, while allowing the numbers of A to grow wildly. Of course this must mean that something very odd is happening in the S->A step - the disease is mutating into an asymptomatic variant. This seems extreely unlikely.

So overall, I consider the hypothesis that there are lots of asymptomatic cases to be sufficiently implausible that it requires very strong evidence to support it - that means actual testing and not just modelling.
Early data, and I see no reason to have changed it, has between 50%-75% asymptomatic, and about 1% death rate. Which also gives about 2-5% of the population as having had it.
Have you considered stupidity as an explanation

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Thu May 28, 2020 5:38 pm

Starting at the beginning of this week, 150,000 Italians are being called at some-sort-of-random across all of Italy and being asked if they would like to have a blood test for covid antibodies. TV adverts have informed us to expect calls from a phone number which looks like 065510____.

Apart from the drawback that people screen their calls and/or think it's a scam when they do get a call, there's another disincentive: anyone who tests positive for antibodies will be obliged to self-isolate until they can get swabbed for virus RNA.

Still, I wouldn't mind being called up and getting testing because I'm genuinely curious about whether I could have picked up the covids without noticing back in February.
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Re: SARS-CoV-2 testing

Post by tom p » Thu May 28, 2020 5:53 pm

shpalman wrote:
Thu May 28, 2020 5:38 pm
Starting at the beginning of this week, 150,000 Italians are being called at some-sort-of-random across all of Italy and being asked if they would like to have a blood test for covid antibodies. TV adverts have informed us to expect calls from a phone number which looks like 065510____.

Apart from the drawback that people screen their calls and/or think it's a scam when they do get a call, there's another disincentive: anyone who tests positive for antibodies will be obliged to self-isolate until they can get swabbed for virus RNA.

Still, I wouldn't mind being called up and getting testing because I'm genuinely curious about whether I could have picked up the covids without noticing back in February.
That's a terrible way of doing things.
If you have someone there, and you're drawing blood, why not also swab for the virus? That way there's no need for any unnecessary self-isolation, since the swabs take a few hours, but the antibody tests (at least here in NL) took a few days.

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Thu May 28, 2020 5:59 pm

Yes, that would be more intelligent, but I can only assume a decision has been made to not divert swab capacity away from where it is currently being deployed.
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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu May 28, 2020 9:57 pm

Based on tests conducted between 11 May and 24 May 2020, we estimate 133,000 people in England had COVID-19
Our latest estimates indicate that at any given time during the two weeks from 11 May to 24 May 2020, an average of 133,000 people in England had the coronavirus (COVID-19) (95% confidence interval: 62,000 to 250,000). This equates to 0.24% (95% confidence interval: 0.11% to 0.46%) of the population in England. This estimate is based on tests performed on 18,913 people in 8,799 households.

[...]

There were an estimated average of 54,000 new COVID-19 infections per week in England
Based on results of people tested throughout the study period, which began on 26 April 2020, we estimate that there were 0.10 new infections per 100 people followed for one week (95% confidence interval: 0.06 to 0.16). This would represent an average of 54,000 new infections per week for people living in private-residential households in the community in England since the study began (95% confidence interval: 34,000 to 86,000).

[...]

Around 6.78% of people who provided blood samples tested positive for antibodies to COVID-19
As of 24 May 2020, 6.78% (95% confidence interval: 5.21% to 8.64%) of individuals from whom blood samples were taken tested positive for antibodies to the coronavirus (COVID-19). This is based on blood test results from 885 individuals since the start of the study on 26 April 2020.

[...]

Of those in our study who reported working in patient-facing healthcare or resident-facing social care roles1, 1.73% tested positive for COVID-19 (95% confidence interval: 0.92% to 2.94%). This includes NHS professionals, such as nurses and doctors, as well as social care workers, such as nursing home or home care workers.

By comparison, the percentage of people reporting not working in these types of roles testing positive for COVID-19 was lower at 0.38% (95% confidence interval: 0.29% to 0.47%).

[...]

Rates of infection for COVID-19 appear higher for individuals who work outside the home compared with those who work from home. An estimated 0.71% (95% confidence interval: 0.46% to 1.04%) of individuals who reported working outside of the home tested positive for COVID-19, compared with 0.23% (95% confidence interval: 0.10% to 0.43%) of individuals who reported working at home.
https://www.ons.gov.uk/peoplepopulation ... urvey-data

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Thu May 28, 2020 10:32 pm

Preprint: "Virus in sewage predicts COVID-19 (a) cases and (b) hospital admissions with 99% accuracy". Fox News runs story.

Reality: Clueless authors (8, all from Yale) used a statistical technique they didn't understand and shot themselves in the foot. Sigh.
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