SARS-CoV-2 testing

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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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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.
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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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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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Re: SARS-CoV-2 testing

Post by Woodchopper » Sat Jun 06, 2020 2:04 pm

Second round of antibody testing in Spain. Similar results as in the first. Only circa 5.2 percent of the population tested positive.
https://www.isciii.es/Noticias/Noticias ... VID19.aspx

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Re: SARS-CoV-2 testing

Post by shpalman » Sat Jun 06, 2020 2:24 pm

I don't fully understand this but about 10000 antibody tests have been made in Como and we have the results for about 9000 so far.

11% of them are positive.

The bit I don't understand is that it seems that most of the tests, about 8000, were carried out on health workers, and we have about 7% of these positive.

But the rest (the other 1000 results we have so far) were "invited" by the health service (under what criteria isn't mentioned) and here we have 42% positive.

So yeah I'd really like to know the invitation criteria because I seriously doubt there's a 42% positive rate in the general non-health-worker population...
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Re: SARS-CoV-2 testing

Post by bob sterman » Sat Jun 06, 2020 3:56 pm

shpalman wrote:
Sat Jun 06, 2020 2:24 pm
I don't fully understand this but about 10000 antibody tests have been made in Como and we have the results for about 9000 so far.

11% of them are positive.

The bit I don't understand is that it seems that most of the tests, about 8000, were carried out on health workers, and we have about 7% of these positive.

But the rest (the other 1000 results we have so far) were "invited" by the health service (under what criteria isn't mentioned) and here we have 42% positive.

So yeah I'd really like to know the invitation criteria because I seriously doubt there's a 42% positive rate in the general non-health-worker population...
Could it be that the people "invited" from the general population were self-selected people who had been ill some time ago and were interested to find out whether the illness was COVID-19? Such people would be motivated to respond to recruitment advertisements.

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Re: SARS-CoV-2 testing

Post by shpalman » Sat Jun 06, 2020 4:51 pm

bob sterman wrote:
Sat Jun 06, 2020 3:56 pm
shpalman wrote:
Sat Jun 06, 2020 2:24 pm
I don't fully understand this but about 10000 antibody tests have been made in Como and we have the results for about 9000 so far.

11% of them are positive.

The bit I don't understand is that it seems that most of the tests, about 8000, were carried out on health workers, and we have about 7% of these positive.

But the rest (the other 1000 results we have so far) were "invited" by the health service (under what criteria isn't mentioned) and here we have 42% positive.

So yeah I'd really like to know the invitation criteria because I seriously doubt there's a 42% positive rate in the general non-health-worker population...
Could it be that the people "invited" from the general population were self-selected people who had been ill some time ago and were interested to find out whether the illness was COVID-19? Such people would be motivated to respond to recruitment advertisements.
I should have read it better. They were invited from those who had been put in self-isolation. (It's not clear if they'd had positive covid RNA tests or just suspected contact or symptoms.)

In any case the national antibody survey is not based on self-selection.
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Re: SARS-CoV-2 testing

Post by Woodchopper » Tue Jun 09, 2020 10:01 pm

57% of Bergamo province were infected.
https://www.reuters.com/article/us-heal ... SKBN23F2JV

That’s actually getting close to the fabled herd immunity.

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Re: SARS-CoV-2 testing

Post by Brightonian » Sun Jun 14, 2020 1:44 pm

Adults in England wanted for testing study: https://www.bristol.ac.uk/translational ... -19-study/

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Re: SARS-CoV-2 testing

Post by JQH » Sun Jun 14, 2020 2:21 pm

Brightonian wrote:
Sun Jun 14, 2020 1:44 pm
Adults in England wanted for testing study: https://www.bristol.ac.uk/translational ... -19-study/
Interesting, thanks. I'll take a good look at this later.
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Re: SARS-CoV-2 testing

Post by tom p » Mon Jun 15, 2020 11:44 am

Has anyone linked to this more or less about antibody testing yet?
I'm certain it will be of interest to many here

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Mon Jun 15, 2020 11:55 pm

My mum has just related this highly reassuring account of how UK testing works, based on her dealings with one of the residents at the old folks' home where she works.

Monday morning. Resident complains of having had a bad cough and a headache since Friday. My mum recommends she phones the GP. The GP tells the resident to isolate until she can be tested. To get her test, she'll need an email address and a mobile phone number. She has neither. She uses my mum's.

Tuesday: my mum is sent a code, which she passes on to the resident. The resident now has to phone the GP's office again, to give them that code. It doesn't work. The GP requests a new code, this time using her own details.

Wednesday: the GP gets the code, and it works, so she is able to order a test for the resident. It will be delivered to the resident the next working day.

Thursday: resident receives the testing kit and instructions, which she needs my mum's help to understand. The swabbing has to be done after 9pm and before 8am. She has to rub a long cotton swab on her tonsils before shoving it up her nose, then put it in a series of plastic bags and boxes, affixing various labels in appropriate places.

Friday: the testing kit is collected by courier.

Saturday: my mum receives a text message with the test results: negative. She calls the resident. "Oh yes, I thought it would be - I always have these symptoms when my hayfever is playing up."
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Re: SARS-CoV-2 testing

Post by headshot » Tue Jun 16, 2020 4:40 pm

A neighbour of ours is a nurse who has been working on a Covid ward. She was symptomatic back in March.

They gave her an antibody test to see if she's had it.

They lost the samples and now she has to get tested again.

(I'm not sure who "they" are, but assume it must be Serco or some other company dealing with the testing regime)

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Tue Jun 16, 2020 6:09 pm

Somehow I forgot the most damning part of the testing anecdote.

The negative results message ended with: "You can go back to work."

Not, congratulations you don't have the potentially debilitating or deadly infection currently ravaging your community. Just, back to work, peasant. Arbeit McFries.
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Re: SARS-CoV-2 testing

Post by Gfamily » Thu Jun 18, 2020 10:15 am

As an aside, a nephew works as a paramedic.

As so many people are having problems remembering what day it is, the test for dementia has now been changed to "do you know what year it is?"
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Re: SARS-CoV-2 testing

Post by jdc » Thu Jun 18, 2020 5:38 pm

Gfamily wrote:
Thu Jun 18, 2020 10:15 am
As an aside, a nephew works as a paramedic.

As so many people are having problems remembering what day it is, the test for dementia has now been changed to "do you know what year it is?"
Apparently they also considered "do you know who the Prime Minister is?" but Boris Piccaninny Watermelon Letterbox Cake Bumboys Vampires Haircut Wall-Spaffer Spunk-Burster f.ck-Business f.ck-the-Families Get-Off-My-f.cking-Laptop Girly-Swot Big-Girl’s-Blouse Chicken-frit Hulk-Smash Noseringed-Crusties Death-Humbug Technology-Lessons Surrender-b.llsh.t French-Turds Dog-Whistle Get-Stuffed FactcheckUK@CCHQ 88%-lies Get-Brexit-Done Bung-a-Bob-for-Big-Ben’s-Bongs Cocaine-Event Spiritual-Worth Three-Men-and-a-Dog Whatever-It-Takes I-Shook-Hands-With-Everyone Herd-Immunity Johnson was considered to be a bit of a mouthful.

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Re: SARS-CoV-2 testing

Post by JQH » Fri Jun 19, 2020 8:53 am

I would accept "That useless lying c.nt" as a valid answer.
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