SARS-CoV-2 testing

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

Post by Woodchopper » Thu Apr 30, 2020 5:13 am

False positives in antibody testing potentially exaggerate the numbers infected and give low infection fatality rates
https://twitter.com/michaelzlin/status/ ... 98565?s=21

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Re: SARS-CoV-2 testing

Post by shpalman » Thu Apr 30, 2020 10:33 am

Antibody responses to SARS-CoV-2 in patients with COVID-19
https://www.nature.com/articles/s41591-020-0897-1
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Re: SARS-CoV-2 testing

Post by shpalman » Fri May 01, 2020 6:01 am

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Re: SARS-CoV-2 testing

Post by bmforre » Sat May 02, 2020 3:47 am

NYTimes:
When senators converge on Capitol Hill for a new session next week, there will not be enough coronavirus tests for all of them — even though White House officials and staff members are well supplied.

Dr. Brian P. Monahan, the tight-lipped doctor who attends to Congress, told senior Republican officials on a private conference call on Thursday that his office could not screen all 100 senators for the virus when they return on Monday.

President Trump and Vice President Mike Pence are tested frequently and have often avoided masks in public. Aides who come into close contact with them are tested weekly, according to officials familiar with the process.

The stark contrast between the testing haves at the White House and the have-nots on Capitol Hill makes clear that Mr. Trump’s pronouncement that “anybody that wants a test can get a test,” as he said in March, is far from true. Although the rich and powerful are clearly favored, not even all the powerful have equal access.
Unbelievable.

Norway has plenty of testing materials, we make them so don't have to quarrel with others. But offering help to the US is probably no good diplomatic idea. And they themselves really ought to be able to make what they need.

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Re: SARS-CoV-2 testing

Post by shpalman » Mon May 04, 2020 7:32 am

John Oliver on the dire testing situation in the US https://youtu.be/7rl4c-jr7g0
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Re: SARS-CoV-2 testing

Post by JQH » Mon May 04, 2020 7:43 am

Doesn't appear to be available in the UK
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Re: SARS-CoV-2 testing

Post by shpalman » Sun May 10, 2020 12:11 pm

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Re: SARS-CoV-2 testing

Post by AMS » Sun May 10, 2020 12:41 pm

I suspect a lot of the issues with test capacity are as much about the logistics. For example, there's the challenge of opening 100,000 sealed packages a day, while treating all of them as potentially contaminated and all needing to be accurately tracked.

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Re: SARS-CoV-2 testing

Post by Brightonian » Mon May 11, 2020 5:47 am


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Re: SARS-CoV-2 testing

Post by shpalman » Mon May 11, 2020 4:29 pm

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Re: SARS-CoV-2 testing

Post by raven » Mon May 11, 2020 11:20 pm

shpalman wrote:
Mon May 11, 2020 4:29 pm
This looks nice: https://twitter.com/StefanTigges/status ... 9919495170
I like that.

I haven't seen any recent figures for Covid-19 tests. Sensitivity seems to be given as something like 70% most places I've seen it. So 3 out of 10 people with Covid-19 test negative, which fits nicely with a paper I read that suggested a third of cases in people travelling out of China very early on in all this were getting missed.

No idea what the specifity is though.

Oh, and to support that twitter thread Brightonian linked to, this account of testing appeared in the Oxford Mail last week. The Oxford test site is run by Serco, so I figured it would be crap. I just didn't realise how crap.

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Re: SARS-CoV-2 testing

Post by Squeak » Mon May 11, 2020 11:47 pm

Not a comment on test accuracy but this seems like a good place to remind folk that Australia's stats are probably a good place to look for things like fatality rates in a modern, western, not-overwhelmed system. At our worst, our positive test rate was between 2% and 3%, so we were already doing a good job of testing people around each positive case. But now it's off the charts. Using the moving five-day average, Australia is currently performing ~33 000 tests per day to find ~15 cases. That's a positive test rate of 0.045%.

Since the UK's population is ~2.5 times Australia's, that ~33 000 translates to about 3/4 of the UK's claimed testing rates, it's just that Australia is actually doing them (And I think they're all being administered by trained folk, rather than DIY) and Australia kept control of the infections so the positive rate is low.

The numbers from Our World In Data are a little older and less exuberant, as our testing has been ramping up insanely this week - they say that on May 9th, Australia was performing 115 tests for every positive case. In contrast, the UK was performing just six test to find each case.

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Re: SARS-CoV-2 testing

Post by Fishnut » Tue May 12, 2020 8:52 am

raven wrote:
Mon May 11, 2020 11:20 pm
shpalman wrote:
Mon May 11, 2020 4:29 pm
This looks nice: https://twitter.com/StefanTigges/status ... 9919495170
I like that.

I haven't seen any recent figures for Covid-19 tests. Sensitivity seems to be given as something like 70% most places I've seen it. So 3 out of 10 people with Covid-19 test negative, which fits nicely with a paper I read that suggested a third of cases in people travelling out of China very early on in all this were getting missed.

No idea what the specifity is though.

Oh, and to support that twitter thread Brightonian linked to, this account of testing appeared in the Oxford Mail last week. The Oxford test site is run by Serco, so I figured it would be crap. I just didn't realise how crap.
This account from someone using the Gatwick suggests this is not a rogue testing site but how the government has decided to 'run' these facilities. It's a complete shitshow and I'm feeling more terrified now that I was at the start of the lockdown.

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Re: SARS-CoV-2 testing

Post by jaap » Tue May 12, 2020 11:37 am

Fishnut wrote:
Tue May 12, 2020 8:52 am
raven wrote:
Mon May 11, 2020 11:20 pm
Oh, and to support that twitter thread Brightonian linked to, this account of testing appeared in the Oxford Mail last week. The Oxford test site is run by Serco, so I figured it would be crap. I just didn't realise how crap.
This account from someone using the Gatwick suggests this is not a rogue testing site but how the government has decided to 'run' these facilities. It's a complete shitshow and I'm feeling more terrified now that I was at the start of the lockdown.
That is the original thread that Brightonian linked to and raven was replying to.

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Re: SARS-CoV-2 testing

Post by Fishnut » Tue May 12, 2020 11:44 am

jaap wrote:
Tue May 12, 2020 11:37 am
Fishnut wrote:
Tue May 12, 2020 8:52 am
raven wrote:
Mon May 11, 2020 11:20 pm
Oh, and to support that twitter thread Brightonian linked to, this account of testing appeared in the Oxford Mail last week. The Oxford test site is run by Serco, so I figured it would be crap. I just didn't realise how crap.
This account from someone using the Gatwick suggests this is not a rogue testing site but how the government has decided to 'run' these facilities. It's a complete shitshow and I'm feeling more terrified now that I was at the start of the lockdown.
That is the original thread that Brightonian linked to and raven was replying to.
sorry, i didn't read back far enough

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Re: SARS-CoV-2 testing

Post by gosling » Wed May 13, 2020 9:06 am

Boots recruiting unpaid volunteers to work a minimum of 25 hours a week at testing sites

The link is for the Wembley IKEA site, but there are adverts for another 35 sites.

I know a lot of people want to volunteer to do their bit to help, but 25 hours or more seems like they're taking the piss. Especially as, presumably, Boots have a contract from the government to run the sites.

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Re: SARS-CoV-2 testing

Post by Fishnut » Wed May 13, 2020 9:27 am

gosling wrote:
Wed May 13, 2020 9:06 am
Boots recruiting unpaid volunteers to work a minimum of 25 hours a week at testing sites

The link is for the Wembley IKEA site, but there are adverts for another 35 sites.

I know a lot of people want to volunteer to do their bit to help, but 25 hours or more seems like they're taking the piss. Especially as, presumably, Boots have a contract from the government to run the sites.
Why on earth is that a volunteer position?! Even minimum wage would be taking the piss really, but volunteer???

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Re: SARS-CoV-2 testing

Post by raven » Wed May 13, 2020 12:57 pm

The Oxford testing site is jointly run by Serco and Boots.

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Wed May 13, 2020 2:37 pm

f.cking embarrassing.
THINK BIG AND UPEND THE SYSTEM

#ShowYourStripes

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu May 14, 2020 6:32 am

Big 70 000 random sample antibody test in Spain. Only 5% infected overall. Implied IFR of 1-1.2%
https://elpais.com/sociedad/2020-05-13/ ... encia.html

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu May 14, 2020 7:03 am

Thread suggests that IFR in New York is 1.07
https://twitter.com/devansinha/status/1 ... 00832?s=21

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu May 14, 2020 7:16 am

Estimate that circa 5% of France has been infected, with an IFR of 0.7%
https://science.sciencemag.org/content/ ... c3517.full

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Re: SARS-CoV-2 testing

Post by bob sterman » Thu May 14, 2020 8:46 am

So now that robust data from New York, Spain and France suggest that John ioannidis' estimate of the IFR from his dodgy Santa Clara study was off by an order of magnitude or more - will he admit this his paper falls into the "Most Published Research Findings Are False" category?

Or has he jumped the shark completely - and will insist that the "most" refers to the findings from New York, Spain and France.

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Re: SARS-CoV-2 testing

Post by lpm » 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/
I'll miss him after he's fled to Riyadh

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Re: SARS-CoV-2 testing

Post by shpalman » Thu May 14, 2020 3:10 pm

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/
i.e. 26% https://www.medrxiv.org/content/10.1101 ... 20072264v1

(ETA as of three weeks ago given the preprint is dated 24th April)
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