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 » Tue Jul 07, 2020 7:14 am

Spain has 28 388 confirmed Covid deaths and according to the FT about 48 000 excess deaths. Making the IFR between about 1.2-2%.

ETA The latter number is pretty high. Could be a sign of what happens when the healthcare system gets overwhelmed which causes higher mortality in milder Covid cases and non-Covid cases who can’t get treatment.

Alternatively, another explanation is that large numbers of people who were infected didn’t have detectable antibodies when they did the tests.

EETA as mentioned here people with a mild infection may not have have detectable antibodies for long: https://www.nature.com/articles/d41586-020-01989-z

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Tue Jul 07, 2020 7:24 am

Woodchopper wrote:
Tue Jul 07, 2020 7:14 am
Spain has 28 388 confirmed Covid deaths and according to the FT about 48 000 excess deaths. Making the IFR between about 1.2-2%.
So for Spain to get herd immunity without the vaccine would mean about half a million people dying, not to mention how many of the survivors would have life-changing long term complications.

Who on earth thought the UK's strategy back in March was sensible?
molto tricky

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Tue Jul 07, 2020 7:36 am

shpalman wrote:
Tue Jul 07, 2020 7:24 am
Woodchopper wrote:
Tue Jul 07, 2020 7:14 am
Spain has 28 388 confirmed Covid deaths and according to the FT about 48 000 excess deaths. Making the IFR between about 1.2-2%.
So for Spain to get herd immunity without the vaccine would mean about half a million people dying, not to mention how many of the survivors would have life-changing long term complications.

Who on earth thought the UK's strategy back in March was sensible?
Half a million is in the ballpark of the 16 March Imperial modeling for the UK. Pity they didn’t predict that earlier.

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Tue Jul 07, 2020 7:51 am

All the 16 March Imperial model really did was put a scale on the y-axis of the graph.
molto tricky

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jimbob
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Re: SARS-CoV-2 testing

Post by jimbob » Tue Jul 07, 2020 8:57 am

shpalman wrote:
Tue Jul 07, 2020 7:24 am
Woodchopper wrote:
Tue Jul 07, 2020 7:14 am
Spain has 28 388 confirmed Covid deaths and according to the FT about 48 000 excess deaths. Making the IFR between about 1.2-2%.
So for Spain to get herd immunity without the vaccine would mean about half a million people dying, not to mention how many of the survivors would have life-changing long term complications.

Who on earth thought the UK's strategy back in March was sensible?
Yes, which is inline with the experience from the Korean church outbreak, which was the best measure of a known population at yhe time.

Quoting myself as that shows the date.



https://twitter.com/ParkinJim/status/12 ... 92800?s=20
Yes, and this has the potential to be about as bad. A mix of symptoms similar to a bad (or possibly even a mild) cold in many, but severe in say, 20% and lethal even in 1-2% is a recipe for a huge impact.
Have you considered stupidity as an explanation

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Gentleman Jim
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Re: SARS-CoV-2 testing

Post by Gentleman Jim » Tue Jul 07, 2020 1:16 pm

My son has not long started as an EMD.
Initially, all the staff (dispatch and ambulance) were tested weekly as a routine, but the government stopped this. Now they can get tested IF they ask for one, and have to justify why they think they need testing
Rules are for the guidance of wise men and the obedience of fools.

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discovolante
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Re: SARS-CoV-2 testing

Post by discovolante » Tue Jul 07, 2020 1:20 pm

Gentleman Jim wrote:
Tue Jul 07, 2020 1:16 pm
My son has not long started as an EMD.
Initially, all the staff (dispatch and ambulance) were tested weekly as a routine, but the government stopped this. Now they can get tested IF they ask for one, and have to justify why they think they need testing
What was their stated reason for stopping it?
don't get any big ideas, they're not gonna happen

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Gentleman Jim
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Re: SARS-CoV-2 testing

Post by Gentleman Jim » Tue Jul 07, 2020 1:50 pm

discovolante wrote:
Tue Jul 07, 2020 1:20 pm
Gentleman Jim wrote:
Tue Jul 07, 2020 1:16 pm
My son has not long started as an EMD.
Initially, all the staff (dispatch and ambulance) were tested weekly as a routine, but the government stopped this. Now they can get tested IF they ask for one, and have to justify why they think they need testing
What was their stated reason for stopping it?
Partly but mostly because it takes an ambulance off the road for a day apparently. That was ok during lock down but now people are getting back to normal, ambulance requirements are vastly increased
Rules are for the guidance of wise men and the obedience of fools.

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Gentleman Jim
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Re: SARS-CoV-2 testing

Post by Gentleman Jim » Tue Jul 07, 2020 3:00 pm

Workers who have coronavirus tests paid for by their employer will have to pay tax on them.

Tax authorities have confirmed that tests will be treated as a "benefit in kind", and so will be subject to extra income tax for employees.

With some companies requiring regular tests, the tax bills will mount, Treasury Committee chairman Mel Stride has warned.

Chancellor Rishi Sunak has promised to look into the issue "very quickly".

"Many employees, especially healthcare and hospitality workers, are required to undergo regular coronavirus testing," said Mr Stride.

He said the new guidance from HM Revenue and Customs "is unclear and will worry a large number of workers".

"Many of our key workers could be faced with the perverse incentive of avoiding employer-sponsored tests in order to reduce their tax bill," he added.
https://www.bbc.co.uk/news/business-53324101

Well, that will help halt the virus :shock: :shock: :shock:
Rules are for the guidance of wise men and the obedience of fools.

TheScientificHippy
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Re: SARS-CoV-2 testing

Post by TheScientificHippy » Wed Jul 08, 2020 5:18 pm

Gentleman Jim wrote:
Tue Jul 07, 2020 1:16 pm
My son has not long started as an EMD.
Initially, all the staff (dispatch and ambulance) were tested weekly as a routine, but the government stopped this. Now they can get tested IF they ask for one, and have to justify why they think they need testing
Wow - Which Ambulance service? In London apart from taking in part in one of the studies of asymptomatic people we have only ever been able to get tested if we are symptomatic.
We have been having antibody testing too but that only really tells us anything at a population level.

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Gentleman Jim
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Re: SARS-CoV-2 testing

Post by Gentleman Jim » Thu Jul 09, 2020 7:34 am

SECamb
Rules are for the guidance of wise men and the obedience of fools.

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Jul 09, 2020 9:32 am

Coronavirus: The inside story of how UK's 'chaotic' testing regime 'broke all the rules'

Insiders reveal that data collection was haphazard, as officials went against accepted practice and "buffed the system".
https://news.sky.com/story/coronavirus- ... s-12022566
Sky News has learned that in the early days of mass COVID-19 testing, the statistical problems were so deep that one minister sat at their desk with Excel spreadsheets in front of them, calling round to try to collect data to use in each daily press conference.

Even as Health Secretary Matt Hancock struggled to get the number of tests carried out up to 100,000 a day by the end of April, the collection of those testing statistics was still so primitive that they were being compiled with pen and paper.

Sky News has uncovered hand-written tables of testing data, allegedly from mid-May, which show national testing figures for different parts of the operation.

[...]

Many working in NHS pathology labs reject that characterisation.

They argue that if the government had turned to them, then testing would be in a far better position - and point to their successes as proof.

Others working in academic labs say they offered their services to the government and PHE to push up testing capacity.

But in March, the government decided to reject those advances and set up an entirely separate network of testing sites and facilities, run in large part by commercial partners.

It was a bold, disruptive move in the face of what was seen as foot-dragging by PHE and NHS labs, but multiple sources from inside government, from labs and from the technology sector told Sky News it was this move more than any other that set in motion the problems with testing results and data that have plagued the system ever since.

[...]

In the face of the unprecedented outbreak, less thought and time than usual was given to putting in place the systems and safeguards that would ensure test results could be robustly reported and tabulated into the data that would help inform Britain's response to COVID-19.

Quantity trumped quality.

[...]

Tom Lewis, a doctor who oversees testing at North Devon Healthcare NHS Trust, says that when tests are carried out by his own labs the results come back within 12 hours.

Most importantly, those results are tied to crucial data points: they are filed alongside each person's unique NHS number, forming a permanent, traceable record of their coronavirus status.

By contrast, when tests are done by the national system, the results take far longer to arrive, in large part because the tests need to be transported to the Lighthouse Labs before processing.

Worryingly, those crucial data points, including links with an NHS number, are not routinely collected - making it extremely difficult to reconcile the test results with a given individual and their accompanying medical records.

This helps explain why DHSC was unable for many weeks to publish data for the number of people tested in England.

[...]

Dr Lewis said the data problems are particularly acute when he attempts to get confirmation of test results for his staff from Pillar 2 centres.

In order to verify that a staff member has been tested, he has been forced to ask for screenshots, which he then enters manually into an Excel spreadsheet.

Handling an outbreak at a care home, he was unable to find out who had been tested and what the results were.

"You know things have happened and you don't know when and to whom," he says. "It's a mess, a total mess."

[...]

Many of those Sky News has talked to referred back to that fateful decision to reject the offers of help from the existing lab community - both in hospitals and the academic sector - as one of the moments things started to go wrong.

[...]

As one senior insider put it: "There's a growing recognition that we may never know for sure what happened with many of those early tests.

"We will probably never know how many people have been tested for the virus."

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Jul 09, 2020 10:30 am

How government blindfolded frontline public health experts fighting Covid’s next phase
After months of battling to get basic information out of government, those tasked with containing the pandemic on the ground have run out of patience
https://www.manchestereveningnews.co.uk ... c-18566511

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Fri Jul 10, 2020 4:38 am

Woodchopper wrote:
Tue Jul 07, 2020 7:14 am
Spain has 28 388 confirmed Covid deaths and according to the FT about 48 000 excess deaths. Making the IFR between about 1.2-2%.

ETA The latter number is pretty high. Could be a sign of what happens when the healthcare system gets overwhelmed which causes higher mortality in milder Covid cases and non-Covid cases who can’t get treatment.

Alternatively, another explanation is that large numbers of people who were infected didn’t have detectable antibodies when they did the tests.

EETA as mentioned here people with a mild infection may not have have detectable antibodies for long: https://www.nature.com/articles/d41586-020-01989-z
Another comment on the likelihood that antibodies aren’t detectable after a period.

https://blogs.sciencemag.org/pipeline/a ... -ignorance

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sun Jul 12, 2020 6:57 pm

molto tricky

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Mon Jul 13, 2020 7:41 am

shpalman wrote:
Sun Jul 12, 2020 6:57 pm
The Guardian too: https://www.theguardian.com/world/2020/ ... y-suggests
Here’s the paper

Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection

https://www.medrxiv.org/content/10.1101 ... 20148429v1

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Woodchopper
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Re: SARS-CoV-2 testing

Post by Woodchopper » Mon Jul 13, 2020 7:43 am

It’s not how old you are. But how old you feel:

COVID-19 severity is predicted by earlier evidence of accelerated aging
https://www.medrxiv.org/content/10.1101 ... 20147777v1

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headshot
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Re: SARS-CoV-2 testing

Post by headshot » Mon Jul 13, 2020 12:57 pm

Got my test results back from the Ipsos Moro/Imperial swab and spit test research: negative. (I showed no symptoms)

Weird thing is the text I got:
Thank you for completing the COVID-19 swab test. Your swab analysis results indicate that you are COVID-19 negative. Although results are not 100% conclusive, it is important that you and your household continue to observe social distancing guidance. If you or anyone in your household has or develops symptoms you must follow the Stay at Home Guidance even if you have a negative result. For the current Government guidance about COVID-19 go to www.gov.uk/coronavirus
My bold. WTF is that about? Do they not trust their own tests?

I thought testing was supposed to be a way for people to get back out of isolation and into the workforce.

Or is it just in case someone gets a negative test and then shows symptoms days or weeks later?

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Gfamily
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Re: SARS-CoV-2 testing

Post by Gfamily » Mon Jul 13, 2020 1:12 pm

headshot wrote:
Mon Jul 13, 2020 12:57 pm
Got my test results back from the Ipsos Moro/Imperial swab and spit test research: negative. (I showed no symptoms)

Weird thing is the text I got:
Thank you for completing the COVID-19 swab test. Your swab analysis results indicate that you are COVID-19 negative. Although results are not 100% conclusive, it is important that you and your household continue to observe social distancing guidance. If you or anyone in your household has or develops symptoms you must follow the Stay at Home Guidance even if you have a negative result. For the current Government guidance about COVID-19 go to www.gov.uk/coronavirus
My bold. WTF is that about? Do they not trust their own tests?

I thought testing was supposed to be a way for people to get back out of isolation and into the workforce.

Or is it just in case someone gets a negative test and then shows symptoms days or weeks later?
That's possible, I think it can take a few days for the test to show as positive.
It's also that you might have picked up an infection since taking the test
My avatar was a scientific result that was later found to be 'mistaken' - I rarely claim to be 100% correct
ETA 5/8/20: I've been advised that the result was correct, it was the initial interpretation that needed to be withdrawn
Meta? I'd say so!

badger
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Re: SARS-CoV-2 testing

Post by badger » Mon Jul 13, 2020 6:24 pm

Did anyone hear the latest More or Less ?

UK Govt admit 2 million tests *not* returned/processed. That's 66% of all sent out so far!!! Not sure why this hasn't been in the headlines today (that I've seen). Surely they should be tearing Hancock a new one?

(also contains interesting Swedish analysis)

bob sterman
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Re: SARS-CoV-2 testing

Post by bob sterman » Mon Jul 13, 2020 8:23 pm

headshot wrote:
Mon Jul 13, 2020 12:57 pm
Got my test results back from the Ipsos Moro/Imperial swab and spit test research: negative. (I showed no symptoms)

Weird thing is the text I got:
Thank you for completing the COVID-19 swab test. Your swab analysis results indicate that you are COVID-19 negative. Although results are not 100% conclusive, it is important that you and your household continue to observe social distancing guidance. If you or anyone in your household has or develops symptoms you must follow the Stay at Home Guidance even if you have a negative result. For the current Government guidance about COVID-19 go to www.gov.uk/coronavirus
My bold. WTF is that about? Do they not trust their own tests?

I thought testing was supposed to be a way for people to get back out of isolation and into the workforce.

Or is it just in case someone gets a negative test and then shows symptoms days or weeks later?
You took the test as part of a research project - right?

Back in May if you requested a home test from gov.uk and it came back negative you got this message....
Your recent COVID-19 test has been processed and has come back NEGATIVE. If you are a key worker, please contact your employer about returning to work. Continue to follow government advice at https://www.gov.uk/coronavirus.
It's pretty standard with many health research projects for participants to be told not to rely on the results for clinical purposes.

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headshot
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Re: SARS-CoV-2 testing

Post by headshot » Mon Jul 13, 2020 8:33 pm

Ah, that makes a lot of sense.

I had a symptomatic test back in June, let me check that message...

Ah yes, you're completely right. "You may return to work if you've not had a fever for 48 hours".

I didn't realised that about clinical trial tests.

EllyCat
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Re: SARS-CoV-2 testing

Post by EllyCat » Wed Jul 15, 2020 6:20 pm

So the Council are leafleting areas of Leicester with high rates asking everyone to get tested, even if you don’t show any symptoms. Which is a good idea but:

1) There are now no testing vacancies at drive through testing centres nearby

2) If you’re sending somebody door-to-door leafleting, why not get them distributing self-test kits instead of relying on people being able/bothered to order them or having people with a low expose risk clog up drive-through slots? Missed opportunity there! Especially when staff/students/alumni of the University of Leicester have been asked to volunteer to do exactly that (so I can’t imagine it’s a manpower problem).

Any good replies for point 2) before I email the council and point out they missed the ball? ‘Cos I imagine they’ll be doing this again - we aren’t coming out of lockdown any time soon... :|

Edit to update: oh, and you can’t book a test at home kit online unless they pass your details on to a third party. That’s going to help uptake.

raven
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Re: SARS-CoV-2 testing

Post by raven » Wed Jul 15, 2020 9:06 pm

EllyCat wrote:
Wed Jul 15, 2020 6:20 pm
Edit to update: oh, and you can’t book a test at home kit online unless they pass your details on to a third party. That’s going to help uptake.
Is the third party the local public health officials, I wonder. Because they were complaining about not having access to the data from the Lighthouse test centres or whatever we're calling them.

That would make sense, and I'd hope that's where Boots/Serco/whoever's doing the testing is passing it on to.

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