SARS-CoV-2 testing

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

Post by Tessa K » Sat Sep 05, 2020 12:10 pm

headshot wrote:
Sat Sep 05, 2020 12:05 pm
I’ll take “corrupt privatisation of public services” please Bob.
With a side order of 'too busy counting my money to give a f.ck'.

I may have over-reacted btw, I think this is just a mild cold but I did feel rough yesterday. Easy to panic at the moment, especially if you're me.

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sat Sep 05, 2020 5:22 pm

shpalman wrote:
Sun Mar 15, 2020 6:45 pm
KAJ wrote:
Sun Mar 15, 2020 6:19 pm
Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?
I posted a link in the wrong thread in which it was found that the body sheds dead non-infectious virus during the recovery phase.
Coronavirus tests could be picking up dead virus

In Italy there is 'screening' for antibodies but if you're positive they do a swab. I wonder if it wouldn't be better to do it the other way around.
molto tricky

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sat Sep 05, 2020 7:32 pm

shpalman wrote:
Sat Sep 05, 2020 5:22 pm
shpalman wrote:
Sun Mar 15, 2020 6:45 pm
KAJ wrote:
Sun Mar 15, 2020 6:19 pm
Am I correct ? in my understanding that
  • the RT-PCR test detects the virus, so is only positive for active infections
  • the described antigen test would also be positive for those who had recovered
If so, would the antigen test be more useful than the RT-PCR test for monitoring the progress of the outbreak?
I posted a link in the wrong thread in which it was found that the body sheds dead non-infectious virus during the recovery phase.
Coronavirus tests could be picking up dead virus

In Italy there is 'screening' for antibodies but if you're positive they do a swab. I wonder if it wouldn't be better to do it the other way around.
... but if people are being tested because they present symptoms it's reasonable to assume it's because the covid is alive, not that it's dead already but they caught something else in the meantime
molto tricky

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shpalman
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Re: SARS-CoV-2 testing

Post by shpalman » Sat Sep 19, 2020 7:26 am

Hospitals told not to test staff or patients for Covid-19

It basically seems to be that they're being told that if they set up something as an alternative to the piss poor Test and Trace system they won't get any money to pay for it. Because the government wants to protect the monopoly it gave to the private sector.
molto tricky

Millennie Al
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Re: SARS-CoV-2 testing

Post by Millennie Al » Wed Sep 23, 2020 2:51 am

shpalman wrote:
Sat Sep 19, 2020 7:26 am
Hospitals told not to test staff or patients for Covid-19

It basically seems to be that they're being told that if they set up something as an alternative to the piss poor Test and Trace system they won't get any money to pay for it. Because the government wants to protect the monopoly it gave to the private sector.
While that might be part of it, I think the major part is preventing other organisations showing up the governement incompetence by showing that it is perfectly practical to do it right.
Covid-19 - Don't catch it: don't spread it.

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Gfamily
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Re: SARS-CoV-2 testing

Post by Gfamily » Sat Sep 26, 2020 9:50 pm

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!

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Re: SARS-CoV-2 testing

Post by shpalman » Fri Oct 02, 2020 6:04 pm

If you remember those images from the beginning of the European outbreak with the army lorries carrying coffins out of Bergamo because the crematoria couldn't cope?

The area of Bergamo in question was actually the low part of the Serio valley: the towns Nembro and Alzano Lombardo were mentioned on the news a lot.

Mass screening finds that 42.3% of the population in that area have antibodies

(The protocol here is that anyone who tests positive for antibodies needs a swab to test for the virus, but out of the subjects who had antibodies only 1.7% of were positive for the swab.)

What I hate about this sort of thing is that they never put that percentage into an absolute number in the context of the population of the area they're talking about and the number of cases and deaths in their official statistics.
molto tricky

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bob sterman
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Re: SARS-CoV-2 testing

Post by bob sterman » Mon Oct 05, 2020 6:03 am

Great - so our "world leading" test and trace system managed to temporarily lose 16,000 cases in one week - more cases than Norway has experience during the entire pandemic.

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Re: SARS-CoV-2 testing

Post by jimbob » Mon Oct 05, 2020 7:47 am

bob sterman wrote:
Mon Oct 05, 2020 6:03 am
Great - so our "world leading" test and trace system managed to temporarily lose 16,000 cases in one week - more cases than Norway has experience during the entire pandemic.
And confusing statements about when those positive cases were told to isolate
Have you considered stupidity as an explanation

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Re: SARS-CoV-2 testing

Post by shpalman » Mon Oct 05, 2020 8:19 am

jimbob wrote:
Mon Oct 05, 2020 7:47 am
bob sterman wrote:
Mon Oct 05, 2020 6:03 am
Great - so our "world leading" test and trace system managed to temporarily lose 16,000 cases in one week - more cases than Norway has experience during the entire pandemic.
And confusing statements about when those positive cases were told to isolate
Worse, their contacts wouldn't have been traced. There could be tens of thousands of extra infections caused because of this.

The doubling time is about a week, and this data came in a week late, but it was "only" maybe ~25% of the cases. Somebody else can work out how many extra deaths this will lead to, assuming this still isn't enough to push the health service into saturation leave-people-to-die triage mode. It's too early on a Monday for me.
molto tricky

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jimbob
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Re: SARS-CoV-2 testing

Post by jimbob » Mon Oct 05, 2020 8:26 am

shpalman wrote:
Mon Oct 05, 2020 8:19 am
jimbob wrote:
Mon Oct 05, 2020 7:47 am
bob sterman wrote:
Mon Oct 05, 2020 6:03 am
Great - so our "world leading" test and trace system managed to temporarily lose 16,000 cases in one week - more cases than Norway has experience during the entire pandemic.
And confusing statements about when those positive cases were told to isolate
Worse, their contacts wouldn't have been traced. There could be tens of thousands of extra infections caused because of this.

The doubling time is about a week, and this data came in a week late, but it was "only" maybe ~25% of the cases. Somebody else can work out how many extra deaths this will lead to, assuming this still isn't enough to push the health service into saturation leave-people-to-die triage mode. It's too early on a Monday for me.
I was thinking it depended on how and where the data went missing. And the answer is - early enough in the process to completely be useless
Have you considered stupidity as an explanation

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mediocrity511
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Re: SARS-CoV-2 testing

Post by mediocrity511 » Mon Oct 05, 2020 9:28 am

shpalman wrote:
Mon Oct 05, 2020 8:19 am
jimbob wrote:
Mon Oct 05, 2020 7:47 am


And confusing statements about when those positive cases were told to isolate
Worse, their contacts wouldn't have been traced. There could be tens of thousands of extra infections caused because of this.

The doubling time is about a week, and this data came in a week late, but it was "only" maybe ~25% of the cases. Somebody else can work out how many extra deaths this will lead to, assuming this still isn't enough to push the health service into saturation leave-people-to-die triage mode. It's too early on a Monday for me.
It also depends who the data was from. A lot of the Nottingham cases seem to be students and I think most unis are running some variety of track and trace themselves, which hopefully will limit the impact somewhat. A massive shitshow though.

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bob sterman
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Re: SARS-CoV-2 testing

Post by bob sterman » Mon Oct 05, 2020 11:30 am

mediocrity511 wrote:
Mon Oct 05, 2020 9:28 am
It also depends who the data was from. A lot of the Nottingham cases seem to be students and I think most unis are running some variety of track and trace themselves, which hopefully will limit the impact somewhat. A massive shitshow though.
Surely the most likely scenario is that the dropped cases are from one lab? Perhaps a new lab facility that came online last week - or one that had some sort of IT "upgrade" last week? Or perhaps a network of labs belonging to a single test providing organisation?

E.g. in early September there was talk of a new "Loughborough lighthouse lab" opening by the end of September. No idea if it actually opened - but anything that opening in that last week of September has got to be a prime suspect.

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RoMo
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Re: SARS-CoV-2 testing

Post by RoMo » Mon Oct 05, 2020 11:56 am

bob sterman wrote:
Mon Oct 05, 2020 11:30 am
E.g. in early September there was talk of a new "Loughborough lighthouse lab" opening by the end of September. No idea if it actually opened - but anything that opening in that last week of September has got to be a prime suspect.
No, it hasn't opened yet and apparently not until the end of October.

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bob sterman
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Re: SARS-CoV-2 testing

Post by bob sterman » Mon Oct 05, 2020 11:59 am

RoMo wrote:
Mon Oct 05, 2020 11:56 am
bob sterman wrote:
Mon Oct 05, 2020 11:30 am
E.g. in early September there was talk of a new "Loughborough lighthouse lab" opening by the end of September. No idea if it actually opened - but anything that opening in that last week of September has got to be a prime suspect.
No, it hasn't opened yet and apparently not until the end of October.
OK - cross Loughborough off the list of suspects!

Actually latest rumour in the news is that it was something to do with an Excel spreadsheet getting too full :shock:

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Re: SARS-CoV-2 testing

Post by Gfamily » Mon Oct 05, 2020 12:05 pm

bob sterman wrote:
Mon Oct 05, 2020 11:59 am
RoMo wrote:
Mon Oct 05, 2020 11:56 am
bob sterman wrote:
Mon Oct 05, 2020 11:30 am
E.g. in early September there was talk of a new "Loughborough lighthouse lab" opening by the end of September. No idea if it actually opened - but anything that opening in that last week of September has got to be a prime suspect.
No, it hasn't opened yet and apparently not until the end of October.
OK - cross Loughborough off the list of suspects!

Actually latest rumour in the news is that it was something to do with an Excel spreadsheet getting too full :shock:
I'm hearing they had 1 column per 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!

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lpm
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Re: SARS-CoV-2 testing

Post by lpm » Mon Oct 05, 2020 12:23 pm

I'm hearing there's another thread where we've already talked about it.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: SARS-CoV-2 testing

Post by raven » Mon Oct 05, 2020 2:27 pm

bob sterman wrote:
Mon Oct 05, 2020 11:59 am
Actually latest rumour in the news is that it was something to do with an Excel spreadsheet getting too full :shock:
Johnson used the word 'truncated' which does, if he wasn't just using a big word to sound clever yet again, have a specific meaning wrt databases. Or so MrRaven tells me. Something something limits on the size of a datadump something something.

Also just read somewhere that PHE have admitted the fault was at their end of the data transfer.

It is sh.t, however. And I'd like to know how no-one noticed for 8 days...

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Re: SARS-CoV-2 testing

Post by sTeamTraen » Tue Oct 06, 2020 9:11 pm

raven wrote:
Mon Oct 05, 2020 2:27 pm
Johnson used the word 'truncated' which does, if he wasn't just using a big word to sound clever yet again, have a specific meaning wrt databases. Or so MrRaven tells me. Something something limits on the size of a datadump something something.
Truncate (or TRUNCATE) is a command in the SQL database language, but it is also a perfectly good computer-related word to describe what happens to any file containing 80,000 records of data when you open them in a system that can't handle that many, and it can be used for a plain text file as well. The use of this word in SQL is derived from its ordinary English meaning. So I think MrRaven is being a little too keen to bash Boris here. (Which is otherwise entirely understandable, of course.)
Something something hammer something something nail

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Re: SARS-CoV-2 testing

Post by Boustrophedon » Wed Oct 07, 2020 12:53 pm

And now there's a shortage of Roche testing kits due to a problem in an automated warehouse. https://www.ft.com/content/aa48893b-9c9 ... bda727bbda

Or to quote my local GP health centre.
URGENT NOTIFICATION
UNFORTUNATELY THERE IS A NATIONAL PROBLEM WITH THE CHEMICALS USED BY LABORATORIES WHEN TESTING BLOOD SAMPLES.
SO, WITH IMMEDIATE EFFECT, WE HAVE BEEN INFORMED TO PAUSE ROUTINE TESTING OF BLOOD SAMPLES. WE DO NOT KNOW WHEN A NORMAL SERVICE WILL RESUME.
REGRETTABLY WE WILL HAVE TO CONTACT MANY PATIENTS TO CANCEL THEIR BLOOD TEST APPOINTMENTS. WE RECOGNISE THIS WILL CAUSE FRUSTRATION AND ANXIETY AND APOLOGISE FOR THIS BUT THIS SITUATION IS COMPLETELY OUTSIDE THE PRACTICE'S CONTROL.
THE DEPARTMENT OF HEALTH IS LOOKING INTO THIS AND WE WILL KEEP YOU UPDATED ONCE WE HAVE MORE INFORMATION.
PATIENTS WHO REQUIRE URGENT BLOOD TESTS WILL BE PRIORITISED BY THE CLINICAL TEAM.
THANK YOU FOR YOUR UNDERSTANDING AT THIS TIME.
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Re: SARS-CoV-2 testing

Post by Sciolus » Wed Oct 07, 2020 1:20 pm

Boustrophedon wrote:
Wed Oct 07, 2020 12:53 pm
And now there's a shortage of Roche testing kits due to a problem in an automated warehouse. https://www.ft.com/content/aa48893b-9c9 ... bda727bbda
Thanks, Brexit.

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Re: SARS-CoV-2 testing

Post by Boustrophedon » Wed Oct 07, 2020 1:36 pm

In case you can't read the FT link, here's the story on the Beeb: https://www.bbc.co.uk/news/health-54435226
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bob sterman
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Re: SARS-CoV-2 testing

Post by bob sterman » Thu Oct 08, 2020 5:41 pm

So the number of new cases reported today was about 17,500 - but the Kings College Zoe symptom study is only estimating 21,903 new cases per day.

Can we really be detecting 80% of infections????

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Re: SARS-CoV-2 testing

Post by badger » Thu Oct 08, 2020 7:50 pm

bob sterman wrote:
Thu Oct 08, 2020 5:41 pm
So the number of new cases reported today was about 17,500 - but the Kings College Zoe symptom study is only estimating 21,903 new cases per day.

Can we really be detecting 80% of infections????
Interesting, because if you spread out today's 17,500 over date of specimen, and then extrapolate (assuming 9 day doubling) you get 21/22k today.

See this thread:
https://twitter.com/RP131/status/1314222917580980224

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lpm
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Re: SARS-CoV-2 testing

Post by lpm » Thu Oct 08, 2020 8:21 pm

bob sterman wrote:
Thu Oct 08, 2020 5:41 pm
So the number of new cases reported today was about 17,500 - but the Kings College Zoe symptom study is only estimating 21,903 new cases per day.

Can we really be detecting 80% of infections????
No of course we can't.

The King College reports have been disasters, week after week.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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