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Re: SARS-CoV-2 testing
Posted: Sat Sep 05, 2020 12:10 pm
by Tessa K
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.
Re: SARS-CoV-2 testing
Posted: Sat Sep 05, 2020 5:22 pm
by shpalman
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.
Re: SARS-CoV-2 testing
Posted: Sat Sep 05, 2020 7:32 pm
by shpalman
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
Re: SARS-CoV-2 testing
Posted: Sat Sep 19, 2020 7:26 am
by shpalman
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.
Re: SARS-CoV-2 testing
Posted: Wed Sep 23, 2020 2:51 am
by Millennie Al
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.
Re: SARS-CoV-2 testing
Posted: Sat Sep 26, 2020 9:50 pm
by Gfamily
Re: SARS-CoV-2 testing
Posted: Fri Oct 02, 2020 6:04 pm
by shpalman
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 6:03 am
by bob sterman
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 7:47 am
by jimbob
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
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 8:19 am
by shpalman
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 8:26 am
by jimbob
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
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 9:28 am
by mediocrity511
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 11:30 am
by bob sterman
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 11:56 am
by RoMo
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.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 11:59 am
by bob sterman
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
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 12:05 pm
by Gfamily
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
I'm hearing they had 1
column per test !
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 12:23 pm
by lpm
I'm hearing there's another thread where we've already talked about it.
Re: SARS-CoV-2 testing
Posted: Mon Oct 05, 2020 2:27 pm
by raven
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
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...
Re: SARS-CoV-2 testing
Posted: Tue Oct 06, 2020 9:11 pm
by sTeamTraen
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.)
Re: SARS-CoV-2 testing
Posted: Wed Oct 07, 2020 12:53 pm
by Boustrophedon
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.
Re: SARS-CoV-2 testing
Posted: Wed Oct 07, 2020 1:20 pm
by Sciolus
Re: SARS-CoV-2 testing
Posted: Wed Oct 07, 2020 1:36 pm
by Boustrophedon
In case you can't read the FT link, here's the story on the Beeb:
https://www.bbc.co.uk/news/health-54435226
Re: SARS-CoV-2 testing
Posted: Thu Oct 08, 2020 5:41 pm
by bob sterman
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????
Re: SARS-CoV-2 testing
Posted: Thu Oct 08, 2020 7:50 pm
by badger
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
Re: SARS-CoV-2 testing
Posted: Thu Oct 08, 2020 8:21 pm
by lpm
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.