COVID-19

Covid-19 discussion, bring your own statistics
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raven
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Re: COVID-19

Post by raven » Sat Oct 09, 2021 9:26 pm

Seagull wrote:
Thu Oct 07, 2021 1:18 pm
I know this article is lifted directly from Kit Yates' twitter.
Pos LFT Neg PCR
But it does seem to be a genuine issue - I know a family for whom this is the case right now:
Child clear positive on routine LFT, asymptomatic so far, negative PCR next day (so back in school). At least 4 others in the same class have had the same thing.
Next day, parent clear positive on LFT, negative PCR next day, now feeling ill.

Anyone else come across this, or have any insight as to what might be going on here??
The teacher my sister works with had symptoms, got a 'faint positive' on LFT, but negative PCR. Sister had the same cold, tested negative repeatedly on LFT, but a fortnight on can't seem to shake the fatigue and is starting to wonder.

Is it maybe another coronavirus that's tripping one test and not the other? Or if you're vaccinated, and you do regular LFTs, that's picking up Covid as soon as you catch it, but by the time you've got a PCR done your antibodies have reduced the virus levels enough that it doesn't show up?

If it's another variant, presumably they're still sequencing enough of the PCR samples to pick that up.

raven
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Re: COVID-19

Post by raven » Sat Oct 09, 2021 10:25 pm

Or - d'oh - maybe it's simply the maths of following a LFT with a very low false positive rate with a PCR test that throws out some false negatives, as this guy says:

https://twitter.com/BristOliver/status/ ... XZpqw&s=19

Also this article on LFTs is very informative:
https://www.medicaldevice-network.com/f ... w-testing/

tl;dr version: LFT as screening for asymptomatic cases may be pointless because a) if you're truly asymptomatic you're much much less infectious anyway, and b) even picking up 'pre-symptomatic' cases might not have much impact, given that stage is so brief.

Grauniad is reportingadvice has been changed to Isolate if you have Covid symptoms but negative PCR.

raven
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Re: COVID-19

Post by raven » Sat Oct 09, 2021 10:26 pm

raven wrote:
Sat Oct 09, 2021 10:25 pm
Or - d'oh - maybe it's simply the maths of following a LFT with a very low false positive rate with a PCR test that throws out some false negatives, as this guy says:

https://twitter.com/BristOliver/status/ ... XZpqw&s=19

Also this article on LFTs is very informative:
https://www.medicaldevice-network.com/f ... w-testing/

tl;dr version: LFT as screening for asymptomatic cases may be pointless because a) if you're truly asymptomatic you're much much less infectious anyway, and b) even picking up 'pre-symptomatic' cases might not have much impact, given that stage is so brief.

Grauniad is reporting advice has been changed to Isolate if you have Covid symptoms but negative PCR.

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sTeamTraen
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Re: COVID-19

Post by sTeamTraen » Sat Oct 09, 2021 10:28 pm

raven wrote:
Sat Oct 09, 2021 10:25 pm
Grauniad is reportingadvice has been changed to Isolate if you have Covid symptoms but negative PCR.
Probably not a bad idea if we are indeed in for a bad flu season.
Something something hammer something something nail

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lpm
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Re: COVID-19

Post by lpm » Sat Oct 09, 2021 10:46 pm

Not sure what the point of Covid testing is at this stage.

Either do both flu and Covid or neither.

We have enough data from surveys and hospitalization info.
What ever happened to that Trump guy, you know, the one who was president for a bit?

raven
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Re: COVID-19

Post by raven » Sat Oct 09, 2021 10:51 pm

sTeamTraen wrote:
Sat Oct 09, 2021 10:28 pm
raven wrote:
Sat Oct 09, 2021 10:25 pm
Grauniad is reportingadvice has been changed to Isolate if you have Covid symptoms but negative PCR.
Probably not a bad idea if we are indeed in for a bad flu season.
That's just what I was thinking. 'Cos there's always some brave fool (ahem, eldest, my brother, etc etc) who overdoses on paracetamol & goes to work with flu. Maybe this way they'll stay at home.

Herainestold
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Re: COVID-19

Post by Herainestold » Sat Oct 09, 2021 11:15 pm

sTeamTraen wrote:
Sat Oct 09, 2021 10:28 pm
raven wrote:
Sat Oct 09, 2021 10:25 pm
Grauniad is reportingadvice has been changed to Isolate if you have Covid symptoms but negative PCR.
Probably not a bad idea if we are indeed in for a bad flu season.

Indeed. Maybe restrictions for flu pandemics could be a thing and save many lives.
Vaccination saves lives. Lockdowns stop transmission.We need both to end this pandemic.

OffTheRock
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Re: COVID-19

Post by OffTheRock » Sun Oct 10, 2021 12:25 am

raven wrote:
Sat Oct 09, 2021 10:25 pm
Or - d'oh - maybe it's simply the maths of following a LFT with a very low false positive rate with a PCR test that throws out some false negatives, as this guy says:

https://twitter.com/BristOliver/status/ ... XZpqw&s=19

Also this article on LFTs is very informative:
https://www.medicaldevice-network.com/f ... w-testing/

tl;dr version: LFT as screening for asymptomatic cases may be pointless because a) if you're truly asymptomatic you're much much less infectious anyway, and b) even picking up 'pre-symptomatic' cases might not have much impact, given that stage is so brief.

Grauniad is reportingadvice has been changed to Isolate if you have Covid symptoms but negative PCR.
That was my initial thought, but I’m not sure it’s the case. There are schools in areas where there is lots of testing going on due to covid outbreaks seeing almost no cases of this whereas schools where the number of cases/suspected cases is lower are seeing dozens of cases. And I’d have thought it would be the other way round if it was just the maths.

LFTs generally require a higher viral load to get a positive than a PCR, I’d think it was unlikely viral load would have dropped enough between the LFT and getting a PCR for that to be the issue.

Other possible explanations:
LFTs picking up something that isn’t SARSCOV2
Dodgy batch of PCR tests
Dodgy testing process at one of the labs
New variant that isn’t picked up on the PCR tests in use in the U.K.

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jdc
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Re: COVID-19

Post by jdc » Sun Oct 10, 2021 4:26 pm

No idea about LFTs picking up something that isn’t SARSCOV2.

Dodgy batch of PCR tests might be a possibility if we've given the contract to a mate of a cabinet minister who's never made them before.

Dodgy testing process at one of the labs sounds plausible. Remember this Panorama? https://www.bbc.co.uk/programmes/m000tqjj

New variant is possible, but unlikely.
Theoretically, a mutation in the virus genome at the site to which either oligonucleotide primer should bind, may destabilise the interaction such that, despite the presence of virus genome, a negative result ensues. To mitigate against this possibility, primers are chosen to highly conserved regions of the genomes. In addition, tests can rely on more than one pair of primers that bind to different conserved regions of the genome, so that any single mutation is unable to prevent a positive test result.

Currently, the low level of changes in the SARS-CoV-2 genome make such false negative results improbable. In addition, the availability of new SARS-CoV-2 genome sequences as they are deposited openly in GISAID, enables the commercial manufacturers of test kits to monitor whether the primers chosen for current tests are likely to remain sensitive and specific, or require updating
https://royalsociety.org/-/media/policy ... alysis.pdf

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shpalman
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Re: COVID-19

Post by shpalman » Sun Oct 10, 2021 4:38 pm

More anecdata https://twitter.com/fascinatorfun/statu ... rWbNA&s=19
H/t @ActuaryByDay (who I trust)

“Anecdote warning: An actuary I trust told me that his son’s school year had 62 positive LFTs, of which 60 were PCR negative. Can’t explain that one away with Bayes Theorem!”
molto tricky

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jdc
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Re: COVID-19

Post by jdc » Sun Oct 10, 2021 4:52 pm

Couple of additional suggestions from Kit Yates - increased reporting, people faking a positive LFT result, or changes in test accuracy due to vaccination or demographic infected. (He also thinks faulty tests and new variant are possible explanations.)

More here, including a diagram based on 1% prevalence https://twitter.com/Kit_Yates_Maths/sta ... 6328343552

OffTheRock
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Re: COVID-19

Post by OffTheRock » Sun Oct 10, 2021 4:56 pm

jdc wrote:
Sun Oct 10, 2021 4:26 pm
No idea about LFTs picking up something that isn’t SARSCOV2.

Dodgy batch of PCR tests might be a possibility if we've given the contract to a mate of a cabinet minister who's never made them before.

Dodgy testing process at one of the labs sounds plausible. Remember this Panorama? https://www.bbc.co.uk/programmes/m000tqjj

New variant is possible, but unlikely.
Theoretically, a mutation in the virus genome at the site to which either oligonucleotide primer should bind, may destabilise the interaction such that, despite the presence of virus genome, a negative result ensues. To mitigate against this possibility, primers are chosen to highly conserved regions of the genomes. In addition, tests can rely on more than one pair of primers that bind to different conserved regions of the genome, so that any single mutation is unable to prevent a positive test result.

Currently, the low level of changes in the SARS-CoV-2 genome make such false negative results improbable. In addition, the availability of new SARS-CoV-2 genome sequences as they are deposited openly in GISAID, enables the commercial manufacturers of test kits to monitor whether the primers chosen for current tests are likely to remain sensitive and specific, or require updating
https://royalsociety.org/-/media/policy ... alysis.pdf
It did seem the least likely of the possible options I could think of. But This story about the Breton variant from March sprang to mind. I'm not sure what the outcome was. I think we identified alpha because some labs were getting a failure of one of the primers in a lot of test samples. As you say, all of the primers in a given test failing seems unlikely, although theoretically possible.

I don't know about LFTs picking up other stuff, either. I'd have thought that would have noticed that before if it were the case.

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jdc
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Re: COVID-19

Post by jdc » Sun Oct 10, 2021 5:55 pm

I've had a wee look and the Breton variant is B.1.616 which is mentioned in the wiki on variants but doesn't seem to have been a VOC or VOI
https://www.medrxiv.org/content/10.1101/2021.05.05.21256690v1 wrote:The 34 cases had clinical, biological and radiological findings in line with classical features of COVID-19, while RT-PCR tests on nasopharyngeal (NP) samples failed to detect SARS-CoV-2 in most patients. Indeed, this gold-standard test was positive in only 15% of the first tests in B.1.616-related COVID-19 patients. Of note, the diagnostic performance of RT-PCR tests was satisfactory on lower respiratory tract samples, suggesting that failure to detect B.1.616 on NP samples would be due to a viral load below the limit of detection in the upper respiratory tract, rather than to genomic mismatches between routine RT-PCR targets and this variant.

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Re: COVID-19

Post by Brightonian » Tue Oct 12, 2021 6:00 am

Via Guardian, report of House of Commons inquiry (led by Tories!) criticises Government, finds that unpreparedness, initial pursuit of herd immunity, late implementation of lockdowns, halting of mass testing, exceptionalism, "fatalism" contributed to high level of deaths compared to places like South Korea. Test & Trace chaotic, Sage and PHE also criticised.

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shpalman
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Re: COVID-19

Post by shpalman » Tue Oct 12, 2021 6:15 am

Yesterday in the Guardian Live Blog Patrick Vallance said his “mantra” throughout the pandemic has been that action needs to be taken sooner than it appears to be needed. This is such obvious gaslighting b.llsh.t compared to what he actually said at the beginning of the pandemic.
molto tricky

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lpm
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Re: COVID-19

Post by lpm » Tue Oct 12, 2021 7:57 am

All of us could have written that report 18 months ago. We did write that report 18 months ago.
What ever happened to that Trump guy, you know, the one who was president for a bit?

sheldrake
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Re: COVID-19

Post by sheldrake » Tue Oct 12, 2021 8:48 am

I would like to see the comparisons they made with Sweden and other states that didn't lock down.

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lpm
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Re: COVID-19

Post by lpm » Tue Oct 12, 2021 8:52 am

Sweden did lock down.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: COVID-19

Post by sheldrake » Tue Oct 12, 2021 9:32 am

lpm wrote:
Tue Oct 12, 2021 8:52 am
Sweden did lock down.
Hmm, we're probably using a different definition of lockdown here. Which measures are you referring to here?

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lpm
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Re: COVID-19

Post by lpm » Tue Oct 12, 2021 9:45 am

Sweden government lockdown had rule of 8, limited numbers permitted in supermarkets, made public transport bookable for limited numbers, all restaurants and bars closing at 8 pm, no crowds at sport events, no indoor concerts.

It's one of those enduring myths that they didn't lockdown, based on the fact that they were such a famous outlier early on before they realised how badly they were f.cking up.

And - as for the UK in March 2020 - the public choose a higher lockdown than the government imposed. Google data etc shows Sweden had a substantial voluntary lockdown during the government abdication of responsibility, although less than Scandinavian neighbours.
What ever happened to that Trump guy, you know, the one who was president for a bit?

sheldrake
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Re: COVID-19

Post by sheldrake » Tue Oct 12, 2021 10:00 am

lpm wrote:
Tue Oct 12, 2021 9:45 am
Sweden government lockdown had rule of 8, limited numbers permitted in supermarkets, made public transport bookable for limited numbers, all restaurants and bars closing at 8 pm, no crowds at sport events, no indoor concerts.

It's one of those enduring myths that they didn't lockdown, based on the fact that they were such a famous outlier early on before they realised how badly they were f.cking up.
They never really adopted measures like ours and kept deaths per million lower though, wouldn't you say?

Similar questions about various US states.

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Re: COVID-19

Post by PeteB » Tue Oct 12, 2021 10:08 am

sheldrake wrote:
Tue Oct 12, 2021 10:00 am
...

Similar questions about various US states.
which ones?

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lpm
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Re: COVID-19

Post by lpm » Tue Oct 12, 2021 10:15 am

FFS Sheldrake, this is basic.

You missed out on this entire sub forum during the pandemic. Here we're pretty expert on the issues. Get up to speed or get out.

For starters, you don't compare countries like this. Sweden has different dynamics to the UK, from demographics to population density to international travellers. In short, UK was particularly vulnerable to the pandemic while a country like Sweden should have had it easy. Their first wave was an even worse failure than the UK's.

But in a way it was helpful to have one European outlier in the first wave. The Sweden death toll guaranteed proper lockdowns everywhere for wave two - including Sweden itself who lockdowned properly in Nov/Dec 2020 and didn't f.ck around trying to "save Christmas". A plausible counterfactual would be everywhere locking down in the first wave, but then someone trying the no lockdown approach in wave two which would almost certainly have been even worse.
What ever happened to that Trump guy, you know, the one who was president for a bit?

sheldrake
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Re: COVID-19

Post by sheldrake » Tue Oct 12, 2021 10:32 am

lpm wrote:
Tue Oct 12, 2021 10:15 am
FFS Sheldrake, this is basic.

You missed out on this entire sub forum during the pandemic. Here we're pretty expert on the issues. Get up to speed or get out.
I expect the same level of groupthink here as I saw in the brexit threads.
For starters, you don't compare countries like this. Sweden has different dynamics to the UK, from demographics to population density to international travellers. In short, UK was particularly vulnerable to the pandemic while a country like Sweden should have had it easy. Their first wave was an even worse failure than the UK's.
But you're comfortable comparing South Korea? Seems pretty different to the UK as well. Sweden is more urbanised than the UK btw.
But in a way it was helpful to have one European outlier in the first wave. The Sweden death toll guaranteed proper lockdowns everywhere for wave two - including Sweden itself who lockdowned properly in Nov/Dec 2020 and didn't f.ck around trying to "save Christmas". A plausible counterfactual would be everywhere locking down in the first wave, but then someone trying the no lockdown approach in wave two which would almost certainly have been even worse.
https://en.wikipedia.org/wiki/COVID-19_pandemic_in_Sweden wrote:Sweden has not imposed a lockdown, unlike many other countries, and kept large parts of its society open. The Swedish Constitution legally protects the freedom of movement for the people, thus preventing a lockdown in peace time. The Swedish public is expected to follow a series of non-voluntary recommendations[note 2] from the government agency responsible for this area, in this case the Public Health Agency of Sweden (Folkhälsomyndigheten). The Swedish Constitution prohibits ministerial rule – politicians overruling the advice from its agencies is extremely unusual in Sweden – and mandates that the relevant government body, in this case an expert agency – the Public Health Agency – must initiate all actions to prevent the virus in accordance with Swedish law, rendering state epidemiologist Anders Tegnell a central figure in the crisis.
The closest Sweden got to a lockdown was less restrictive than our 'rule of 6' when people started meeting up and going to restaurants again.

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lpm
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Re: COVID-19

Post by lpm » Tue Oct 12, 2021 10:48 am

Lol, you post an extract from wiki, but cut it short. You "accidentally" forgot to include the next section about the new laws in Dec 2020 and Jan 2021.

Let's all pretend you made a mistake, led astray by the bad wiki editing that retains old present tense language such as "Sweden has not imposed a lockdown" despite the next section being on subsequent lockdown laws.

Even Trump slammed Sweden's response. Yes, Sheldrake, you are being even more stupid than Donald Trump. An achievement few can dream of.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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