Michael McNamara TD getting to the truth, Cases, PCR testing flaws.

drunkmonkey

Victor wrote: »

Assuming (not unreasonable) this 78 days hasn't changed, then reporting like-for-like numbers isn't a problem.

I'm not getting you Victor, if there not active cases why base policy on them. There's a lot more relevant figures they could look at, symptomatic people presenting to GP's, hospital admissions, ICU admissions etc.

Everything our whole road map/restrictions are based around positive test results.

myfreespirit

drunkmonkey wrote: »

It's all tests, That's one issue the other is the false positive rates, it's estimated 9 out of 10 positives are false.

You have been asked several times to provide independent corroborating evidence that "9 out of 10 positives are false"

Do you have reliable sources that show this to be factual?
If it is in fact correct, it would be deeply concerning.

_Kaiser_

3xh wrote: »

^^^ So Glynn’s strategy is to change nothing for the next 6-9 months, hope something new like treatments or vaccine appears before then, if not, they’ll look to alter the NPHET advice on how we ‘live’ with Covid beyond next summer.

Pretty much. He is pinning the hopes and finances of the nation to the hope that someone will develop a vaccine somewhere. He can't see beyond his brief or his medical objective to "get covid to zero"

Unfortunately a country isn't the same as a lab or theoretical model.

sabat wrote: »

How did he get the job? Is it a direct appointment or voted on somewhere?

He stepped in when Tony H stood aside over the summer. It's clear to me anyway that Glynn isn't up to the task.

As to how either of them are in the role, I presume it's internal appointment?

Sir Guy who smiles

drunkmonkey wrote: »

What exponentially smaller number are you suggesting, let's say 100 tests what percentage will only be picked up for 39 days?
Isn't the detection time depending on the number of cycles the lab runs.

A study in Singapore found 30% of cases negative by day 15, 68% by day 21, 88% by day 28 and 95% by day 33.

https://codeblue.galencentre.org/2020/06/01/positive-sars-cov-2-rt-pcr-test-virus-dead-or-alive-dr-tan-poh-tin/

You have to dig through the references to find the CT cycles but it turns out they use 45 cycles.
(The recent NYT article that claimed the cycle rates used there were too high was criticising US testing for using 35 to 40 cycles.)

ElTel

myfreespirit wrote: »

You have been asked several times to provide independent corroborating evidence that "9 out of 10 positives are false"

Do you have reliable sources that show this to be factual?
If it is in fact correct, it would be deeply concerning.

The meta data on the cycle threshold number could be useful. It would be a travesty if this info is not on hand given we have so much data out there in this info age.

Do the CT numbers show the same distribution for symptomatic and asymptomatic cases? How many of the test give a CT of say 10, 20 30 40?

My limited understanding is that a "real infection" with a CT number of say 34 means you "found" them in that small window at the start of their infectious period.

This infectious period looks like a front loaded bell curve where (lets say 80%) of the viral shedding occurs in 5 days, starting 2 days before symptoms. If people are getting their results a week after symptom onset how likely are they to be infectious?

Regarding testing figures, breaking them down into the 3 categories Community Acute and Serial should be published. Are retests significant?

drunkmonkey

Sir Guy who smiles wrote: »

A study in Singapore found 30% of cases negative by day 15, 68% by day 21, 88% by day 28 and 95% by day 33.

https://codeblue.galencentre.org/2020/06/01/positive-sars-cov-2-rt-pcr-test-virus-dead-or-alive-dr-tan-poh-tin/

You have to dig through the references to find the CT cycles but it turns out they use 45 cycles.
(The recent NYT article that claimed the cycle rates used there were too high was criticising US testing for using 35 to 40 cycles.)

There's a lot in that, I see what your saying but the same article makes reference to people testing positive up to 82 day after onset of symptoms. the take away as the report says..
"Recovery Phase RT-PCR Positive Doesn’t Mean Infectious"
It's probably why were picking up so many asymptomatic especially in meat factorys/hospitals etc. The virus is dead and gone in those people.

I think there has to be a better metric to base policy on.

Sir Guy who smiles

drunkmonkey wrote: »

It's probably why were picking up so many asymptomatic especially in meat factorys/hospitals etc. The virus is dead and gone in those people.

Actually you have less grounds to say it's an old infection in asymptomatic cases.

If you had classic covid signs four weeks ago, then test positive, you have some grounds for saying it's a four week old infection.

In the absence of symptoms there is nothing to guide you- you could have got it yesterday, could have got it two weeks ago.

ShineOn7

wellwhynot wrote: »

.I am just so fed up with this. It must be the only ‘pandemic’ in history with 50 - 80% asymptomatic, low deaths and empty hospitals.

Any yet both are on the rise again

MadYaker

Hilarious thread.

DaSilva

Cillian De Gascun wrote a very informative twitter thread about PCR testing and many of the details of it here: https://threadreaderapp.com/thread/1305250887246458880.html

Suggests to me that there might not be simple straight forward answers to questions the TD had like, "how many cycles are used", it seems it depends on the actual test (manufacturer/lab/equipment) being used.

drunkmonkey

DaSilva wrote: »

Cillian De Gascun wrote a very informative twitter thread about PCR testing and many of the details of it here: https://threadreaderapp.com/thread/1305250887246458880.html

Suggests to me that there might not be simple straight forward answers to questions the TD had like, "how many cycles are used", it seems it depends on the actual test (manufacturer/lab/equipment) being used.

This is the whole problem were basing restrictions around a test that doesn't tell us if someone is infectious or not.
Those different test he mentioned are feeding into our overall number.
It's fine for Cillian to say that the false positive rate is .2% but it's incorrect as he doesn't know for all tests were counting.

We have Chantelle then today launching a 10 minute test for the country, what's the accuracy of that and the false positive rate. Nobody knows.

myfreespirit

drunkmonkey wrote: »

That's one issue the other is the false positive rates, it's estimated 9 out of 10 positives are false.

So, no evidence from you that the above statistic is true?
None at all.

It is probably safe to assume that this is not true.

drunkmonkey

myfreespirit wrote: »

So, no evidence from you that the above statistic is true?
None at all.

It is probably safe to assume that this is not true.

I linked to the evidence if you go back and read my posts long before you asked the question.

UK are estimating, .8% and someone linked to an Irish newspaper article claiming .2% but nothing to back it up.

I was wrong about the private testing feeding into our daily numbers as it's says there not in the independent this morning. The private tests like Stephen Donnelly had aren't accurate enough for the HSE to use. Pretty amazing seen as the Dail was back in session a few hours after a test the HSE don't recognize.

OscarMIlde

drunkmonkey wrote: »

There you have it folks CCO of the HSE admits PCR testing picking up covid weeks after infection...these are recorded as positive covid results.

https://www.youtube.com/watch?v=y_cl63FgAhQ

How cases are recorded is also questionable.

https://www.youtube.com/watch?v=4ZolPvWW8oo

Will the general public ever understand what the daily cases actually mean rather then just getting frightened by them, we really need the Media to start getting at the truth of what's happening.

Mix all the above in with the false positive rates and they're little justification for how the Government are behaving.

This is absolutely fundamentally untrue. PCR amplifies genetic material, it cannot amplify what's not there. The covid 19 test is specific for sars-cov2 RNA, and will only amplify if viral RNA is present. The only way it will show a false positive result is if the sample has been contaminated in some way.

The RT-PCR assays used are used to give a yes/no answer to whether covid 19 RNA is present or not. They are not used to imply a level of viral load or how infectiousness a person is. However, since the only people being referred for testing are close contacts of known positives or symptomatic people then it is highly likely these people are infectious, and should quarantine.

Happydays2020

drunkmonkey wrote: »

This is the whole problem were basing restrictions around a test that doesn't tell us if someone is infectious or not.
Those different test he mentioned are feeding into our overall number.
It's fine for Cillian to say that the false positive rate is .2% but it's incorrect as he doesn't know for all tests were counting.

We have Chantelle then today launching a 10 minute test for the country, what's the accuracy of that and the false positive rate. Nobody knows.

What is that 10 minute test?

OscarMIlde

drunkmonkey wrote: »

What do you mean by this, are you suggesting that once the virus is no longer active that it won't be picked up, for someone with years of experience of these tests you should know that the number of cycles will effect the result. The CCO could not give the number of cycles were using yesterday. If were using the same as the UK which I think someone said we are that time limit for picking up traces of RNA for a positive result of Covid is 78 days.
The CCO said it himself yesterday it's for week after infection.

I don't know where that estimate of 78 days is coming from. What CT value was given for this result? Is it above what Irish labs are using as the limit of detection? Irish labs are testing only close contacts of confirmed cases or symptomatic people so it's unlikely that anyone being tested isn't infectious.

drunkmonkey

OscarMIlde wrote: »

I don't know where that estimate of 78 days is coming from. What CT value was given for this result? Is it above what Irish labs are using as the limit of detection? Irish labs are testing only close contacts of confirmed cases or symptomatic people so it's unlikely that anyone being tested isn't infectious.

It's 45 from what I understand, Irish labs are testing anyone that goes for a test plenty of asymptomatic people are being tested. Take one of the meat factories with blanket testing for example, 83 asymptomatic, 2 Symptomatic.
Completely untrue to say were only testing symptomatic.

drunkmonkey

https://www.youtube.com/watch?v=nZ5GKKvOVlo

drunkmonkey

Happydays2020 wrote: »

What is that 10 minute test?

Dragon’s Den star Chanelle McCoy plans to launch 10-minute finger prick test for Covid-19 nationwide.

https://www.independent.ie/business/dragons-den-star-chanelle-mccoy-rolls-out-ten-minute-covid-19-test-nationwide-39575738.ht

drunkmonkey

OscarMIlde wrote: »

However, since the only people being referred for testing are close contacts of known positives or symptomatic people then it is highly likely these people are infectious, and should quarantine.

That's completely untrue, did you even watch what you dismissed.

OscarMIlde

drunkmonkey wrote: »

It's 45 from what I understand, Irish labs are testing anyone that goes for a test plenty of asymptomatic people are being tested. Take one of the meat factories with blanket testing for example, 83 asymptomatic, 2 Symptomatic.
Completely untrue to say were only testing symptomatic.

Or close contacts of confirmed cases, as I said.

Consider how a viral infection works. A virus enters the body, and invades a cell. There it uses the cell machinery to replicate itself (viruses are unable to replicate independently). Once more virus copies have been made they burst out of the initial cell to invade nearby cells and repeat the process. This will continue until the immune system controls the infection, or a treatment can halt the viral life cycle (as can be done for HIV), or the oatient dies.

Now consider the testing process. A swab is rubbed at the back of the throat and nasal passage to try and grab some virus. The RT-PCR assay can replicate and amplify viral RNA. It can only do so if the swab took hold of some virus in the first place. If someone was at an early stage of infection, there may not be much virus present as it is still replicating itself. Alternatively if someone is at a late stage of infection where the immune system is clearing the virus only a small amount of viral material may be swabbed. In both these cases (early/late infection) a high CT value will likely be obtained. This is NOT a false positive, as the person still has covid 19 virus in their system.

The other reason for a late CT might be that despite the fact the person has a high viral load and is infectious, the swab itself may not have picked up enough viral material through poor technique or just bad luck. There is no control gene so poor swabbing cannot be controlled for.

For this reasons labs are retesting late CT values. The process described has a lot of steps and false negatives are much more of a worry.

Also with regards that 78 day study. This is a novel virus which our immune systems have not encountered before. We have no specific targeted treatment against the virus itself. We are relying on the immune response to control it. We know that some people don't do that well, especially given the long tail of disease severity. It is possible that the virus detected in that study WAS active viral particles in an immumocompromised oerson who failed to clear the virus. I find that more likely than dead virus hanging around as we have very active clearance mechanisms for such issues. Many viral infections can remain latent for a few months and reappear if not fully cleared by the immune system.

drunkmonkey

OscarMIlde wrote: »

Or close contacts of confirmed cases, as I said.

Were testing tens of thousands of asymptomatic people every week and they are not all close contacts of confirmed cases you need to admit that as your completely wrong or trying to deliberately mislead in your posts.
There is nobody saying we're not testing Asymptomatic people, that's not even up for questioning.

OscarMIlde

drunkmonkey wrote: »

Were testing tens of thousands of asymptomatic people every week and they are not all close contacts of confirmed cases you need to admit that as your completely wrong or trying to deliberately mislead in your posts.
There is nobody saying we're not testing Asymptomatic people, that's not even up for questioning.

We are in certain high risk industries, where known outbreaks have occurred that contributed to community spread (e.g. meat factories, direct provision centres) or where there is a high risk if infections take hold (e.g. nursing homes). This is a perfectly sensible measure to take, and one that anyone should welcome. There is abundant evidence that asymptomatic people can spread covid 19, it's part of the reason it is so difficult to eradicate within the community. That does not alter my substantive point that there is no real risk of false positives skewing our figures, the more likely issue is that false negatives are underestimating the rate of covid 19 within the community. The growth in positives PCR tests within the community in the Dublin area has been matched by increased detection of covid 19 levels within waste water, further validation that there is an increased infection rate.

Sir Guy who smiles

OscarMIlde wrote: »

This is absolutely fundamentally untrue. PCR amplifies genetic material, it cannot amplify what's not there. The covid 19 test is specific for sars-cov2 RNA, and will only amplify if viral RNA is present. The only way it will show a false positive result is if the sample has been contaminated in some way.

The RT-PCR assays used are used to give a yes/no answer to whether covid 19 RNA is present or not. They are not used to imply a level of viral load or how infectiousness a person is. However, since the only people being referred for testing are close contacts of known positives or symptomatic people then it is highly likely these people are infectious, and should quarantine.

This is the best summary, undecided readers listen to this guy.

If you get a positive a week after being near someone who has Covid, whic is more likely?

1. You got it off them a week ago?

Or

2. You are one of the tiny % who will show positive after they got it 70 days ago, even though there is nothing to suggest you were exposed to it back then?

Stormyteacup

OscarMIlde wrote: »

I don't know where that estimate of 78 days is coming from. What CT value was given for this result? Is it above what Irish labs are using as the limit of detection? Irish labs are testing only close contacts of confirmed cases or symptomatic people so it's unlikely that anyone being tested isn't infectious.

Ok so might have missed something but is the positivity rate not about 3%?

3xh

Stormyteacup wrote: »

Ok so might have missed something but is the positivity rate not about 3%?

Yep. It’s been 2.9% - 2.8% in the very recent past.

ElTel

Sir Guy who smiles wrote: »

This is the best summary, undecided readers listen to this guy.

If you get a positive a week after being near someone who has Covid, whic is more likely?

1. You got it off them a week ago?

Or

2. You are one of the tiny % who will show positive after they got it 70 days ago, even though there is nothing to suggest you were exposed to it back then?

Why not use the CT number especially in asymptomatic positives?

OscarMIlde

ElTel wrote: »

Why not use the CT number especially in asymptomatic positives?

There's no point in using the CT number, as there is no control gene to account for an ineffective swab. An early CT indicates a lot of viral material on the swab, and it can be extrapolated that a person definitely has active covid 10 circulating.

A late CT value indicates less viral material on the swab. The reasons for this can vary from an early stage infection were viral load hasn't climbed high yet, a diminishing infection where viral load has been significantly controlled by the immune system, or a poor swab where viral material wasn't picked up.

We also know that asymptomatic people spread covid 19 just as much (possibly more as they have no 'cue' to limit their social interactions) as symptomatic people, so any positives should be quarantining.

Stormyteacup

OscarMIlde wrote: »

There's no point in using the CT number, as there is no control gene to account for an ineffective swab. An early CT indicates a lot of viral material on the swab, and it can be extrapolated that a person definitely has active covid 10 circulating.

A late CT value indicates less viral material on the swab. The reasons for this can vary from an early stage infection were viral load hasn't climbed high yet, a diminishing infection where viral load has been significantly controlled by the immune system, or a poor swab where viral material wasn't picked up.

We also know that asymptomatic people spread covid 19 just as much (possibly more as they have no 'cue' to limit their social interactions) as symptomatic people, so any positives should be quarantining.

Still puzzled - if only 3 out of 100 of all tests return a positive test result, what are you saying? What percentage of the 97% testing negative are false negatives?

Why would everyone tested be considered infectious if 97% test negative?

OscarMIlde

Stormyteacup wrote: »

Still puzzled - if only 3 out of 100 of all tests return a positive test result, what are you saying? What percentage of the 97% testing negative are false negatives?

Why would everyone tested be considered infectious if 97% test negative?

When did I say everyone would be considered infectious? I meant any late positive CT value within the test cut off range (as in the CT value below which results are considered positive) should be considered infectious.