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No FDA approved PCR tests so far for newer SARs CoV 2 variants..

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jmc
Posts: 615
 jmc
Topic starter
(@jmc)
Joined: 2 years ago

It seems  the FDA have yet to approve for conditional use any of the PCR reagents being used for older SARs Cov2 variants. Some pick them up, but most dont. 

https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests?ACSTrackingID=USCDC_2146-DM71408&ACSTrackingLabel=Lab%20Alert%3A%20CDC%20Update%20on%20the%20SARS-CoV-2%20Omicron%20Variant%20&deliveryName=USCDC_2146-DM71408

https://www.cdc.gov/csels/dls/locs/2021/12-03-2021-lab-alert-CDC_Update_SARS-CoV-2_Omicron_Variant.html

There are no authorized, cleared, or approved diagnostic tests to specifically detect SARS-CoV-2 variants (Omicron or other variants). Currently, COVID-19 tests are designed and authorized to check broadly for the SARS-CoV-2 virus, not for specific variants.

The standard PCR test tested for the presence of three molecular patterns that should be unique to SARs CoV 2. Only if all three match is it considers a positive. The best match pattern was the S protein which is where the recent variant mutations are. 

Labs it seems are now considering a two match a positive. Which is why the positive rate has gone up so much. With a two match  the sensitivity and specificity drops markedly which means that for mass screening the false positive rate must be close to 99% by this stage.

Given that the S protein was the only long high probability unique molecular match pattern for SARs Cov 2. And the other two match patterns were bases on a search of the genomic database for sequences that dont appear in other viruses. I decided to look up the database for just how much effort was put into tracking the other human corona virus (HCOV) variants 

This the entry for SARs CoV2

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=2697049

Lost of data on variants.

Here is how much they have for 229E and OC43.

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=11137

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=31631

Basically nothing in comparison.

All four general circulation HCOVs's have been spinning off variants at the same rates as SARs Cov2. Every few weeks to months. So as a rough estimate over 99% of all  HCOV variants of the last few decades are not in the genomic databases.

Which makes the analytical accuracy PCR test even in a high prevalence clinical setting very problematic. If there is so little genomic data for even the closest relatives to SARs CoV 2

 

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Stop believing start thinking
(@stop-believing-start-thinking)
Joined: 7 months ago

Posts: 202
Posted by: @jmc

 

Labs it seems are now considering a two match a positive. Which is why the positive rate has gone up so much. With a two match  the sensitivity and specificity drops markedly which means that for mass screening the false positive rate must be close to 99% by this stage.

 

 

I have watched your similar comments over the months and have seen them challenged, but there is no sign of learning.

Are you aware of what the definition of false positive rate actually is?

Your estimate of 99% is ludicrous, so perhaps you could look up the equation, collect some stats on tests performed, corresponding positive results. That would give you the theoretical maximum for FPR (assuming all positive results were false).

Go ahead, do this and show us your working out. It will be educational for you.

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jmc
 jmc
(@jmc)
Joined: 2 years ago

Posts: 615

@rational 

Never pick a fight with someone who has done very complex maths for a living for many decades. And has had a serious medical condition almost as long. 

So here goes.

These are clinical diagnostic tests. For active infections.

All numbers quoted by you and other are the ANALYTICAL accuracy not the CLINICAL accuracy for the RT/PCR tests.

The Analytical accuracy of a test is the probability of a true positive when presented with pure reference sample in a highly controlled laboratory environment.  So 95% to 97% sensitivity and claimed 99% selectivity for the currently approved FDA reagents. 

The Clinical accuracy of a test is the probability of a true positive for an active infection in the test subject.

The test sample for the RT/PCR mass screening test is a deep nasopharyngeal swap. The published literature for viral upper respiratory infections shows that these deep swabs have only around a 60% / 70% probability of collecting a valid sample amount. The published literature for viral upper respiratory infections shows that there is little correlation between upper respiratory system viral density and severity of symptoms. In fact 10% to 20% of symptomatic upper respiratory viral infections have negligible / no upper respiratory system viral density.

Starting to see a pattern here? And I have not even started.

 

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Stop believing start thinking
(@stop-believing-start-thinking)
Joined: 7 months ago

Posts: 202

@jmc 

You could try applying some of your advanced maths once you have read the definition of false positive rate, for which you make claims.

Try fitting the results of mass screening using PCR into this see your reasoning crumble.

 

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jmc
 jmc
(@jmc)
Joined: 2 years ago

Posts: 615

@rational

If you research the literature you will find that the usual error rate in mass processed lab testing is in the 4% to 10% range. It's a big problem much discussed. But only in the professional literature. 

And we have not even got to the statistics of low prevalence.  Or the Type I or Type II error rates for valid clinical tests. So yes. For the vast majority of SARs CoV 2 tests the false positive rates before omicron was 90%.  Unless the test subject already had early clinical symptoms sign of pneumonia. 

And for RT/PCR the icing on the cake was the match probes used  for the SARs CoV 2. The protein pattern used to match by the test reagents. One strong, on the S protein, two acceptable. On the N. Omicron modified the S so most of the approved reagents failed to match one probe. So the Analytical sensitivity of the regent was not 97% but closer to 50%. Because two probe matches were now counted as a positive result.

I could go into the subject of stand specific PCR and how that is the only correct PCR test for active infection but still only catches 5 of the typical 10 day infection duration. 

But I am certain this (as well as most of the above) is well beyond your level of comprehensions.

But the CLINICAL accuracy of the current RT/PCR test for SARs CoV 2 will give 99% false positive rates when used for mass screening. 

 

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Stop believing start thinking
Posts: 202
(@stop-believing-start-thinking)
Joined: 7 months ago

After all this time, and you making repeated claims about false positive rate, you still haven't looked up the definition of false positive rate.

Go on have a look.. it will tell you that such 99% a claim is incompatible with the definition and the regular results of mass screening using PCR.

I tell you what,, I'll tell you the definition....

 

FPR = false positives / (All negatives)

 

Have a big think and see why you are wrong..

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jmc
 jmc
(@jmc)
Joined: 2 years ago

Posts: 615
Posted by: @leek

After all this time, and you making repeated claims about false positive rate, you still haven't looked up the definition of false positive rate.

Go on have a look.. it will tell you that such 99% a claim is incompatible with the definition and the regular results of mass screening using PCR.

I tell you what,, I'll tell you the definition....

 

FPR = false positives / (All negatives)

 

Have a big think and see why you are wrong..

Ever heard  the phrase not even wrong?

Someone who knows so little about the subject that they dont realize that what they wrote is total garbage. 

You obvious dont have the mathematical or scientific background to understand such concepts as Type I and Type II errors, low prevalence sampling errors, analytical v clinical accuracy, or threshold detection levels etc which I have posted about before.

Try reading a basic textbook like this..

https://www.amazon.com/Biostatistics-Epidemiology-Primer-Biomedical-Professionals/dp/1493921339

..pages 133 to 169 will give enough background to start to have a clue about the subject of misuse of clinical screening tests.

Dont forget the first chapter either. Thats the basic maths bit.

And when you can show that you have even the most basic understanding of the subject I can walk you through the mathematics of how to calculate the CLINICAL ACCURACY of the RT/PCR test and it equivalent.

For a CLINICAL TEST the false positive rate is the number of positives minus the number of true positives for subjects with an active infection. Also remember that that PCR test has a false negative rate of > 50% for active SARs coV 2 infections which makes it invalid as an acceptable clinical diagnostic test. Which should have false negative rates of < 5%. 

And in the case of SARs CoV 2 since March 2020 the PCR test when used as a clinical screening test in complete contraction of how it was used in a clinical environment before March 2020. Only in a high probable prevalence, low probable candidates clinical test environment and purely as a confirmation test not a diagnosis test.  

The false positive rate for the non strand specific RT/PCT screening test used since March 2020 has gone from 90% with the early variants to up to 99% with the current variants and almost all the currently approved reagents.

Due to some very basic mathematics.

Get back to us when you have actually done your basic research on the subject that what looks like a cut and paste from wikipedia. 

 

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lordsnooty
(@lordsnooty)
Joined: 1 year ago

Posts: 582

@jmc yes, it's an  version of what Nietzsche really said that ignorant people remember, the real words are Mystical explanations are thought to be deep; the truth is that they are not even shallow.

 
And that's what you are jmc, not even shallow.
 
 
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Stop believing start thinking
Posts: 202
(@stop-believing-start-thinking)
Joined: 7 months ago

But you still have not shown how your claim of false positive rate can be true.

You spout on about basic maths, but never do any.

Quite simply... how can your claim of FPR be true. Using actual definition and results and actual maths.

Your attempts so far have avoided these. You claim to be a high level mathematician (amongst other things) so give it a go. 

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2 Replies
ScepitcAl
(@scepitcal)
Joined: 2 years ago

Posts: 31

@leek so with a 99% false positive rate this suggest 2 ludicrous outcomes!

1) covid does not exist! 🤦🏻‍♂️ 

2) covid has a ridiculously high death rate, well in excess of that of ebola! 

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Stop believing start thinking
(@stop-believing-start-thinking)
Joined: 7 months ago

Posts: 202

@scepitcal 

Yes, you have highlighted some more methods of discrediting the nonsensical 99% FPR claim from JMC.

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