RT-PCR TESTING
 
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RT-PCR TESTING

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Posts: 7
Topic starter
(@fact-or-fiction)
Joined: 4 years ago

Can someone explain why a CT value of 40 is used. Surely way to high. I have read that a value of around 30 is more reasonable for this ropey test.

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Posts: 133
(@splattt)
Joined: 3 years ago

Because its nowhere near as simple as that.

There is no magic Ct where below which its a non issue.

They've managed to culture virus from Cts of 38+ but also failed on some samples of 20.  Loads of viable cultures at 35 or so.

Its a distribution curve of probabilities.

Using 40 or whatever isn't specifically a problem.  The problem relies on using a simple yes/no as a diagnostic.

They should be reporting the Ct and combining that with symptoms or close contact data to determine infection probability.  As far as im aware this is only done in some hospital settings, not at lighthouse labs.

The problem isnt the test - its how the results from it are used.

 

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Posts: 7
Topic starter
(@fact-or-fiction)
Joined: 4 years ago

Many Thanks. I know the test can't determine between live or dead virus. But what would generally be recognised as the confidence level for detecting "dead or alive" viral RNA, or is there a fear of missing "positive" cases by trying to detect a low viral load.

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Posts: 133
(@splattt)
Joined: 3 years ago

If you're worried purely about disease prevention then a false negative is more dangerous than a false positive.
Standard public health there.

Ultimately you cant just set a Ct (also each different assay has a different threshold so its not just viral rna related) and use it.

It has to be combined with other factors such as symptoms and/or likely exposure to someone infected. The problem we have is its not. The test is the only diagnostic.

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3 Replies
(@ewloe)
Joined: 3 years ago

Posts: 319
Posted by: @splattt

If you're worried purely about disease prevention then a false negative is more dangerous than a false positive.
Standard public health there.

Ultimately you cant just set a Ct (also each different assay has a different threshold so its not just viral rna related) and use it.

It has to be combined with other factors such as symptoms and/or likely exposure to someone infected. The problem we have is its not. The test is the only diagnostic.

I cannot say this often enough, the message never gets through. We are not only concerned with disease prevention. We are just as concerned about disease exageration, since the biggest effect of covid19 is not illness, death or disability, the worst effect of covid19 is its econopolitical impact. If you are worried about the econopolitical impact, then a false positive is more dangerous than a false negative. Standard economics there.

We should use a Ct  level  that  does not cause disease exaggeration, sure we'll miss some cases but they will be balanced by false positives if the Ct is OK.The goal can never be to detect all cases, as that is impossible.

It only has to be combined with other factors if we are interested in the accuracy of an individual test, i.e when considering treatment options. Else not.If the Ct value is OK, we don't care about the result of a particular result, we just count it up. The totals (what's economically/politically important ) will be right.

 

 

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(@splattt)
Joined: 3 years ago

Posts: 133

@ewloe 

"We should use a Ct level that does not cause disease exaggeration, sure we'll miss some cases but they will be balanced by false positives if the Ct is OK"

You can't.  There isn't one.

Some virus will culture at 40, some refuses to at 20.

Each different assay used for the tests (there are lots of manufacturers) also need different Cts for the same outcome.

Simply wouldn't work at all.

What is needed is treat it as designed - a diagnostic confirmatory test alongside a clinical diagnosis based on symptoms or exposure.

LFTs are similar to what you want.  They produce some false positive but also a lot of false negatives - they're rubbish with low viral loads.  As a diagnostic or screening tool, they're absolutely useless.

 

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(@ewloe)
Joined: 3 years ago

Posts: 319
Posted by: @splattt

@ewloe 

"Some virus will culture at 40, some refuses to at 20.

 

That  does not matter since we are only exaggerating this virus.If we are exaggerating (we are) ct is too high. End of matter. cheers.

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Posts: 133
(@splattt)
Joined: 3 years ago

No its not. There is no "right" Ct.

There is no number you can pick and say "if its below this its probably fine".

It doesnt work like that and cant be used like that.

If you can culture virus from a particular same at a Ct of 38 then 38 is not too high *in that situation*.

PCR is supposed to be a confirmatory diagnostic in conjunction with a clinical diagnoses.  Its not designed to be a stand alone test.

 

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