මොකක්ද මේ CT Value (COVID 19 PCR Report)

[divoomdelux]

Godak than wala karanne na machan. Strips out of stocks godak than wala.

DGH wala athi mchn

 

[warwickuni]

This is an extract from a post I made in 14 November 2020 - on the interpretation of the Ct values... This figure clearly shows how the Ct values can reflect on infectivity.

<snip>

On a previous post on a Covid Megathread, I have explained in detail how a RT-PCR is done. The Ct value does play a part. The Ct is what's known as the Cycle Threshold - is the number of Cycles needed for the fluorescent signal to cross the threshold above the background. A PCR is done usually to a max of 40 cycles...
Cts < 29 are strong positive reactions indicative of abundant target nucleic acid
Cts of 30-37 are positive reactions indicative of moderate amounts of target nucleic acid
Cts of 38-40 are weak reactions indicative of minimal amounts of target nucleic acid which could represent an infection state or environmental contamination.

So a high CT value is dubious. You cannot rely on Ct after 37 at all. In which case you do another PCR test a few days later. These can be false positives.

A team of scientists recently did a study more than 3000 cases the graph below shows the results. Ct against infectvity. They did a PCR test and also they did a viral culture using the same swab to independently grow the virus to confirm. The number of Samples N is the PCR test, The number of Samples n is the Virus detected in the culture.
One can easily see at high Ct values the results are inaccurate. The Global percentage value graph is 100% at low Ct values and then keeps on falling down to zero at Ct around 36. This is well known but only probably not known by an average person.

Also studies done in several countries (most recently in Brazil) has shown that nearly 35% of patients Ct value of 25 or below were more likely to have severe disease or die.
<snip>

View attachment 138922

can this be elaborated more as to what Cycle Threshold means and how it become relevant to this result.(this is how it is used , but the molecular biology explanation to this phenomenon.

 

[imhotep]

can this be elaborated more as to what Cycle Threshold means and how it become relevant to this result.(this is how it is used , but the molecular biology explanation to this phenomenon.

It's as stated in the post...

"The Ct is what's known as the Cycle Threshold - is the number of Cycles needed for the fluorescent signal to cross the threshold above the background."

The RT_PCR process requires a temperature cycling reaction called the amplification cycle. For a single test, the amplification cycle is repeated at least 40 times before obtaining the results. The total number of amplification cycles required to detect the virus’ genetic material or viral RNA is defined as the ‘CT’ value or the Cycle Threshold.

Note: Background (Baseline) - very little fluorescence. Cycles between cycles 0 and 15, as shown above is known as the background signal.

Expotential Phase - This is when the amount of PCR product doubles for every PCR cycle. This can be seen in cycles 15 and 25

Plateau - amplification slows down and ultimately plateau

The placement of the line is often determined by the qPCR software, however, users can manually place this line as well.

 

[willpower]

TFS

 

[warwickuni]

Please read the first para on the extract I copied. If you could locate my post on the PCR that explains how the PCR is done.

Very briefly, a PCR is done to quantify a target sequence and it involves amplifcation of the target in real-time via a target-specific fluorescent signal emitted during amplification.
The process is just like a molecular photcopier. To amplify a small segment of DNA using PCR, the sample is first heated so that it separates into two pieces of single-stranded DNA. Next, an enzyme called "Taq polymerase" is used to synthesize- two new strands of DNA, resulting in the duplication of the original DNA, with each of the new molecules containing one old and one new strand of DNA. Then each of these strands can be used to create two new copies, and so on, and so on. This process is done to 40 times max (cycles) as I mentioned before.

However, in practice even though the PCR dyes and probes are sequence specific, there's considerable background fluorescence occurs. This signal to noise issue is addressed by two things - a threshold line and the Ct value.
Threshold line is the level of detection point where the reaction reaches a fluorescent intensity above background levels and the Ct value is the PCR cycle number at which your sample’s reaction curve intersects the threshold line.

How it relates to infectivity is the graph on my post....

Thanks.