Someone asked me what the PCR does if it doesn’t test for viruses. You may be aware that the PCR test is the most accurate test for COVID-19. And for us to have a good understanding of the PCR test, it is helpful to understand DNA.
WHAT IS DNA?
DNA stands for Deoxyribonucleic Acid. DNA is regarded as the building block of life because it contains all the information needed to create and maintain the human body and indeed, all life forms. Every living thing contains DNA, the blueprint of life. Humans, dogs, flies even bacteria and viruses contain DNA.
DNA has a unique structure, a double helix shape, like a twisted ladder. Imagine the ladder legs as 2 strands of DNA and the strands are held together by rungs of base (protein) pairs – Adenine-A, Thymine-T, Cytosine-C and Guanine-G. A always pairs with T and C pairs with G.
The strands of DNA are always complementary. So if one strand is made from the proteins A, A, T, G, on the opposite side you will have T, T, A, C.
The ‘ twisted’ strands of DNA can be untwisted into 2 single strands of DNA.
If you untwist DNA and you add the 4 proteins – Adenine, Thymine, Guanine and Cytosine), the single strands will regrow the missing complementary strands. So from 1 DNA, you can make 2 DNAs. And from 2 you can make 4 and 8 and 16 and so on.
THE PCR ( POLYMERASE CHAIN REACTION)
The PCR is a DNA manufacturing technology. It was invented by Kary Mullis, a brilliant biochemist who won the 1993 Nobel price for chemistry for his invention.
The PCR is a cutting edge technology for replicating DNA.
It does not test for viruses.
This fact was reiterated many times by the inventor the Late Dr Kary Mullis.
HOW THE PCR WORKS
The PCR aims to produce a lot of DNA from a negligible amount. And it does this by continually doubling the DNA in a sample.
Remember that DNA is made up of 2 twisted strands, the PCR heats DNA to untwist it. So instead of one twisted DNA, you have 2 single strands of DNA.
Remember the 4 base proteins – Adenine, Thymine, Cytosine and Guanine. A primer containing these proteins is added to the PCR so that the single-strand DNA can regrow the missing strand. So from 1 DNA, you make 2 DNA. And from 2 you create 4 and 8, 16, 32 and so on. After doing this 10 times, you have 1000, and after 20 times you have a million. If you do it 30 times, you get a billion and 40 times you get a trillion. The PCR denotes each doubling as a cycle, and so you have 20, 30 or 40 cycles.
The PCR starts with a sample barely containing DNA, and by the time the process has completed 40 cycles, you have a trillion times the DNA you began with, enough to run some tests.
Usually, the PCR produces enough DNA from 20 cycles, and at 40 cycles, if no DNA is detected, the process is terminated.
HOW THE PCR WORKS IN A REAL-LIFE SCENARIO
Let’s say a detective walks into an apartment where he believes a crime had occurred. He’s looking for evidence, like a bloodstain to prove that the victim was in the house. But the apartment has been scrubbed squeaky clean, and there’s no chance he will find anything. Now his instincts take him to a spot where he suspects foul play. He scrapes the floor and sends the sample to the Lab.
In the Lab, the technicians prepare the sample and then load it inside a PCR machine. The PCR machine starts the cycling process. What the PCR is doing is doubling the amount of DNA that may be present in the sample. After 20 cycles, the technicians would expect about a million times more DNA. The system uses ‘fluorescent lighting’ to check if enough DNA has been produced. After 30 cycles, about a billion times more DNA is present. Perhaps, after 37 cycles, the PCR will detect a sizable amount of DNA.
And the DNA produced will be compared to the DNA from the victim for a match.
That’s how the PCR machine works. It is used to produce a sufficient amount of DNA for further testing.
The PCR machine on its own is not a testing machine.
HOW THE PCR WAS USED BEFORE DEC 2019
Let’s say a patient is not feeling well, and doctors are suspecting a blood infection, perhaps a viral infection. So a sample of blood is taken for PCR analysis. There are other ways to analyse the blood, such as by cell culture or electron microscopy, but these are not very reliable, so the more reliable PCR, is preferred.
The technicians will purify the blood sample before introducing it into the PCR machine. Firstly they’ll filter out every particle larger than a virus from the sample, including blood cells, bacteria and parasites. The reason for filtering out these particles is because they contain DNA and may contaminate and compromise the PCR test.
The PCR test produces significant false-positive results because samples are easily contaminated by anything containing DNA.
And so technicians working with the PCR machine must filter impurities from samples before starting the cycling process.
If DNA is detected, perhaps after 35 cycles, then the detected DNA is compared to a database of known viral DNAs to see if there’s a match. If there is a match, the doctors will know the virus responsible for the patient’s problems.
Notice that the PCR machine does not know the virus in the sample. It can only produce a sufficient amount of DNA for further analyses.
You will need to decode the DNA produced by the PCR test to determine what it is, whether it is DNA from a human, bacteria or virus. Or perhaps a mixture of all 3.
In the next newsletter, I will write about the new and debased interpretation of the PCR reading.
Now that you understand how the PCR technology functions, let us see how it is applied today for the COVID test.
As you now know, the PCR is a DNA manufacturing technology.
It makes or amplifies the amount of DNA present in a sample by doubling the original amount in a cyclical process. For example, after 10 cycles of doubling, you will have 1000 times the initial amount of DNA you started with, and after 20 cycles you have a million times more, and 30, a billion times more.
The PCR produces a sufficient amount of DNA between 20 and 50 cycles. If no DNA is produced after 50 cycles, the process is terminated, and it is assumed that DNA is not present in the sample.
The PCR does not detect DNA; it makes DNA. And when sufficient amounts are produced, it is compared to a database of known DNA to establish a match. If there’s no match, the DNA is considered a new DNA perhaps from a new virus or bacteria.
Because the PCR amplifies or multiplies DNA, it will amplify any DNA present in a sample. So if a sample contains a mixture of viruses, bacteria and human cells, the PCR will amplify the DNA from all 3 cells present in the sample.
For this reason, samples are filtered and purified before being analysed by the PCR machine.
For example, if you have a sample from the throat, it may contain viruses, bacteria as well as human cells. If you want to see if it contains viruses, you will have to filter out all other cells larger than a virus such as the human cells and the bacteria and anything else in between. Then you use the PCR to amplify any DNA left behind. You can then safely assume that any DNA you find will not be DNA from a human cell or bacteria or parasite.
The PCR can amplify a single DNA or many DNAs. You can only establish the content of a sample if you compare the DNA produced in the PCR to a database of known DNAs. And when you find a match, you can establish the source of the DNA.
What is vital with the PCR is that you filter the sample to reduce the risk of contamination and amplifying all sorts of DNA in the sample, and making it difficult to identify the DNA in the sample.
Now that you understand how the PCR works let us see how it is interpreted to diagnose COVID-19.
If you remember, the PCR machine amplifies a tiny amount of DNA by doubling it in a continual cycle until a sufficient amount is produced, usually between 20 and 50 doubling cycles.
Sufficient DNA is usually detected after 30 to 40 cycles, or after multiplying the DNA a billion to a trillion times. After then, you will have enough DNA for further studies to confirm the source of the DNA.
Also, remember that you have to purify your sample to reduce the risk of contamination with other sources of DNA which then makes it challenging to identify the source of the DNA.
When the PCR is used for the COVID test, it uses a predetermined number of cycles as a cut-off point for a positive or a negative test.
Here is a real-life example. Imagine a lab somewhere in a city that performs a COVID-19 test. So throat swabs are sent to this lab to test for COVID-19.
The lab will add reagents or chemicals to the swab to dissolve the secretions and without filtering the sample start the PCR process at a predetermined number of cycles say 31. This number then determines who tests positive or negative for COVID-19.
In other words, what they mean is that if the PCR machine does not produce sufficient DNA after 31 cycles, then the COVID-19 test is negative. And if DNA is produced before 31, then the test is positive.
While some Labs chose 31 as a cut-off, others chose 35, or 36 or 37 or 45.
In a review of 33 PCR based tests approved by the FDA, it was found that manufacturers recommended 30, 31, 35, 36, 37, 38, 39, 40, 43 and 45 cycles.
Remember that the PCR machine doesn’t have a clue how much DNA or what DNA you have in a sample. If there is very little DNA in a sample, the PCR will require more cycles to produce a sufficient amount than if there was a lot of it.
So using the number of cycles as a determinant for a positive or negative test is nonsensical.
If DNA is detected at 31 cycles, it just means that the sample tested contains DNA. The PCR cannot tell the type of DNA present. It could be the DNA from a coronavirus. But It could also be the DNA from an influenza virus or Rhinovirus or Adenovirus. And it could be the DNA from bacteria or human cells, especially as no attempt is made to filter and purify the sample before the PCR process.
If the DNA from the sample is not compared to a known database of DNA, it is impossible to say what the DNA is. The inventor of the PCR test Kary Mullis was very outspoken about misapplying his technology. You will find a number of his videos on Youtube.
Here is how the COVID-19 test is used today
A sample is collected by sticking a long cotton-tipped tube into the nose or throat, and scrappings are collected. These samples are not filtered our purified before the PCR is started. Without purification, the sample could contain DNA from any living thing, human cells, bacteria, fungi and viruses.
The PCR starts doubling the contained DNA to a set cycle, say 31 cycles. If DNA is detected before 31 cycles, the sample is considered positive, and you have COVID. And if no DNA is detected after 31 cycles, the sample is negative, and you don’t have COVID. The number of cycles or doubling could be anything from 25 to 45, and there is no scientific guideline for this number.
Remember that an unpurified sample will contain DNA from all sorts of living things, and the number of cycles required to produce enough DNA will depend on the amount of DNA in the original sample.
While a lot of these COVID results are solely based on a predetermined cut-off point in the PCR process, other tests compare the DNA detected to a known database. But there is a catch.
The labs that run a confirmatory test on the detected DNA only compare 1% of the total ‘ DNA genome’ of COVID-19.
If you consider that humans and chimpanzees have a 96% genetic similarity, you realise that comparing only 1% of our DNA will show false positive errors 96 times out of 100 times.
Even then, many scientists have pointed out that the Samples used to confirm the COVID-19 DNA genome were not purified; therefore, we cannot say that the 1% DNA tested even belongs to a COVID-19 virus.
What you have just read is the entire process of how the COVID-19 test is being performed.
And so it begs the question of what exactly is being detected by the test and how valid is the test?
Yes, DNA is detected in the test, but what DNA?
When you realise that the PCR test is the most accurate test for detecting the COVID virus, it makes you wonder what exactly is going on.
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