Dr Sam Bailey: The Truth About PCR Tests

Přepis obsahu videa Dr Sam Bailey: The Truth About PCR Tests.

2020 seemed to be the year when PCR tests became a household name riding on the wave of corona mania. Prior to this PCR tests were far less well-known to the public and even much of the medical community had little engagement with them now it seems everyone has something to say about them. 
However like my recent video exploring what exactly is a COVID-19 case, it is useful to go back to the basic science to understand what the foundations are so we can see where it can lead and often where it can go wrong.

So what is PCR? PCR stands for polymerase chain reaction. Polymerase means an enzyme that catalyses the formation of a polymer or long chain molecule from smaller units.
In this case we are talking about DNA.
The molecule that carries the vital genetic information for much of the life on our planet. Chain reaction means that the process is carried out multiple times in sequence.
This amplification process means a minute sample of dna is multiplied millions of times to produce sufficient material to allow for genetic and molecular analysis.
The history of PCR started in 1976 with the discovery of tech DNA polymerase. The enzyme was found in thermos aquaticus: a bacteria discovered living in hot springs in yellowstone national park. Because the enzyme could withstand temperatures of 95 degrees centigrade - it was a practical molecule for the thermally dependent PCR process. Prior to this fresh enzyme would have to be added at every single cycle. Things really took off in the 1980s when Carrie Mullis realised how to put tech polymerase to use... and the enzyme became commercially promoted. Mullis was awarded the nobel prize in chemistry in 1993,
and is generally considered to be the inventor of PCR.

I won't get into all the technical details of PCR - is for our purposes the principles and application are more important than all the biochemistry. However for those of you interested I'll include links with more detail below in the description.

In summary the process starts with heating the sample of DNA. This separates this double-stranded DNA into two pieces of single-stranded DNA. 
Primers are then added these are short pieces of DNA that are designed to flank the target section of DNA for amplification.
Usually two primers are used one to bind to each of the opposite strands of the target DNA section. The polymerase then synthesizes a new DNA strand that is complementary to the target DNA section. It builds this from nucleosides present in the reaction mixture. This essentially completes a cycle and the amount of target DNA has been doubled. 
The cycle then starts again but this time with around twice as much target DNA as the first time. (The DNA learning center had produced a nice little video outlining the PCR process in 3d, which you can check out in the link if you're interested.)
The cycle is typically repeated 25 to 40 times and it is important to realize the exponential amplification of material that occurs with these numbers for example
at 40 cycles, there would be around a thousand billion copies produced! However tech DNA polymerase has a certain number of mismatch errors - so higher cycle numbers are more likely to produce inaccurate results. It is also important to realize that a typical PCR test only detects a small sequence of genetic material it does not detect anything close to the entire genome of a purported organism.
Okay, so we have a pretty neat way of detecting tiny amounts of DNA and actually RNA. What could possibly go wrong? 
Well, quite a bit when the technique is used to draw conclusions beyond that for which it was designed. The inventor of PCR himself warned that the PCR test doesn't tell you that you are sick. These tests cannot detect free infectious viruses at all. 
And as I've discussed in previous videos the manufacturers of PCR tests usually have disclaimers stating that they are not suitable for diagnostic purposes and that they are non-specific. Let's explore some of the reasons why this is so.
Firstly the very nature of the biological samples is problematic. When a biological specimen for example a nasal swab is taken from a living host it contains all sorts of things including genetic material from any
number of microorganisms. Humans are covered in billions of microorganisms. Most of them living in symbiosis with us, meaning they don't cause any harm or any disease. In fact many of them are essential to our very existence experiments with newborn animals have revealed that attempting to raise them in sterile conditions leads to rapid death. Most microorganisms found in and around us have nothing to do with illness so the mere apparent detection of their prisons is not a cause for alarm additionally as Carrie Mullis pointed out a PCR test does not detect an infectious agent. This is because it is an indirect test that only detects genetic fragments of organisms. Your body may have encountered a potential pathogen that your immune system rapidly destroyed but the PCR test still detects remaining fragments. It also needs to be established that a genetic sequence is absolutely specific to a certain organism and this is where diagnostic PCR can fall apart. 
Due to the almost incomprehensible amount of genetic material on the planet it is rash to assume total specificity when it comes to particular sequences. What about SARS-CoV-2? Was it even formally isolated prior to the development of a PCR test?
As you are aware we are currently working on the third english edition of virus mania and this has been something we have been looking into. We asked the groups that reported that they had identified the novel virus by electron micrograph - whether they had formally purified the virus. The responses were all the same: "no". Even Michael Laue from the Robert Koch institute wrote in an email that we received on september 4th 2020. 
"I am not aware of a paper which purified isolated SARS-CoV-2. Hence it cannot be concluded with any confidence that the so-called COVID-19 PCR-tests were specifically calibrated to a brand new viral pathogen." (Michael Laue, Sept. 4,2020)

The research work of geneticist Barbara McClintock (Geneticist, 1902-1992) is also with a mention here. In her nobel prize speech from 1983, she reported that the genetic material of living beings can constantly alter by being hit by shocks. These shocks can be toxins, but can also be from other materials, that produce stress 
in the test tube. This in turn can lead to the formation of new genetic sequences which were unverifiable - both in vivo and in vitro previously. So this raises another complicating factor when considering where genetic sequences are actually  originating from and how different conditions in life and the lab - can change genetic expression. 
But even if the PCR test was known to be reliably correlated to a particular organism something more is required to prove beyond any doubt that the PCR can truly measure if a person is affected by a disease-causing microorganism. We need to do a blinded experiment; and you guessed it this hasn't happened to date! It cannot be emphasized enough (!) how problematic it is when a test has no connection to actual illness. 
To put it in perspective there is little doubt that some tests are very useful and have strong relationships to illness. For example if we have a patient who reports fatigue and a blood test reveals a hemoglobin of 65 grams per liter, we have a very strong indication that they are anemic and need  further investigations and treatment. This is not the case with many PCR tests where a positive result doesn't tell you anything meaningful about the test subject; and as we saw in 2020 even athletes at the top of their game were testing so-called positive with the covered PCR tests.
To go back to our hemoglobin example we would not expect Ronaldo to make it through the first 10 minutes of the game if his hemoglobin was 65. So I'm sure the soccer star would have much more confidence in this test.
* * *
PCR tests may be qualitative or quantitative. Essentially qualitative PCR is the traditional technique which is used to decide whether a DNA fragment is present or not. Whereas quantitative PCR or qPCR is used to determine how much of the DNA fragment is present in the sample.
There has been confusion with regards to this as the product descriptions of the RT-qPCR tests for SARS-CoV-2 state - they are qualitative tests. Contrary to the fact that the q and qPCR stands for "quantitative". In fact one of my co-authors Thorsten Engelbrecht applied pressure to the charity with regards to the Drawston Corman PCR test... and received the following response: "If real-time RT-PCR is involved to the knowledge of the charity in most cases these are limited to qualitative detection."

Mmmm. Clear as mud. In any case as I've previously discussed in this video: 
( Co je případ COVID-19?
https://www.youtube.com/watch?v=g2aR2UInnug; 
Kdo kontroluje kontrolory faktů?
https://www.youtube.com/watch?v=T5dWbxwoCZI )
for some reason the FDA and other health authorities have failed to collect any significant data on PCR cycle thresholds despite dr thatchy saying it was an
important value for the clinician to consider. Check out that video for more about
cycle thresholds ("What's COVID-19 case?", Dr. Sam Baily, p.p.).

With regards to SARS-CoV-2 there is an additional issue in that the target genetic material is for a presumed RNA virus. This means that before starting the actual PCR process the target RNA must be converted to complementary DNA with the enzyme reverse transcriptase. Professor of Molecular Medicine Stephen A. Bustin pointed to the problem that in the course of this conversion process the amount of DNA obtained with the same RNA-based material can vary widely even by a factor of 10 ! So this initial step can also cause variation in whether the subsequent PCR test is considered positive or not. Interestingly Bustin who helped develop the miqe guidelines to standardize PCR protocols had the following to say about COVID-19 PCR tests:
"We demonstrate that elementary protocol errors and appropriate data analysis and inadequate reporting continue to be rife and conclude that the majority of published RT-qPCR data are likely to represent technical noise." In other words ... total ... mess.
So why are PCR tests being promoted as fit for purpose for COVID-19?
It's hard to know all the reasons but there are huge profits to be made and advancements of certain agendas. There is also likely to be many conflicts of interest by those with links to political power and public funds for their work. A viewer sent me an article that was written by a New Zealand scientist called Susie Wiles. She states there was a misinformation video about PCR tests circulating. New Zealand is a small place so presumably this is one of mine? Unfortunately she doesn't exactly explain which part is wrong, only that it is chock-full of false information. Goodness me what a highly scientific rebuttal? Firstly it seems that the spin-off website has received 222 thousand dollars in funds from creative New Zealand which is a division of the New Zealand government. So perhaps the nature of the article is not that surprising. Anyway let's have a look at where susie goes astray and how she has cut more than a few corners with her claims. The PCR looks for specific genetic sequences that are only found in the SARS-CoV-2 virus. As we've discussed this is a dubious claim as the virus was never fully isolated and purified prior to the development of the PCR test. It also suggests that we have sequenced the genomes of all significant organisms on the planet. And know about every change in genetic expression as per Barbara McClintock's work the manufacturers of the PCR test certainly don't share Susie's enthusiasm and in
fact include disclaimers like "This product is for research use only and is not intended for diagnostic use and may react to other organisms." That makes it very suitable as a screening tool as it has such a low false positive rate - people are highly unlikely to test positive unless the virus is present in the sample.

I can only view this as confused or disingenuous. Where has it been established that it is a suitable screening tool when it wasn't even established as a suitable diagnostic tool? The Corman Drosten paper that triggered the worldwide promotion of COVID PCR tests never established how it should be applied in clinical use. And this is one of the many reasons why a consortium of scientists have requested its retraction.
It is also unsound medical practice to claim that COVID-19 is diagnosed by a PCR test and that the definition of COVID-19 is a positive PCR test as a standalone. As I've discussed in previous videos there can be no estimate of false positive rates as there is nothing to compare it to - no gold standard  - she can only be referring to the false positive rate in the lab setting with control samples - not real world application in the community. I've talked about the gross limitations of this in my fact-checking video we know this is true from all the thousands of negative tests we've seen here in New Zealand. This bizarre statement is a complete non-sequitur in (and?) no way establishes the suitability of a test.
It tells us nothing about the status of the people being tested there have been no blinded trials to establish the validity of the test for actual illness. Anyway you can see that she is attempting to build the case for PCR tests but already the foundations are inadequate. Some of the article is fine and talks about cycle thresholds, but then she gets into hypotheticals and a "(1) test,  (2) trace, (3) isolate" mantra. Public education campaign perhaps to her it seems that mass testing can only be beneficial but this ignores the huge costs that include a financial costs an official information act request in New Zealand a country of 5 million people revealed 74 million in PCR swab and lab costs alone over a mere six week period. The total cost will be far in excess of this... and be psychological and social costs to people who believe that they are actually ill and isolate because of a positive test result. However most conspicuous by its absence in the article is where it was established that positive PCR test results have anything to do with illness? She completely misses this crucial point. And this is not surprising because as I discussed in my video what is a COVID-19 case it has never been established as my co-author and season campaigner class coonline would say she has been swept up in the PCR pandemic. Unfortunately scientists like Susie seem to have become detached from the very nature of human health as they focus on molecular test results and top-down political policies. Interestingly some of the authorities that heavily promoted the COVID PCR tests are now softening their positions with a european court declaring the tests not fit for purpose and potential lawsuits brewing. Last month the who quietly issued a statement suggesting more caution with so-called positive tests. Could this be the beginning of a gradual back down from unsound science? Over a decade before PCR tests appeared on the scene noble laureate for medicine sir Frank Macfarlane Burnet made a precise warning. By the beginning of the 1970s he had become very skeptical about "... the usefulness of molecular biology especially because of the impossible complexity of living structures and particularly of the informational machinery of the cell. [Certainly molecular biologists are] rightly proud of their achievements and equally rightly feel that they have won the right to go on with their research. But their money comes from politicians, bankers, foundations who are not capable of recognising the nature of a scientist's attitude to science and who still feel as I felt myself 30 years ago that medical research is concerned only in preventing or curing human disease. So our scientists say what is expected of them, their grants are renewed and both sides are uneasily aware that it has all been a dishonest piece of play acting but then most public functions are."
As a quick comment I can also say that when PCR tests are used out of context they can also appear to provide evidence of a new strain of a virus again this indirect method does not suffice and full evidence of the virus needs to be carried out with formal purification and isolation as well as the characterization of the full genome and shell and if there is evidence of any new strain we still need evidence that it poses any threat to humans as its mere detection is no reason to cause panic. In summary I'm not saying that there is no use for PCR tests. They are an incredible tool of human discovery and have a vital role in scientific research as well as genetic and forensic medicine. However their use with regards to infection diagnostics has generally been overplayed in recent years and I suspect 2020 will be viewed as the year in which they went completely out of control.

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