The PCR Test

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  • CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel For Emergency Use Only
  • WHO finally admits the problem of PCR tests.
  • PCR test what is it? The PCR test is primarily used to to see if it contains any genes from the SARS-CoV-2 virus the virus that causes COVID-19. Note that the PCR test is looking for specific genes in the COVID-19 virus not the whole virus. US FDA describes the Coronavirus Disease 2019 Testing Basics here
  • Public Health England publishes "Understanding cycle threshold (Ct) in SARS-CoV-2 RT-PCR" found here that provides a very good and concise description of the PCR test and its Cycle Threshold (Ct).
  • The polymerase chain reaction (PCR) test has many limitations and issues associated with its use as a diagnostic tool.
  • The CDC is now requiring that clinical specimens for PCR sequencing should have an RT-PCR Ct value ct28 when conducting tests for vaccinated individuals, refers to cycle threshold or number of times sample is amplified. The PCR test and their associated cycle thresholds is explained by Public Health Ontario quote "The cycle threshold (Ct) value is the actual number of cycles it takes for the PCR test to detect the virus. It indicates an estimate of how much virus was likely in the sample to start with not the actual amount. If the virus is found in a low number of cycles (Ct value under 30), it means that the virus was easier to find in sample and that the sample started out with a large amount of the virus. Think about it like the zoom button on your computer, if you only have to zoom in a little (zoom at 110%), it means that item was big to start with. If you have to zoom a lot (zoom at 180%), it means that the item was small to start with." So the much higher threshold cycle counts previously used could be generating a high false positive rate. For example Oxford Academic published an article which stated, quote "It can be observed that at Ct25, up to 70% of patients remain positive in culture and that at Ct30 this value drops to 20%. At Ct35, the value we used to report a positive result for PCR, 3% of cultures are positive." This would seem to indicate that a higher cycle count is correlated with a lower actual viral load. The obvious implication being that infection cases and death counts using earlier higher cycle counts may have considerably overstated the real figures. The image below shows the inverse relationship between cycle threshold value and live virus found when cultured. Basically finding a viral signal at low cycle threshold (Ct) counts correlates well with being able to culture live virus. High cycle threshold (Ct) indications have a low probability of producing a positive viral culture. Click here for a big version of image below. All rights to image remain with Oxford Academic. pcr cycle count image

     

  • Some COVID-19 tests contain EtO - poison. Ethylene oxide is used as a fumigant in agriculture and sterilant in the medical industry. EtO is also used in COVID-19 tests.
  • Lateral flow tests do not cause cancer While ethylene oxide is a carcinogen widely used to sterilise medical equipment, the sterilisation process is tightly controlled to ensure any residue left over is negligible!
  • Ethylene glycol is a clear liquid used in antifreeze and de-icing solutions. The Agency for Toxic Substances and Disease Registry states Your health is not likely to be seriously affected by very small amounts of ethylene glycol accidental or intentional ingestion of larger amounts of ethylene glycol can cause serious illness or death.
  • The extreme sensitivity of Polymerase Chain Reaction (PCR) can easily result in contamination. This is a major problem in using these techniques routinely in a regulatory agency such as the Food and Drug Administration (FDA).
  • The Flawed PCR Test: Even CDC Admits Virus May Not Cause Symptoms or Disease. a Positive [test] results are indicative of active infection with 2019-nCoV but do not rule out bacterial infection or co-infection with other viruses. The agent detected may not be the definite cause of disease.
  • The CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. This document contains the following under Warnings and Precautions pg10
    • This test has not been FDA cleared or approved;
    • this test has been authorized by FDA under an EUA for use by laboratories certified under CLIA, 42 U.S.C. 263a, that meet requirements to perform high complexity tests.
    • This test has been authorized only for the detection of nucleic acid from SARS CoV-2, not for any other viruses or pathogens.
    • This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Federal Food, Drug and Cosmetic Act, 21 U.S.C. 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.

The World Health Organisation released a document entitled WHO Information Notice for IVD Users dated 14 December 2020 which, interestingly enough, seems to have disappeared from their web site "This page cannot be found" but was archived here.

  • Purpose of this notice: To ensure users of certain nucleic acid testing (NAT) technologies are aware of certain aspects of the instructions for use (IFU) for all products.
  • Description of the problem: WHO has received user feedback on an elevated risk for false SARS-CoV-2 results when testing specimens using RT-PCR reagents on open systems.
  • In some cases, the IFU will state that the cut-off should be manually adjusted to ensure that specimens with high Ct values are not incorrectly assigned SARS-CoV-2 detected due to background noise.

How many PCR test cycles should be standard if we want 80% of the positives to represent an inoculable sample i.e. virus can actually be cultured from the sample provided by the patient? At a of Ct25 80% of the samples termed positive by the RT-PCR test will be inoculable. However, 20% of the positives will be false, if inoculation is a bench-mark for efficacy of the RT-PCR"