PCR Tests Unraveled

Dec 10, 2020 | COVID-19, The MockingJay Project

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Oregon Governor Kate Brown is using results from PCR tests to determine public policy in Oregon. The current metric (as of December 2020) is calculated using positive tests divided by total tests given. Is this an effective or accurate way to determine actual infection rates in the state? In this article, you will learn what a PCR test is and how it works. You will learn its deficiencies and exactly why it is unreliable.

What is the PCR Test?

The Polymerase Chain Reaction (PCR) is a process designed by Dr. Kary Mullis in 1984 used to “amplify” or copy small segments of DNA.1,2 It  uses a series of chemicals (primers) to detect segments of DNA in a test sample, like those taken with a nasal swab.3  Amplification using PCR can create over a billion copies very quickly, and continues until predetermined cycle thresholds (Ct) are reached.The higher the Ct value, the higher the amplification.4 The copies are then compared to a master copy genetic sequence to determine results.5

DNA Master Copies

The key to developing a successful PCR test is using a master copy of the genetic sequence that is pure and isolated. If the master copy is contaminated in any way, the test is considered unreliable. The SARS-CoV-2 (the virus that causes the illness Covid-19) master copy, used for PCR testing, was derived from a synthetic RNA strand combined with viral fragments manufactured by Chinese scientists.6 In other words, scientists made an educated guess at the genetic sequence for SARS-CoV-2. At the time of publishing this article, labs continue to use the synthetic virus even though a pure and isolated SARS-CoV-2 virus has been isolated.7

The Corman-Drosten Paper: The Blueprint for PCR Tests

On January 25th, 2020 a paper titled “Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR” was published in the Eurosurveillance journal. The purpose of the paper, commonly known as the Corman-Drosten paper, was to “develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.”8 This paper has been used around the world by laboratories as a blueprint to design their own PCR tests9 and gain Emergency Use Authorization (EUA).10

The Corman-Drosten Paper Debunked

A request to retract the Corman-Drosten paper was submitted on November 28th, 2020.11 The report accompanying the retraction request lists “10 major scientific flaws on the molecular and methodological level.”12 One of these flaws of the PCR test includes using a master copy RNA sequence, supplied by China, for testing. Using a sequence that is based upon an educated guess, scientists were forced to only test against 2 sections of viral RNA.13 Because of this, the test does not possess the ability to accurately distinguish between SARS-CoV-2 and other coronaviruses,14 of which there are many, including the common cold. Another flaw is that while the Corman-Drosten paper is listed as peer-reviewed, the time between submission and publication is less than 24 hours,15 an impossibly short time for peer review.

Cycling Thresholds

When the Food and Drug Administration issued an Emergency Use Authorization (EUA) for PCR testing, using the Corman-Drosten paper as a blueprint, a recommended Ct was not listed.16 Oregon is using the Thermo Fisher PCR test which lists a Ct of just under 40.17 According to University of Oxford scientists, any test with a Ct above 30 is completely unreliable.18 The higher the Ct value, the more times the sample had to be amplified to find any trace of the virus, and the less likely the person is infected. According to researchers who wrote the retraction request, when a Ct above 35 is used, “the probability that said person is actually infected is less than 3%, the probability that said result is a false positive is 97%.”19

Viral Fragments

Another serious flaw with PCR testing is that it will show a positive match even if the sample only contained viral fragments. A person cannot infect another person with viral fragments20 and therefore is not contagious even though fragments can remain within the body for up to 31 days.21 This renders the PCR test incapable of determining whether or not a person is contagious. A Portugese appeals court recently deemed the PCR test unreliable and will longer use it to drive policy or lockdowns.22 They stated, “Based on the currently available scientific evidence this test the RT-PCR test is in and of itself unable to determine beyond reasonable doubt that positivity in fact corresponds to infection by the SARS-CoV-2 virus.”23

Testing Positive for SARS-Cov-2 Using a PCR Test

If a person were to test positive for SARS-Cov-2, it means that after amplifying the test using just under 40 cycles, viral fragments were found that match the theoretic sequences created by China. The test does not differentiate between the presence of live or dead virus, nor does it state at which cycle threshold (number of times the sample was amplified) the RNA was detected. Essentially, it’s useless as the sole means of determining if a person is contagious. This is why Dr. Mullis and PCR test manufacturers agree it cannot be used to diagnose an active infection.24

For any other virus, a person would need to present with clinical signs of infection, such as cough or shortness of breath, for which a doctor could order confirmatory medical tests.25 Historically, medical professionals only order tests with the presence of signs and symptoms in their patient. For SARS-Cov-2 however, a single PCR test is used to diagnose a person without symptoms to be an active case.

Calculating Cases

Each new positive PCR test, with all of its flaws, is counted as a new COVID-19 case, regardless of how many times the same person is retested. This is due to the CDC’s decision to adopt26 a fatally flawed position paper by the Council of State and Territorial Epidemiologists (CSTE) on April 14, 2020.27 In Section VII.B, it cites that it is “not applicable” to ensure a person is not counted twice.

To make matters worse, it was recently brought to public attention that the Oregon Health Authority (OHA) has been omitting certain negative tests when calculating Oregon’s infection rates. Any negative tests that were from individuals who had already been tested were not being used. The State’s positivity rate was 12.9% but should have been 6.7% if all negative tests were included.28 The OHA has stated that they will change the way they report positivity rates but gave no clear deadline as to when this would happen.

Should the PCR Test be Used to Drive Policy?

In the words of the late Dr. Kary Mullis, the PCR test’s designer, “Anyone can test positive for practically anything with a PCR test, if you run it long enough.” Dr. Mullis was a strong advocate against using the PCR test as a means of diagnostics because cycle thresholds above 30 are unreliable. Additionally, he warned that we should never use this technique for diagnosis due to the complexity of the process and due to a relatively high rate of false positive results when administered to asymptomatic individuals.29

Using the PCR test as a sole indicator of infection is ineffective and unreliable at determining COVID-19 policy for Oregon. We are losing jobs, livelihoods, and children due to an alarming increase in suicide rates.30,31
Knowing what you now do about PCR tests, do you think it is reasonable or responsible for Oregon’s Governor to use data produced with flawed tests when dictating public health, business, and lockdown policies?

 

References:

  1. Farber C. Interview with Kary Mullis. Spin Magazine. 1994. https://web.archive.org/web/20200110115958/http://aidswiki.net/index.php?title=Document:Farber_interviews_Mullis. Last modified August 15, 2015. Accessed December 3, 2020.
  2. National Human Genome Research Institute. Polymerase Chain Reaction (PCR) Fact Sheet. https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet. Updated August 17, 2020. Accessed December 4, 2020
  3. Drummond H. A basic introduction to the Covid PCR test. https://hectordrummond.com/2020/10/12/a-basic-introduction-to-the-covid-pcr-test. Published October 11, 2020. Accessed December 7, 2020.
  4. Bradburn S. What is a cycle threshold (Ct) value in qPCR? https://toptipbio.com/ct-value-qpcr. Accessed December 7, 2020.
  5. Thermo Fisher Scientific. Real-time PCR: understanding Ct. https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-learning-center/real-time-pcr-basics/real-time-pcr-understanding-ct.html. Accessed December 7, 2020.
  6. Borger P, Malhotra BR, Yeadon M, et al. External peer review of the RTPCR test to detect SARS-CoV-2 reveals 10 major scientific flaws at the molecular and methodological level: consequences for false positive results. https://cormandrostenreview.com/report. Published November 27, 2020. Accessed December 3, 2020.
  7. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):pii=2000045. doi:10.2807/1560-7917.ES.2020.25.3.2000045#abstract_content
  8. Corman et al., op cit.
  9. Borger, Malhotra et al., op cit.
  10. Thermo Fisher Scientific, Inc. Fact sheet for health care providers: Coronavirus Disease 2019 (COVID-19). https://www.fda.gov/media/136111/download. Updated October 9, 2020. Accessed December 3, 2020.
  11. Borger P, Kämmerer U, Steger K, et al. Retraction request letter to Eurosurveillance editorial board. https://cormandrostenreview.com/retraction-request-letter-to-eurosurveillance-editorial-board. Published November 2020. Accessed December 3, 2020.
  12. Borger, Malhotra et al., op cit.
  13. Corman et al., op cit.
  14. Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-269. doi:10.1038/s41586-020-2008-3.
  15. Borger, Malhotra, et al., op cit.
  16. Food and Drug Administration. CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. https://www.fda.gov/media/134922/download?fbclid=IwAR1oqq13b9d87qaTJ0OtZcGbIwQwd53FGJkQ8Ph2qjIl-Ou3l9la7S3OyMQ. Effective December 1, 2020. Accessed December 8, 2020
  17. Thermo Fisher Scientific, Inc. TaqPath™ COVID-19 Combo Kit and TaqPath™ COVID-19 Combo Kit Advanced: instructions for use. https://www.fda.gov/media/136112/download. Published 2020. Accessed December 3, 2020.
  18. Jefferson T, Spencer E, Brassey J, Heneghan C. Viral cultures for COVID-19 infectivity assessment. Systematic review. medRxiv. 2020;08.04.20167932. doi:10.1101/2020.08.04.20167932.
  19. Corman et al., op cit.
  20. Department of Physics and Technology, UiT The Artic University of Norway. PCR positives: what do they mean? https://www.cebm.net/covid-19/pcr-positives-what-do-they-mean. Published September 17, 2020. Updated September 23, 2020. Accessed December 7, 2020.
  21. The COVID-19 Investigation Team. Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States. Nature Medicine. 2020;26:861-868. https://www.nature.com/articles/s41591-020-0877-5. Published April 23, 2020. Accessed December 8, 2020.
  22. Tribunal da Relação de Lisboa. Acordam em conferência na 3a secção Criminal. https://drive.google.com/file/d/1t1b01H0Jd4hsMU7V1vy70yr8s3jlBedr/view. Published November 11, 2020. Accessed December 7, 2020.
  23. Weaver. Portuguese Appeals Court Deems PCR tests unreliable. http://tapnewswire.com/2020/11/portuguese-appeals-court-deems-pcr-tests-unreliable. Published November 16, 2020. Accessed December 8, 2020.
  24. Thermo Fisher, TaqPath™, op cit.
  25. Maria T. Vazquez-Pertejo l. Diagnosis of Infectious Disease. Merck Manual, consumer version. June, 2020. https://www.merckmanuals.com/home/infections/diagnosis-of-infectious-disease/diagnosis-of-infectious-disease.
  26. Centers for Disease Control. Coronavirus Disease 2019 (COVID-19) 2020 Interim Case Definition, Approved August 5, 2020. https://wwwn.cdc.gov/nndss/conditions/coronavirus-disease-2019-covid-19/case-definition/2020/08/05/. Approved April 5, 2020. Accessed December 8, 2020.
  27. Council of State and Territorial Epidemiologists. Standardized surveillance case definition and national notification for 2019 novel coronavirus disease (COVID-19). https://www.med.ohio.gov/Portals/0/CSTE%20COVID-19%20Case%20Definition_1.pdf. Accessed December 7, 2020
  28. Dooris P. Oregon changes the way it counts COVID-19 tests after KGW report. https://www.kgw.com/article/news/health/coronavirus/oregon-changes-the-way-it-counts-covid-tests-after-kgw-report/283-e883b1dc-3099-47fb-8556-90e94a707ab7. Published November 20, 2020. Accessed December 3, 2020.
  29. Farber, op cit.
  30. Sullivan D, von Wachter T. Job displacement and mortality: an analysis using administrative data. Quart J of Econ. 2009;124(3):1265-1306. doi:10.1162/qjec.2009.124.3.1265.
  31. Oregon Health Authority. Oregon death data. https://www.oregon.gov/oha/ph/BirthDeathCertificates/VitalStatistics/death/Pages/index.aspx. Updated December 1, 2020. Accessed December 4, 2020.