The PCR problem explained
To understand the flaws in using the PCR to determine the number of active cases of COVID-19 in this epidemic we need to understand the role of the PCR and what it does.
Kary Mullins invented the PCR as a laboratory tool that could be used to multiply genetic material. Its intended use was to multiply small genetic samples that resulted from laboratory experiments or to enable the identification of the smallest snippet of genetic material that was present in samples from patients.
It is an excellent invention that Kary Mullins was awarded the 1993 Nobel Prize for chemistry and it was worth $300 million in the year 2000 when Roche bought the rights to PCR from Cetus.
The PCR was never intended to be a stand-alone diagnostic tool but it is a valuable tool that can be used to support a doctors diagnosis. Kary Mullins explains that the PCR is so powerful, that when used properly, it can find almost anything in anyone because we all have small parts of everything inside us. Therefore, the results can be easily misinterpreted if not taken in context by a doctor.
In the case of viruses, he explains that the PCR cannot determine if the particle that has been found was a whole viable virus or if that particle could multiply in the body to cause disease. Only after culturing the sample in living cells can the presence of whole viable viruses be confirmed.
The PCR is a tool that doubles the amount of genetic material each time it goes through a cycle. The number of cycles needed to multiply the genetic material enough for it break the threshold and become measurable is referred to as the “cycle threshold (Ct)” number by scientists. A table of doubling numbers has been included as a "pop out pdf" below for you to understand how large the numbers become when continuously doubled. There is no limit on the number of times one sample can be doubled using PCR. If you double something 17 times you finish up with 131,972 times more material than what you started with and if you double it 40 times, as most European countries do, you finish up with a colossal 1 trillion times more genetic material than when you started.
In the case of COVID-19 the PCR is set to find a small part of the COVID-19 virus. If that small part is attached to a whole virus then a large amount of genetic material will be doubled and a positive result will be noted before 17 cycles. If the small part of the virus found by the PCR is not attached to a whole virus then a positive result will still be noted but not until many more cycles have been completed.
This leads to a phenomenon known as ‘false-positives’ in which the PCR has found positive proof of the presence of COVID-19 genetic material but the person is not contagious because no whole viable viruses are present in that person. Most likely the COVID-19 material found belongs to small particles of COVID-19 after the viruses have been destroyed by the immune system by cutting them into small pieces.
Scientists have checked the reliability of the positive results from PCR by culturing the samples in a lab to see if whole viable viruses are actually present. They found that with Ct values of 25, only 70% of patients remained positive after culture. At Ct values of 30, only 20% of patients remained positive after culture and at Ct values of 35 or more, less than 3% of patients remained positive by culture (Jaafar 2020).
Another study found that when Ct values above 35 were used only 8.3% of the samples were positive for whole viable viruses (Singanayagam 2020).
Another study noted that positive results from Ct values above 33–34 found people who were “not contagious and thus can be discharged from hospital care or strict confinement.” They found that Ct values between 13 and 17 all led to positive cultures, however, “culture positivity rate then decreased progressively according to Ct values to reach 12% at 33 Ct.” They added that “no culture was obtained from samples with Ct greater than 34” (LaScola 2020).
These study findings were replicated in the field by Ben Warne. He prepared a report for the COVID-19 investigation involving 12,544 students from the University of Cambridge. They found 10 students who were positive representing 0.5% of the student population. On further investigation, they found 0 true positives and confirmed that all of the positive results were in fact false (Warne 2020).
The problem of false-positives has also been confirmed in law. A Portuguese Court of Appeal ruled on a case of 4 German tourists who were denied their liberty while on holiday in Portugal after one of them gave a positive PCR result. The court confirmed “that if a person has a positive PCR test at a cycle threshold of 35 or higher (as in most laboratories in the USA and Europe), the chances of that person being infected was less than 3%. The probability of a person receiving a false positive is 97% or higher.” The court ruled in favour of the 4 German tourists and deemed their detention illegal. The cite the fact that “no one may be totally or partially deprived of liberty, unless as a result of a condemnatory judicial sentence for the practice of an act punishable by law with imprisonment” (Lisbon Regional Council 2020).
Another consideration is that a large portion of the population have already been exposed to COVID-19 because it has been circulating for a longer period of time than we are aware.
A study found evidence of it in the wastewater from Barcelona from as far back as March 2019 (Chavarria-Miró 2020). Another study found evidence of it in blood samples from October 2019 (Apolone 2020). Therefore, it is highly likely that people are being found in the community using Ct values above 17 who have recovered from previous infections and are being labelled as ongoing cases when they are not.
It can be seen from these scientific investigations, real life studies, Court rulings and the large population exposures, that the PCR will produce a vast number of ‘false-positive’ results and that these ‘false-positives’ are directly related to the number of cycles used to amplify the sample. Controls and recommendations should be made with regard to the number of cycles used and the Ct values should be reported back to the doctor with the results. If the PCR is going to be used as a stand-alone diagnostic tool then proof of COVID positive should only be claimed when the Ct value is less that 17 and then a culture of the sample should be ordered by way of confirming this preliminary finding.
Considering the weight that is given to the results of PCR findings and how this alone is being used to determine government lockdown procedures which deprive people of the basic human rights through lockdowns and restrictions on travel it is surprising to find that the system is not as refined or as definitive as it could be.
China has returned to this method of diagnosis and that is the reason they have had no new cases since April 2020 (woldometers.info 2020). All other countries should do the same, it is a medical travesty to rely on the PCR alone as a diagnostic tool and to then use that false information to deprive the healthy of their freedoms is considered criminal by the Portuguese Courts.
All countries should return to the recognised method of gaining a diagnosis from a doctor and only after that diagnosis should patients be asked to undergo a PCR and then a culture of the sample.
References:
Apolone, G., Montomoli, E., Manenti, A., Boeri, M., Sabia, F., Hyseni, I., Mazzini, L., Martinuzzi, D., Cantone, L., Milanese, G. and Sestini, S., 2020. Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy. Tumori Journal, p.0300891620974755.
https://journals.sagepub.com/doi/10.1177/0300891620974755
Chavarria-Miró, G., Anfruns-Estrada, E., Guix, S., Paraira, M., Galofré, B., Sáanchez, G., Pintó, R. and Bosch, A., 2020. Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases. MedRxiv.
https://www.medrxiv.org/con.../10.1101/2020.06.13.20129627v1
Jaafar, R., Aherfi, S., Wurtz, N., Grimaldier, C., Hoang, V.T., Colson, P., Raoult, D. and La Scola, B., 2020. Correlation between 3790 qPCR positives samples and positive cell cultures including 1941 SARS-CoV-2 isolates. Clin Infect Dis, p.ciaa1491.
La Scola, B., Le Bideau, M., Andreani, J., Hoang, V.T., Grimaldier, C., Colson, P., Gautret, P. and Raoult, D., 2020. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. European Journal of Clinical Microbiology & Infectious Diseases, 39(6), p.1059.
https://covid19-evidence.paho.org/handle/20.500.12663/920
Lisbon Regional Council of the Bar Association. 2020. Case number 1783/20.7T8PDL.L1-3, Habeas corpus, illegal detention, November 11, 2020.
https://crlisboa.org/wp/juris/processo-n-o1783-20-7t8pdl-l1-3/
Warne, B. 2020. UoC Asymptomatic COVID-19 Screening Programme: Week 9 (30th November – 6th December 2020). Cambridge University.
https://www.cam.ac.uk/sites/www.cam.ac.uk/files/documents/pooled_testing_report_30nov-6dec.pdf
Singanayagam, A., Patel, M., Charlett, A., Bernal, J.L., Saliba, V., Ellis, J., Ladhani, S., Zambon, M. and Gopal, R., 2020. Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Eurosurveillance, 25(32), p.2001483.
worldometers.info 2020 https://www.worldometers.info/.../coronavirus/country/china/