PCR Testing

EVERYTHING YOU NEED TO KNOW!

FAQ's

What is a PCR test?

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA or RNA sample, allowing scientists to take a very small sample and amplify it to a large enough amount to study in detail.

Mullis developed the PCR in 1983 awarded the Nobel Prize in Chemistry

Animation of how a PCR test work

https://www.youtube.com/watch?v=ThG_02miq-4
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What are the problems with a PCR test?

Firstly, let us become familiar with an important PCR test concept: the cycle count. Every cycle of a PCR doubles the genetic material. A viral swab that becomes positive after 20 cycles has >1000 (2^10) times the viral load compared to a swab that becomes positive after 30 cycles.

Secondly the genetic material being tested is usually a fragment of a virus not the whole virus.

A number of problems arise from these factual properties of the PCR test.

  • Result is binary – positive or negative. All positive results are treated the same way but some positive results require more cycles than others
  • The cycle count is not shown on the test report (and doctors do not readily have cycle count information when they receive a positive test report)
  • The test does not test for the presence of a virus, but rather, a fragment of the virus. Question arises then is the fragment specific to coronavirus or more specifically the SARS-CoV-2 virus (which is one of coronaviruses known to infect human – most of human coronaviruses causes common cold)

https://www.youtube.com/watch?v=kcONxyAJ8S4 New Zealand doctor talking about PCR testing for COVID-19 from her experience in NZ

https://www.youtube.com/watch?v=iWOJKuSKw5c Kary Mullis (inventor of PCR) talking about mis-interpretation of PCR testing in general

https://www.facebook.com/groups/282967603146622/permalink/364988611611187/ Allen Cheng (Deputy CHO Victoria) talking about PCR being too sensitive for purpose

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The most important question when managing a pandemic must be “is the patient infectious?” Does the PCR test answer this question?

The short answer is NO. Let’s have a look at what experts and government agencies actually say about the PCR test.

Harvard University epidemiologist (Michael Mina – expert in viral testing protocol):

"Positives produced with more than 30 cycles are unlikely to find infectious patients. Such tests detect tiny fragments of viral RNA even after the patient has recovered. The vast majority of PCR positive tests we currently collect in this country are actually finding people long after they have ceased to be infectious"
"Results can’t be relied on to guide the epidemiological efforts of public-health officials, which are focused on preventing transmission and controlling outbreaks"

Source: https://harvardmagazine.com/2020/08/covid-19-test-for-public-health

Canadian Study:

"Researchers cannot grow viral cultures from samples in COVID-19 patients whose positive PCR tests required more than 25 cycles or whose symptoms had occurred more than 7 days prior to testing"

In other words, no virus has been found in patients who test positive on the PCR test, when the cycle count is 25 or above, or patients who test positive more than 7 days after symptoms start.

Covid Medical Network - PCR Test Diagram

UpToDate: advises doctors not to use cycle threshold data, doctors do not receive cycle thresholds with positive test results

Department of Health:

"“It should be noted that PCR tests cannot distinguish between “live” virus and noninfective RNA.”"

Source: https://www.health.gov.au/sites/default/files/documents/2020/03/coronavirus-covid-19-information-for-clinicians.pdf?fbclid=IwAR0sTlOk3KO32Bb8n6T97MSEi6omt0ZimWyb-rl0TJB2Pgqus6eB5jfsH5U

Peter Doherty Institute: Post-market validation of the Beijing Genomics Institute (BGI) SARS-CoV-2 Real Time PCR platform

Best practice would be to use a second assay using a different gene target for this retesting, consistent with Australian guidelines.

Source: https://www.health.gov.au/resources/publications/post-market-validation-of-the-beijing-genomics-institute-bgi-sars-cov-2-real-time-pcr-platform

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What does a False Positive mean?

Every test has its limits, even a wonderful invention like PCR. A very sensitive test used on a low prevalence population will lead to false positives.

Let’s familiarise ourselves with two very simple to understand statistical terms.

Prevalence (of a disease): The total number of cases of a disease in a given population at a specific time.

Specificity (of a test): the percentage of healthy people who are correctly identified (probability of a negative test if patient is well).

Assume a disease affects 0.03% of the population.

And the test is 99.9% specific

What would be the false positive rate of such a test?

So, a calculation is like below:

Prevalence of the disease = 3/10,000.

In other words, out of 10,000 people, 9,997 are well, not infected.

If such a test is run on these 9,997 people.

99.9% of them will be correctly identified as well, not infected.

0.1% will be falsely identified as unwell, or infected.

0.1% of 9,997 is 10.

Together with the 3 truly unwell, or infected patients we have a group of 13 reported cases.

Therefore, the false positive rate is 10/13 or 76.9%.

This is the problem with mass testing a low prevalence disease. Even with a test that is 99.9% specific.

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So how should a PCR test be used?

The higher the pre-test probability, the more meaningful a test becomes. Therefore, the DHHS in Victoria for example provided the following criteria

Current testing criteria in Victoria can be found here: https://www.dhhs.vic.gov.au/assessment-and-testing-criteria-coronavirus-covid-19

Victorian coronavirus (COVID-19) testing criteria

20 June 2020

Fever OR chills in the absence of an alternative diagnosis that explains the clinical presentation*.

  • Acute respiratory infection (e.g. cough, sore throat, shortness of breath, runny nose, loss or change in sense of smell or taste).

as of 31 August, 2020

  • *Clinical discretion applies; consider potential for co-infection (e.g. SARS-CoV-2 and influenza).
  • ** Older people may present with other atypical symptoms including functional decline, delirium, exacerbation of underlying chronic condition, falls, loss of appetite, malaise, nausea, diarrhoea and myalgia.

Additional testing note:

People who are at higher risk of infection due to their environmental exposure or higher risk of severe illness should also be tested if they have new onset of other clinical symptoms associated with coronavirus (COVID-19) (e.g. headache, myalgia, stuffy nose, nausea, vomiting, diarrhoea) AND meet the following epidemiological criteria:

  • Close contacts of a confirmed case of coronavirus (COVID-19).
  • Returned overseas travel in the past 14 days.
  • Health care or aged care workers.
  • Residents of an aged care facility or older people in the community

Who should not be tested for coronavirus (COVID-19)?

Patients without symptoms should not be tested except in special circumstances such as:

  • Recovered cases wishing to return to work in a healthcare facility or aged care facility.
  • Where requested by the department as part of outbreak management or enhanced surveillance.

The Victorian Government has also provided these financial supports for people undergoing tests.

  • If you are worried you will lose pay while you wait for your results you may be eligible for a $450 Coronavirus (COVID-19) Test Isolation Payment.
  • If you are worried you will lose pay because you need to stay home to isolate, you may be eligible for a $1500 Coronavirus (COVID-19) Worker Support Payment
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Our recommendations to the Australian Health Authority on the PCR testing and testing for COVID-19 in general

  • Testing must be limited to a population with high enough likely prevalence and pre-test probability to reduce false positives.
  • Testing must be more transparent to medical professional involved in the treatment of patients, including disclosure of cycle count information.
  • Any positive tests must be followed up with a confirmatory test, either with a PCR test on a different platform, or serological tests, or viral culture. (as recommended by the Doherty Institute)
  • No case should be reported as a positive case until confirmation of findings.
  • Any person who tests positive should self-isolate until confirmatory test result becomes available.
  • More emphasis should be placed on early treatment (link here to treatment page with info on HCQ).
  • Case numbers alone must be used only as an adjunct to policy making, not an absolute target the public must sacrifice everything to attain.

ABOUT COVID-19 MEDICAL NETWORK LIMITED

We are a group of senior medical doctors and health professionals who are concerned about the health impacts of the lockdowns used in response to the SARS-CoV-2 outbreaks in Victoria and across Australia.

We are also concerned about the lack of good information available to the general public and the misleading use of data. These factors have created an unwarranted state of fear in our community.

We aim to detail the harms of the lockdowns, describe clearly the virulence and risks of the SARS-CoV-2 virus, critique aspects of the management policies and make this information readily available to the general public.