Use of PCR tests to determine COVID-19 cases

What is a PCR Test

The term PCR test is understood by the majority of the public to be a well established, reliable and accurate way of determining whether someone does or does not have COVID-19 disease. This is the line strongly promoted by most governments and the MSM. That is far from the case and as the saying goes "it's more complicated than that "- in this case much, much more complicated. 

The Wikipedia definition of PCR is :

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail. PCR was invented in 1983 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to many of the procedures used in genetic testing and research, including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory research for a broad variety of applications including biomedical research and criminal forensics.^[1][2]

A COVID-19 PCR test is based on the PCR process and essentially amplifies by repeated cycles the DNA/RNA from e.g a sample nasal swab. If target SARS- CoV2 viral RNA is detectable at or below a chosen number of cycles designated the Cycle threshold  (Ct)  the test is positive and the person providing the sample is deemed to have COVID-19 and if not detected by the designated Ct the test is  negative and the person is deemed not to have COVID-19. 

Limitations of mass COVID-19 PCR Testing 

If your understanding of PCR tests is as described at the start of post alas your understanding is unfortunately almost entirely wrong. Consider these extracts from official and mainstream sources (not some random ill informed  site on the web):         

• Public Health England (PHE )  

"RT-PCR detects presence of viral genetic material in a sample but is not able to distinguish whether infectious virus is present." 

 A single Ct value [i.e one PCR test] in the absence of clinical context [i.e The subject being tested has not been assessed by a clinician] cannot be relied upon for decision making about a person’s infectivity.  n.b. the inserted text in [ ] are my clarifications  

• article in the British Medical Journal website  (my highlighting)

It’s also unclear to what extent people with no symptoms transmit SARS-CoV-2. The only test for live virus is viral culture. PCR and lateral flow tests do not distinguish live virus. No test of infection or infectiousness is currently available for routine use.678 As things stand, a person who tests positive with any kind of test may or may not have an active infection with live virus, and may or may not be infectious.9

• the Oxford University Centre for Evidence-Based Medicine (CEBM) says[1, 2]:

“PCR detection of viruses is helpful so long as its accuracy can be understood: it offers the capacity to detect RNA in minute quantities, but whether that RNA represents infectious virus may not be clear.”  

• fullfact.org -  A site that often presents a highly misleading conclusion but from some good research. 

 "The exact relationship (between Ct value and infectivity) is still being researched, and interpreting these results depends on the clinical context.

So picking apart the widely held understanding of mass of PCR tests for COVID 19 as outlined above:

• Well established ? - NO
• relationship between the Ct values used in test and infectivity and is still being researched
• Reliable ? - NO 
• a person who tests positive with any kind of test may or may not have an active infection with live virus, and may or may not be infectious.
• majority of PCR tests e.g home /school administered PCR tests have no clinical context 
• single PCR test cannot be relied upon 
• Determine whether you do have COVID-19 - Not reliably 
• see points above  and note that simply because some specific disease virus/bacteria are present in your body does not necessarily mean you have the associated disease (see notes )
• Determine whether you don't have COVID-19 - Not reliably    
• With a high Ct a PCR test will detect even minute quantities of viral particles so one might think if these aren't detected it is basically impossible to have the disease. However, the amount of virus present in an individual varies greatly as an infection progress and in cases of respiratory disease as opposed to e.g blood borne diseases the virus is not evenly distributed in the body. In the early stages of an infection where the level of virus - the viral load - is usually minute and a PCR test, especially one using a sample taken by a non medical professional, may falsely produce a negative result hence the PHE caution that 
•  A single Ct value in the absence of clinical context cannot be relied upon ..."

Flawed Statistics - Virus vs. Disease 

It should be self-evident from the above that officially published statistics on the number of COVID-19  cases where numbers are presented as simple facts e.g. like taking a count of passengers on a plane grossly misrepresents the true situation which is that nobody knows with any real confidence how many cases of the disease/illness COVID-19 there are or have been. 

The self contradictions in the process used to produce the official statistics can be seen by these extracts from the key UK government publication ref.  https://coronavirus.data.gov.uk/details/about-data

First we have this clear and factual statement:   

"Polymerase chain reaction (PCR) tests are lab-based and test for the presence of SARS-CoV-2 virus."

Yet two sentences later in the same documents we have this  :

"Daily and cumulative numbers of cases

Number of people with a positive COVID-19 virus test (either lab-reported or rapid lateral flow test) on or up to the specimen date or reporting date (depending on availability)."

and somehow a PCR test for "the presence of SARS-CoV-2 virus" has become,  i.e a lab reported "positive COronaVIrusDisease-19 virus test" despite, as shown above the government knowing  full well that a single PCR test is neither a reliable indicator of whether an individual or doesn't have COVID-19 nor whether they are or are not infectious.  

This mixing of true statements about the well established PCR process for testing the presence of a virus with falses statement/implications about PCR tests without any clinical context being a reliable test for cases of COVID-19 disease are endlessly repeated on the Internet, the mainstream media and those self appointed and misnomered "fact check"sites . Taking this example from  https://fullfact.org/health/cycle-threshold-values/ 

The summary is far from being a non-partisan impartial fact check and closer to a lawyer's summary putting their case i.e. to defend PCR tests in the best light and deliberately misrepresenting their opponents argument to present it in the worst  i.e   

• they have omitted to specify whether the original claim (n.b  no longer available on the web ) was about PCR tests for disease, where they are flawed, or for simple presence of virus where they are not   
• while they have correctly stated that interpreting high Ct result requires clinical context they have disingenuously omitted to acknowledge that with advent of mass PCR testing the huge majority of tests have no clinical context whatever in which to interpret them so in a very real sense they can be considered invalid.    

So how many COVID-19 Cases are there?

Well it should be abundantly clear I don't know and nor does anyone else - but as ever there are polarized arguments either way with some factions arguing that cases are under reported and others that they are over reported. The flaws in PCR test for identifying diseases and hences cases (I'll leave the thorny topic of asymptomatic cases to another post!) can result in both false negatives and false positives.

It is generally the case in the early stages of an outbreak of disease that cases are under-reported with the true number of people infected not being known due to there not being a perfect testing process i.e there is no cheap, 100% reliable, instant test you can simultaneously administer to everyone to know the true number of people infected. 

However COVID-19 is unique in that by early March 2020 there was already widespread fear of  the disease in the UK inflamed by extensive and almost universally alarmist media reporting on the COVID outbreaks in China and Italy. The UK government along with most others were already preparing to impose policies they knew would be incredibly expensive and far reaching in their impact  on society as a whole i.e the lockdown. In such a scenario I contend there were actually very strong vested interests in seeing over reporting of cases to justify the policies already committed to and there are numerous other areas of concern regarding the attribution of COVID deaths - this however requires another post to cover it in any in detail.

Summary - Can it really be that bad ?

Alas the situation is even more complicated in that, along with the serious limitations of mass COVID-19 PCR tests, there is not even general agreement on what constitutes a COVID-19 case with different countries and organisations have differing definitions. This is all presented clearly by the CEBM here:

 https://www.cebm.net/covid-19/when-is-covid-covid/

Government policies on lockdown, school closures, mass testing, quarantine for travellers, imposed isolation after positive test are all to a greater or lesser extent based on an assessment of COVID cases and how fast they are spreading. To me it is genuinely shocking that despite the difficulties in even defining what is a case of COVID-19 and the acknowledged, understood and accepted limitations of PCR tests in identifying disease and infectiousness governments have still used mass PCR tests (see notes) as a cornerstone for the most far reaching, draconian and costly polices ever imposed outside of war time. 

It is equally shocking how the mainstream media, the majority of medical, health and scientific organisations -who know full well the PCR tests limitation - and even opposition politicians, have not just gone along with but acted as active proponents of the simplistic and misleading narrative/propaganda used by the Government. 

I remain convinced this is not all part of a world wide strategic plan, "the great reset", but is primarily the result of fear induced groupthink and a tragically flawed "end justifies the means" way of thinking - see my COVID part 3 post. However the idea there were/are no cynical opportunists developing lucrative careers and numerous companies and organisations making massive profits from the COVID crisis and hence active in supporting and promoting disinformation when is suits their interests and discouraging analysis criticism when its doesn't is to my mind more than simply naieve.  

Notes  

• Lateral flow tests outside of a clinical context are acknowledged as even more unreliable then PCR tests at identifying COVID-19
• One in 10 people i.e 6.6 million people in the UK  would test positive for meningitis on a PCR Test. See https://vk.ovg.ox.ac.uk/vk/meningococcal-disease#:~:text=Between%205%25%20and%2011%25%20of,in%20the%20winter%20each%20year.