Thursday 23 September 2021

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.bthe 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:


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  

Tuesday 21 September 2021

COVID-19 : Part 3 Pandemic ?


It's now September 2021, some 18 months after the start of the "pandemic" (see below), and over 15 months since my last post. I had hoped something approaching normality would have returned by now along with an understanding of the SARS CoV2 virus, the associated disease COVID-19 and how best to treat /contain it from a medical and public health policy perspective. Alas that is not the case and while many aspects of the virus and associated disease are now relatively well understood many remain contentious e.g. the extent of asymptomatic spread, the level of transmission by touch, the effectiveness of social distancing and so called "lockdowns", the effectiveness of vaccines in preventing the spread of COVID-19, concerns over vaccine side effects and many more. Since my first post many of the polices adopted in early 2020 to try and deal with COVID-19 e.g. masks, restrictions on travel, work at home orders, forced isolation etc remain in place to some extent while others, compulsory testing, forced vaccination (for some), quarantines for travellers have been introduced. 


What is however clear is that governments, many scientists and medical professionals and the majority of the mainstream media have not provided the public with clear, accurate and balanced information on the situation. The mainstream media have largely acted as both an uncritical and supportive mouthpiece for the prevailing government narrative and as click-bait alarmists providing endless highly emotive stories of individual suffering, ever rising death tolls", "spikes" "surging", highly deadly variants of the virus etc etc . 


I consider that it is self evident that Governments and their uncritical supporters remain firmly in the grip of "groupthink" whereby they are so convinced of their own "rightness" they refuse to consider, and in many cases try to suppress and discredit, anyone and anything that questions or challenges the position they hold and policies they are implementing. A key element of groupthink is an "end justifies the means" mentality whereby those stuck in groupthink believe that any negative consequence of their actions however terrible are both morally and practically justified i.e. a price worth paying.


My aim remains to try and provide a more accurate and balanced view of what has happened over the last 18 months by analysing the main elements of the mainstream position and in some cases the counter narratives e.g. it’s all a fake "scamdemic". To start however it is essential to try and characterise the true extent of COVID-19 crisis - a term I will use as, whatever the true causes, there has been and remains a crisis - to help assess to what extent the polices imposed to deal with it were and remain justified. 

Pandemic or Scamdemic? - Definitions 

If asked last last year what I considered a pandemic I would have said something like the medieval black death or the Spanish flu of the early 1900s that killed 10's of millions of otherwise healthy people world-wide. This understanding would probably be held by many others. A typical dictionary definition:

Definition of pandemic (Entry 1 of 2)

: occurring over a wide geographic area (such as multiple countries or continents) and typically affecting a significant proportion of the population

with an examples of usage being;

"The 1918 flu was pandemic and claimed millions of lives".

The definition of a flu pandemic used by the WHO until 2009 was: .

“An influenza pandemic occurs when a new influenza virus appears against which the human population has no immunity, resulting in several simultaneous epidemics worldwide with enormous numbers of deaths and illness.”

This definition was altered in 2009 by WHO to: 

“An influenza pandemic may occur when a new influenza virus appears against which the human population has no immunity.”


The current COVID-19 crisis does meet the first criterion of the 2009 onwards WHO definition of a pandemic i.e there is a consensus [see later posts on disputes about this] that SARS CoV2 is a new (corona) virus. However, as immunity to any given disease is in reality a complex and variable phenomenon and I can't see how a total lack the immunity of the "human population" could ever be proven, meeting the second criterion of the WHO definition can never be determined in practise. 


Taking the earlier WHO definition and generic dictionary definition of a pandemic in addition to having to be novel and for no prior human immunity to exist, to be considered a pandemic COVID-19 has to affect a "significant proportion" of the population and/or cause "enormous deaths and illness" - to what extent is this true?

Pandemic or Scamdemic? - The numbers 

If we ignore for the moment concerns over the reliability of COVID-19 deaths statistics from Our World in Data site the numbers of people who died in UK during 2020 were :

 All causes: 604,045 

 Confirmed COVID-19 73,622 


So, from a UK population of 66.65 million 73,622 deaths represent just over 1 in 900 people with COVID deaths accounting for about 12% of the deaths on 2020.


Looking at worldwide statistics: 

 All causes 58.32 Million 

 COVID-19 1.88 Million 


From a world population of 7.674 billion the 1.88 million attributed to COVID-19 represents 0.02% or about 1 in 4000 people and about 3% of all deaths in 2020. Before considering these numbers, one must also consider to what extent COVID-19 affects the "human population” i.e affects everyone equally. 


It was established early on in 2020 from Italy that the distribution of COVID-19 deaths was massively unequal. The vast majority of deaths being in the elderly and those with one or more existing serious conditions (comorbidities). According to the ONS for England and Wales the average age of people dying from COVID-19 was 80.3 years whereas the average of people dying from all causes was actually two years younger i.e 78.2 years. The number of people under 24 who died in 2020 whose death involved i.e some may not have been caused by, COVID was some 55 out of a total of 4579 deaths whereas the number of 65 year olds and over whose deaths involved COVID was 77,987 which is 1400 times greater. 

Pandemic or Scamdemic? - Analysis 

From the above :

  • It is arguable whether COVID-19 is truly a pandemic in the sense of the term generally understood and the definition by the WHO, prior to 2009

  • Given that most people know less than 900 people it is actually unlikely that the average individual in the UK - a country with one of the highest level of infections and deaths due to COVID-19 - will personally know someone who has died from COVID-19. If they do it is highly likely that person will have been “elderly” and /or with other comorbidities 


Given the above some have concluded, perhaps not that unreasonably, that as they and possibly many of their friends' and family don't know anyone who has died of COVID this is somehow all a “scam” or fake issue - this is not a valid conclusion to draw. Despite the true impact of COVID-19 being deliberately exaggerated and serious questions about the accuracy of the official statistics regarding deaths attributed to COVID (see post on PCR tests) excess mortality statistics confirm that many hundreds of thousands of people around the world have died due to some new cause and SARS COV2 is the only credible cause I am aware of. Attempting to claim therefore this is all "fake", a "scamdemic" is simply not true. 


European published excess mortality clearly show the impact across Europe of the “first wave” of SARS COV2. The first wave was largely over by week 20 of 2020 yet resulted in an increase in excess mortality across Europe relative to 2018 of some 50 thousand deaths. 


Source https://www.euromomo.eu/graphs-and-maps


I must be noted that, particularly for the second wave, it is impossible to accurately determine from excess mortality statistics alone how much of the increase was caused directly by COVID-19 and how much was due to other factors e.g the policies implemented in early 2020 to deal with it e.g massive cancellation of operations, vastly reduced GP and A&E services, curtailment of screening for diseases like cancer, shortages of medical staff due to enforced isolation, reluctance to visit hospitals and GPs due to fear of infection. Even some mainstream news outlets (but of course not the BBC) reported on a UK ONS public health modelling study carried out in 2020 where the percentage of excess mortality due to the lockdown policies themselves rather than the virus could be as high as 40%.


https://news.sky.com/story/coronavirus-lockdown-may-have-indirectly-caused-16-000-excess-deaths-study-12044923 

 

Even assuming 40% of excess deaths resulted from government policies rather than the virus by the end of 2020 COVID-19 would have been the cause of 150,000 excess deaths across Europe relative to 2018. [i.e 60% of the 250,000 difference at week 52 - see graph above]

Conclusion 

The use of the terms pandemic and scamdemic are both to some extent flawed and to differing extents misleading characterizations of the true situation and continue to have serious consequences. Future posts will take a critical look at the consequences of these flawed characterisations. 


Notes / References


Groupthink https://www.britannica.com/science/groupthink


Our World in Data Example Plot

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