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COVID CHAOS: A Closer Look At Coronavirus Testing

A remarkable story made headlines last week — a goat, a quail and a papaya tested positive for coronavirus.

Following a request by the president of Tanzania to evaluate the country’s coronavirus test kits, state security services sent a series of non-human samples to the national health laboratory to be tested. The samples — which included goat, quail and papaya, as well as inorganic substances such as motor oil — were labelled with human names and ages, while technicians at the lab were not told of the plot.

After the fruit and animal samples received their positive results, President John Magufuli said there was a “dirty game” playing out at the lab, and that the imported test kits were faulty and had “technical errors”. He also questioned whether there was a possibility of bribes or sabotage taking place:

“People could be used, the test kits could be used too. It could also be a sabotage because this is war… So when you notice something like this, you must know there is a dirty game being played in these tests… that there are unbelievable things happening in this country. Either the laboratory workers in there are bought by people with money, either they are not well-educated, which is not true because this laboratory is used for other diseases… Because even the reagents are imported, because even the swabs are also imported, so it’s a must that something is actually going on.”

Importantly, the president then expressed concern about false positive test results, saying that some people are being told they are infected when they are not actually carrying the virus.

“Through the extra information I have here, there must be people who are told they are positive, while they are not really corona patients, and some might even die from worry.”

The lab’s director as well as its quality assurance manager were suspended, while the Ministry of Health announced a 10-person committee to investigate operations at the lab — not only procedures for handling and processing samples, but also the test kits themselves.

In response, the Africa CDC, who provided the tests in conjunction with the Jack Ma Foundation, defended the tests, as did the World Health Organization. Jack Ma, the richest man in China and the man behind Alibaba, has been on a mission to supply over 150 countries with medical supplies, including a shipment of 1.1 million coronavirus tests kits to Africa.

Note that instead of acknowledging a possible problem with test kits or procedures, MSM reporting on this story repeatedly mentions President Magafuli’s endorsement of a Madagascan tonic as a COVID-19 treatment, his wish for Tanzanians to “pray away” the virus, and Tanzania’s failures with respect to its coronavirus response. Mainstream outlets tend not to mention that he has a PhD in chemistry, his comments about sabotage, or his concerns over faulty tests and false positive results.

Flaws in Testing

This is not the first time coronavirus tests have come into question. In Britain, tests produced under Public Health England (PHE) protocols were found to lack sufficient accuracy and were abandoned. Similarly, in the United States, the CDC’s own tests were also found to be flawed. Other countries including the United States, Spain, Czech Republic, Slovakia, Turkey and India have all reported faulty or inaccurate tests from Chinese suppliers.

Obviously, bad tests means bad results. False negative test results return people who are actually infected with COVID-19 back into the community, confirmed to be safe to enjoy their remaining freedom. If the virus spreads and behaves as the MSM would have us believe, a small number of false negatives could spell disaster.

False positive results are dangerous for another reason — they cause people to be diagnosed with COVID-19 when they don’t actually have it. Considering those people and possibly their entire households may then be quarantined, this is not a good outcome. It gets worse when you add in the possibility of all their contacts being traced, notified that they might have COVID-19, and also possibly being isolated, based on bad test results.

Bear in mind that when large numbers of people are tested, a small percentage of false positives will falsely inflate case numbers, possibly giving the appearance of outbreaks occurring where there may be none. Considering much of the world has been placed on lockdown and large chunks of the global economy held for ransom, we ought to have an exceptionally high degree of confidence in the tests being used to detect coronavirus.


Preparation for extraction of SARS-CoV-2 genome using RT-PCR (Photo: Dean Calma/IAEA. Source: Wikicommons)

A Closer Look

Unfortunately, taking a closer look at the details of the testing process does not inspire confidence. Rather, it brings up a number of potential pitfalls, which, taken together cast a different light on the entire coronavirus crisis.

The following brief analysis by virus researcher David Crowe summarises his discoveries regarding the ‘PCR‘ or RT-PCR test, the main method being used to test people for COVID-19. His research points to what are potentially massive flaws, including:

  • the arbitrary nature of test procedures and the ambiguous nature of test results
  • documented cases in which test subjects alternately test positive, then negative, and then positive again on successive tests
  • the inability of the test to prove that a virus is functional or even present
  • the possibility of both false negative AND false positive results
  • variability in test procedures (which sequence portions of the virus are being sought, etc) among dozens of different test kits
  • the possibility of the ultra-sensitive tests being contaminated.

Before we mortgage our freedom and the global economy alike on the back of these tests, it should be a prerequisite that their results are at least accurate — but neither the tests themselves nor the public health bureaucrats pushing them even attempt to claim total accuracy.

So, who will test the tests? How accurate would you like your test to be?

More on this from David Crowe’s The Infectious Myth:

A lot depends on the result of your COVID-19 test, whether it is positive, indicating infection or, big sigh of relief, negative, indicating that you are not infected. But is there such a thing as “the” COVID-19 test? Indeed there is not. There are many and each is looking for different things and making different decisions about whether those things are present or not.

The Test is Not Binary

It is important to understand that the COVID-19 test does not inherently have only two values. The test uses multiple cycles of the PCR (Polymerase Chain Reaction) technology, with an arbitrary count of cycles being the boundary between positive and negative, usually interpreted as infected and uninfected. Not only is this division arbitrary, but we know that it does not work that well because there are numerous published examples of people testing positive, then negative, then positive again, within a few days. There is, so far, no explanation of this phenomenon amongst people who are unwilling to question the test technology, test implementation or viral theory, although manufacturers do obliquely refer to this problem in their technical documentation by admitting that false positives can be caused by “non-specific signals in the assay” or, more directly, “As with other tests, false-positive results may occur.”

Imagine a game dreamed up by Harry Potter and Lewis Carroll. It is played in a field and the bounds are a circle that is not marked. If someone yells “out of bounds” the referee goes to the centre with a curled-up flamingo and rotates it a number of times, a number chosen arbitrarily by the referee. Some choose 30, and some choose other numbers up to 45. Additionally, different referees have flamingoes of different sizes, and sometimes they are curled up more tightly than at other times. But, if you are within the, say, 37 flamingo turns, you are safe, and if not, out of bounds. Welcome to the world of testing for the coronavirus.

Complexity

Coronavirus tests are performed by sophisticated machines with simple interfaces. Program the parameters of the test, pop in the samples, and in a relatively short time, the results are displayed, sometimes as a graph, or other times as simply as “Positive”, “Negative” or “Invalid”. But the process is not simple. First the RNA needs to be extracted from the sample, which will include a lot coming from your cells, from bacteria, or other sources, as well as possibly some from viral particles, all of which could possibly react with a later stage, causing a false positive. It is also important at this step to eliminate non-RNA substances that could interfere with following steps.

Secondly, the RNA needs to be converted into DNA, because PCR only works with DNA. This process uses the enzyme Reverse Transcriptase, hence the moniker RT-PCR for the combination of RNA conversion followed by standard PCR. The RNA to complementary DNA (cDNA) conversion process is quite inefficient. Stephen Bustin, a professor at Anglia Ruskin university, and perhaps the world’s leading expert on quality control of RT-PCR, told me in a recent interview
(infectiousmyth.podbean.com/e/the-infectious-myth-stephen-bustin-on-challenges-with-rt-pcr) that the amount of DNA obtained can vary widely, easily by a factor of 10. Since the PCR cycle number is a measure of the amount of material obtained, different efficiencies at the RT step essentially invalidate the simple use of the PCR cycle number. Two different test setups in two different labs, that both use the PCR cycle number 35 as a cutoff, may actually have the cutoff between negative and positive at wildly different places.

Finally, the third step, pure PCR occurs. As described above, this is repeated many times. On each cycle the DNA is unrolled from the double helix into two strands, the portion of interest is duplicated, and the DNA rolls up again.

You may think this explanation is complicated. Yes. It is a complicated process. And although a fancy machine makes it simple to operate, it doesn’t mean that every machine, every lab and every operator gets comparable results. Your situation is even worse than the operators because you will likely just be told either “Infected” or “Clear”.

A Potpourri of Tests

The NHS does not exert much control over the choice of COVID-19 test, allowing in-house validation of test kits (http://www.england.nhs.uk/coronavirus/wp-content/uploads/sites/52/2020/03/guidance-and-sop-covid-19-virus-testingin-nhs-laboratories-v1.pdf) although, more recently, it started to insist that commercially available, rather than in-house tests be used (www.telegraph.co.uk/news/2020/04/21/public-health-england-admits-coronavirus-tests-used-send-nhs). The US Food and Drug Administration, on the other hand, requires at least a façade of test approval through their Emergency Use Authorizations. I downloaded 33 of the test kit instructions, hopefully a representative sample, to try to see how the tests differed in what they were looking for, how long they were looking, and how they decided whether they had found it or not. I also scanned the test limitations, to see whether the manufacturers thought their tests were perfect or not. If you are a true masochist, you can check my analysis at:
https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations

The Number of Flamingo Turns

For some tests in the FDA list, the number of PCR cycles to distinguish positive from negative is not specified, but for most, it is. In general, the more PCR cycles, the more likely that a false positive will be obtained, and the fewer cycles, the more likely a false negative will be obtained. One manufacturer each recommended 30 cycles, 31, 35, 36, 37, 38 and 39. 40 cycles was most popular, chosen by 12 manufacturers, and two recommended 43 and 45. The MIQE (Minimum Information for Publication of Quantitative RT-PCR Experiments) guidelines for operation and reporting of RT-PCR states that the use of 40 or more cycles is unwise (academic.oup.com/clinchem/article/55/4/611/5631762). Bustin’s advice in my interview with him was that not more than 35 cycles be used. With either 35 or less than 40, the majority of COVID-19 RT-PCR tests approved by the FDA may be pushing RT-PCR to its limits or beyond.

What is Being Looked For?

The RT-PCR tests look for only a tiny fraction of the COVID-19 genome. And different tests look for different tiny fractions. Most do not specify the size of the portions, but a test developed by Charité Berlin (not on the FDA list) looks for the RdRp and E genes, which amount to 213 bases out of about 30,000 for the entire genome, or less than one percent. On the FDA list, the tests reference the E, N and S genes and portions of the ORF (Open Reading Frame). What is most important to know is not what the function of these RNA segments is, but simply that the tests are looking for very different things. It is as if we went looking for leopards with one person using spots as the guide, another the claws, another the teeth and another the eyes.

Worse than differences in what they are looking for is the way of defining whether they have found it. Some tests look for one portion that must be present for the test to be declared positive. Others look for two portions and both must be positive, while others only require one of the two to be positive. Some tests look for three portions, and generally only require two to be detected, although one test requires all three.

This is worth thinking about. A test that looks for three portions of the genome is generally happy if two are found. That means that we can have a leopard without spots as long as it has leopard-like claws and teeth. Or spots and teeth, but different claws. What does it mean to have a genome of a very simple creature like a virus, for which any part can be missing, but we still say it is what we are looking for? And if we only have 1% of an animal, is it possible we will decide it is a leopard when it is actually an ocelot?

Limitations of the Test

Each test comes with a list of limitations. And the majority probably apply to all tests, even though they are only listed in some. These include noting that the test is only looking for RNA, and does not prove that a virus is present, and certainly cannot prove that the virus is functional. Some note that RNA from the virus may persist after the infection has been resolved.

A variety of reasons for false negatives and false positives are given. While public health agencies are generally not interested in false positives, this problem has the power to magnify the epidemic, as well as turning people’s lives upside down. Some tests note correctly that false positives increase as the number of actual infections in the population being tested decrease. Also, RT-PCR is so ultra-sensitive, that a tiny amount of contamination at any stage of the process can result in a false positive, and the manufacturers warn about this. Some tests indicate that other coronaviruses may cause positive test results, but many coronaviruses are not believed to be very pathogenic, so this is equivalent to a false positive to the person receiving the misleading result. A mix-up of two specimens may cause one false positive and one false negative, as people are given the wrong results.

Some tests indicate correctly that the presence of the coronavirus RNA, even if taken as proof of viral infection, does not prove that it is the cause of any symptoms being experienced.

Many also recommend that the test alone not be used to make a diagnosis but that clinical information (such as symptoms) and a doctor’s opinion be incorporated.

Many tests admit they have not been tested on immunocompromised people or on people with symptoms, indicating that the manufacturers are concerned about the accuracy in these groups.

Impact on Your Life

One story from China illustrates the absurdity of the current situation with COVID-19 testing, the impact on people’s lives, and the unwillingness of medical professionals to consider that the test could ever be a problem.

The story of an elderly Chinese man is found in a pre-publication medical article
(https://www.researchsquare.com/article/rs-23197/v1):

A 68-year-old man was admitted due to fever, muscle pain, and fatigue. He was initially diagnosed with COVID-19 according to two consecutive positive results for SARS-CoV-2 RNA plus clinical symptoms and chest CT findings, and was discharged from hospital when meeting the discharge criteria, including two consecutive negative results. He was tested positive for SARS-CoV-2 RNA twice during the quarantine and was hospitalized again. He was asymptomatic then, but IgG and IgM [antibodies, with IgG indicating immunity] were both positive. He was discharged in the context of four consecutive negative test results for SARS-CoV-2 RNA after antiviral treatment. However, he was tested positive once again on the 3rd and 4th day after the second discharge, although still asymptomatic. IgG and IgM were still positive. After antiviral treatment, the results of SARS-CoV-2 RNA were negative in three consecutive retests, and he was finally discharged and quarantined for further surveillance.

The most disturbing thing about this article is that, at no point, did the authors raise the possibility of false positive test results. Perhaps the unnamed 68-year-old man would disagree, arguing that his life being turned upside down, being forced to take drugs while healthy, and being isolated from his family was more disturbing.

More Information

For more information, discussion and references, see David Crowe’s critique of the COVID-19 pandemic theory at:
http://theinfectiousmyth.com/book/CoronavirusPanic.pdf

Continue reading at The Infectious Myth

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