The Little Pandemic That Could

The PCR test is coming under fire for missing its target: detecting COVID-19 infectiousness

The late Dr. Kary Mullis, a biochemist who won the Nobel Prize for the invention of the polymerase chain reaction (PCR) process that is used in COVID-19 testing since January 2020, said that “with PCR … you can find almost anything in anybody” in a video (around minute 49:00) from a 1997 meeting on “Corporate Greed & AIDS” in Santa Monica, California. He responded to an audience question about the possible misuse of the PCR test in medical diagnoses, stating that the technique cannot be “misused” in a narrow sense, but that the test results are prone to misinterpretation when doctors “claim that it is meaningful” when a virus is discovered based on a minimal amount of genetic material present in a patient. “It doesn’t tell you that you’re sick“, as Mullis says in an extract of the video created by Bright Light News. In this context, he also referred to the “Buddhist notion that everything is contained in everything else.” While the statements were made in conjunction with HIV/AIDS, where Mullis held a highly contested view, they increasingly prove true in the ongoing SARS-CoV-2/COVID-19 testing fiasco.

Dr. Kary Mullis, inventor of the PCR technique, speaks at an event in 1997. Source: screen capture from video at https://lbry.tv/@marengeti:c/corporate-greed-aids-santa-monica-1997-07-12-part2:5

While researching this post, I came across an interesting Reuters “fact check” of social media posts claiming that the COVID-19 PCR test is a fraud. The fact checkers actually revised their initial finding that a quote that the PCR test “can’t be used in virus detection” was falsely attributed to the PCR inventor Dr. Mullis to a more nuanced assessment that the statement “may have been a fair reflection of Mullis’s views, even if not a direct quote.” These so-called fact checkers that are employed by news organizations and social media corporations use questionable tactics discussed by other analysts. Their verdicts inevitably lead to suppression and removal of dissenting opinions in public debate, most recently seen for example in the cancellation of microbiologist Prof. Sucharit Bhakdi’s Youtube account. Two months earlier, psychologist Dr. Rafael Bonelli had posted a critic of journalists aptly titled “When Intellectual Dwarfs Assess a Giant Like Sucharit Bhakdi”…

PCR technique for amplification of genetic sequence, resulting in 2^n copies after n cycles. Source: https://commons.wikimedia.org/wiki/File:Polymerase_chain_reaction-en.svg (CC BY-SA 4.0)

One of the most-cited deviations from the mainstream narrative in a traditional newspaper was the New York Times’s August 29 article “Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be.” The article outlines the PCR technique as an amplification of genetic material with the all-important cycle threshold (Ct), which determines how often the material will be duplicated. The Times examined a dataset from multiple states and found that “up to 90 percent of people testing positive carried barely any virus”, meaning that they are likely not infectious. The author noted that among 45,000 new “cases” at that time, possibly only 4,500 should be required to self-isolate and be subject to contact tracing. A September 29 article in Science magazine, “One number could help reveal how infectious a COVID-19 patient is. Should test results include it?“, refers to a recently pre-published French study, which “found that 70% of samples with Ct values of 25 or below could be cultured, compared with less than 3% of the cases with Ct values above 35.” In other words, a positive test result after 25 or fewer cycles likely indicates an infectious carrier of SARS-CoV-2, while positive tests above 35 most likely should not be considered “cases”.

Across Canada, the provinces recommend different cycle thresholds, but nearly all of them are at or above 35, making a joke of your PCR test results. The Ct values used in the map below were collected by Marie Oakes, senior editor of the independent news outlet Westphalian Times, for her September 25 article “International experts suggest that up to 90% COVID cases could be false positives“.

Cartographers do not normally include symbols in the legend that do not appear on the map, yet to illustrate the recommended Ct values of up to 25 according to the French study or up to 30 according to the Westphalian Times article, I included green and yellow “aspirational” classes. The orange representing the least harmful over-testing in Canada applies to Newfoundland & Labrador(33), Nova Scotia (33-35), and Alberta (35). The worst offenders are the large provinces of Ontario (38-45) and Quebec (45). Ontario today reported 1,855 new “cases” – coincidentally found in a record number of 58,000 tests. If we apply the French study proportions for tests turning out positive after more than 35 cycles, then only 56 Ontarians (3% of 1,855 positive tests) should be considered newly “infected” in a meaningful way (including that they may be infectious), and take the corresponding precautions. The other 1,799 test-positives along with the 56,145 test-negatives and the rest of Ontario’s 14,500,000 residents should be given a break and return to their healthy, social lives and economic activities.

To help us get back to some kind of normality, lawyers around the globe are collaborating in the preparation of major law suits focused on the role of the PCR test in misjudging the pandemic. A couple of weeks ago, a Portuguese appeals court upheld a lower court’s ruling that declared a quarantine order unlawful. Importantly, the appeals court stated that a positive PCR test is not a reliable indication of a person’s infectiousness. And this week in Germany, lawyer Dr. Reiner Fuellmich submitted an injunction and claim for damages on behalf of lockdown critic Dr. Wolfgang Wodarg against the self-declared anti-fake news blog “Volksverpetzer” (literally “people’s snitch”). This court action also revolves in part around the validity of the PCR test for diagnostic purposes and could serve as a stepping stone to a larger class action lawsuit in North America.

Adapted figure caption from original: Comparison of delay between symptom onset and test to probability of successful cultivation of virus (probability positive) and SARS-CoV-2 PCR test (E gene) cycle threshold (Ct) value. Source: Bullard et al. (2020), https://doi.org/10.1093/cid/ciaa638

UPDATE: Things are developing fast these days. Within 24 hours of posting, I became aware that a higher administrative court in Germany has also confirmed that a positive PCR test does not mean that an individual is infectious. The court refers to a summary by the German Society for Neurology of a Canadian study titled “Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples” published as early as 22 May 2020 in the journal Clinical Infectious Diseases. Most interestingly, the researchers from the University of Manitoba and the National Microbiology Laboratory of the Public Health Agency of Canada found that positive test results with a Ct value above 24 could not be cultivated, thus setting an even stricter validity threshold for the PCR test than what I had found and used in the first part of this post. The authors also examine the impact of the delay between symptom onset and test on the patients’ infectiousness, as illustrated in the above figure.