The coming reset in coronavirus testing
With Trump gone, expect an adjustment to PCR testing parameters to reduce false positives, thereby reducing case numbers and making Biden look like a hero
When it comes to coronavirus testing, there are basically three kinds of tests to consider. There are tests that look to see if you have antibodies to the SARS-CoV-2 virus that causes COVID-19 disease, which doesn’t tell you whether you currently are infected but rather whether you’ve been infected at some (fairly recent) point in time. There’s the so-called “rapid test”, which looks for active infection but is thought to be less sensitive than the lab test for infection. And then there’s the lab test itself, almost always based on reverse transcription-polymerase chain reaction (RT-PCR) technology, with its very considerable shortcomings that I’ve described before.
The rapid test, while being less sensitive, is thought be very accurate in terms of reported positives. If you have a positive rapid test, clinicians feel very certain you’re infected, and in many cases won’t even follow up with a lab test. If you have a negative rapid test but exhibit symptoms that are consistent with COVID-19 (there are no symptoms that are unique to COVID-19), they may follow up with an RT-PCR test to see if the rapid test missed an active infection.
The problem is, the design of the RT-PCR tests being used widely in the United States and many other parts of the world is seriously flawed, as I described earlier and as The New York Times described before me (though it got lost in the hysteria of the time).
In the simplest of terms the PCR tests take biological material from the swab, convert the RNA within it to DNA, and then through dozens of cycles “manufacture” with each cycle exponentially more of the DNA they’re targeting (the DNA previously identified as being that of the SARS-CoV-2 virus). Because the manufacturing process is exponential, a single strand of SARS-CoV-2 viral DNA, small enough to be undetectable, can be amplified to billions or trillions of strands over a couple of dozen cycles.
If viral DNA is present, at a certain point in its cyclical amplification there’s enough of it to produce a chemical reaction that causes a “probe” to fluoresce, or glow. The number of cycles it takes for viral DNA to be detected in this way is called the “cycle threshold” (Ct). Depending on how much of the viral DNA there is from the sample (indicating the “viral load”), the probe will fluoresce earlier or later in the cycle process (or not at all if there is no target viral DNA present). Earlier fluorescense — say, within 25 cycles or fewer (Ct<=25) — should mean higher viral load and high confidence of active coronavirus infection. Later fluorescense (such as 30-33 cycles) means it’s taken much more amplification to create a detectable level of viral DNA, and means there’s less confidence of active infection or there’s a lower viral load.
The reason there’s less confidence of active infection is that lab tests involving viral cell culturing alongside PCR tests, used to benchmark the latter, have definitively shown that positive PCR tests with a Ct greater than or equal to about 34 are almost certainly detecting inactive (“dead”, if that word can be used to describe a virus) viral fragments left over in the mucus and other tissues of the body from a previous infection. If the person was asymptomatic or had very mild symptoms during this previous, now-inactive infection, they may never have known they had it. But if their PCR test counts Ct>=34 as a positive, then the result will be reported as an active coronavirus infection even though the person is likely not actively infected and is almost certainly not contagious.
In one study, reported in April 2020 in the European Journal of Clinical Microbiology & Infectious Diseases, any sample that required more than 34 cycles to detect virus did not in fact include enough virus to be grown in culture as a benchmark against the RT-PCR test. Researchers concluded that any positive based on a cycle threshold over 34 should not be considered a positive as the patient was not likely ill and was not shedding virus (i.e., was not contagious). They recommended such a patient be discharged and released from any quarantine. (As an aside, part of this study involved significantly shortening the time in which infected patients were cleared of infection using a combination of hydroxychloroquine [yes, hydroxychloroquine] and azithromycin, confirmed by RT-PCR and cell culturing).
Even Anthony Fauci has admitted (from 4:00 - 5:10 in this podcast clip) that positives from PCR cycles of 35 or higher are likely dead nucleotides from a previous infection, and can’t be detected with cell culturing for coronavirus.
So you’d think that would mean labs would cut off their cycles at around 35 if the cycle threshold hasn’t been reached at that point, meaning no virus has been detected. But you’d be wrong. At least in most cases.
Of the dozens of PCR tests approved by the FDA in the United States and by comparable bodies in other countries, the range of recommended cycle cutoffs is all over the place. But by one researcher’s count, test manufacturers recommended varying cutoffs ranging from 30 to an eye-watering 45 cycles. The majority recommendation was 40, but many were in the upper 30s as well.
As I reported in September, the Department of Health’s Public Health Lab in my state of Arkansas uses a cycle cutoff of 42. With a cutoff that high (even higher than the cutoffs used by states The New York Times accused of producing an extremely high number of false positives), it’s no wonder that Arkansas’s case numbers were regularly hitting records over a number of months. At that time, at least a quarter of testing results reported by the governor on any given day (and on some days as many as half the results) were from the ADH Public Health Lab.
Beginning in December, the State of Florida began requiring testing labs to report Ct thresholds to the state along with their positive test results. Thus far, Florida appears to be the only state to have done so. When I questioned the Arkansas Department of Health on this in December, their dismissive response made clear to me that they were in no way considering doing the same.
But now Trump has been ousted, and the desired narrative is changing from one of intentionally ratcheting up the fear to one of portraying a nation with new leadership and a light at the end of the tunnel. In that context, the way is now paved for an adjustment to the CDC and WHO guidelines on coronavirus PCR testing to lower cycle cutoffs and eliminate the large numbers of false positives that have likely been reported as new active cases over the previous year.
The first inklings of this are already appearing. As Zero Hedge reported just yesterday, “within an hour of Joe Biden being inaugurated and signing an executive order mandating masks on all federal property, the WHO sent out a notice to lab professionals using the PCR test.” It stated:
“WHO guidance Diagnostic testing for SARS-CoV-2 states that careful interpretation of weak positive results is needed (1). The cycle threshold (Ct) needed to detect virus is inversely proportional to the patient’s viral load. Where test results do not correspond with the clinical presentation, a new specimen should be taken and retested using the same or different [nucleic acid testing] technology.”
It’s a tentative step, but one that’s likely to be reinforced at some point with stronger CDC guidance finally pouring cold water on positives with thresholds above 34 or so. At that point, the number of new active cases should plummet, and any retrospective analysis of cycle thresholds for previous cases should show a significant inflation of positives toward the latter half of the initial bell-curve of COVID-19 disease back in the summer, and especially during the so-called “resurgence” thereafter.
If a significant number of these positives were actually artifacts of rapidly increasing testing, detecting inactive infection from weeks or months earlier when the virus first began passing through the population, then the picture of what was happening later in the summer and fall could have been significantly distorted. That’s especially true if the virus first passed through the population much earlier than previously thought.
The new coronavirus, first identified in China in December 2019, may also have been in France and the United States as early as December 2019. Doubtless you’ve heard anecdotal accounts from people who are sure they had it much earlier than it is known to have existed in the United States.
That’s not to say people weren’t dying of COVID-19 in the late summer and fall. No doubt they were. It’s just a question of whether the number of cases and number of deaths attributed to the disease were being inflated, intentionally or through negligence in testing design and procedure. Even in the pre-COVID era, doctors often had a difficult time determining precise cause of death in patients with multiple advanced chronic diseases. With a disease like COVID that has no clinical symptoms unique to it that are not shared by other respiratory, cardiovascular, and related diseases, determining whether someone died of COVID, with COVID, or without COVID but with a positive test is not an easy task. That’s especially true when the median age of death with COVID exceeds 80, higher than average life expectancy, and most deaths are accompanied by advanced comorbidities.
And it’s difficult to dismiss the fact that every possible effort to undermine Trump’s popularity was being pursued at the time by his enemies in officialdom. The domestic and global health agencies that are in a highly symbiotic relationship with the multi-national pharmaceutical industry and related power structures distrusted and despised Trump for being a most reluctant and clumsy spear-carrier for them (and for daring hype hydroxychloroquine, a drug that’s been successfully used for years with other conditions and showed real efficacy against coronavirus in trials reported in European journals, including those that have been quoted by Dr. Fauci related to other aspects).
But they really had little to fear. Trump detected the political winds and quickly married himself to the vaccine efforts, authorizing and hyping as his personal project the very Operation Warp Speed that allowed brand-new vaccine technology, never before approved for human use, to be rushed through abbreviated testing and then into production. Wall Street expects Pfizer and Moderna to make no less than $30 billion in 2021 from their experimental vaccines, absolutely free and clear from any liability for harm they may cause. And tens of millions will be clamoring for them, in abject fear due to numbers that just might bear little relation to reality.
The only question is, now that those numbers have served their purpose, how soon will they be brought back down to reality, and how will public health officials rationalize their failure to address the problems with excessive PCR cycle thresholds that have been known since the inception of the pandemic, and obfuscated for just as long? My guess is heads will never roll. They never do with these people.
Richie Graham is based in Little Rock Arkansas USA and writes from a free-market libertarian, anti-interventionist perspective.