We’ve been doing it all wrong?

Wednesday, 2 September 2020 00:20 -     - {{hitsCtrl.values.hits}}

If a patient had several “comorbidities” (cancers, pneumonia, heart disease), and the cause of death could well have been from these contributing factors, the consensus was to downplay these confounding factors and assign the death to the “novel” coronavirus which has yet to be clinically isolated and even proven as a new pathogen in science – Pic by Shehan Gunasekara 


 

Here from the frontlines are insights and learnings and distinctions that can further inform our medical response to COVID and hopefully inspire our emerging policy towards travel and tourism and the profits they bring with them for Sri Lanka’s national solvency and recovery.

Onto the findings:

Hackery is giving us fresh dosages of “whackiness” as COVID conundrums multiply.

Even the fabled NY Times could not resist reporting this. I have frequently flagged the inconsistencies of PCR testing…too many “false positives,” possibly “false negatives,” widely divergent quality of tests, never meant for “diagnosis” instead for “detection” and more.

But we have breaking news! Let me simply quote, “The standard tests are diagnosing large numbers of people who may be carrying relatively insignificant amounts of the virus.” Okay, gently on now.

Finally, finally, the authorities are copping to the eventually unavoidable reality that a “qualitative” read-out, absent a “quantitative read-out” that tells you about viral load, is distorting. The CDC recently said we needn’t be compelled to test people without symptoms. Despite the drumbeat of “asymptomatic spread,” as indicated recent studies show any such contagiousness to be nominal at best (studies emerging from Guangzhou and other locations), and this is consistent with what WHO has said, based on “data” rather than “modelling” overall.

However, the alternative is more rapid, widespread testing, even if the tests are less sensitive. Why?

Because most of these people so tested are not likely to be contagious and so identifying them “per se” without a look at “viral load” may create bottlenecks, and delay finding those who are truly contagious.



The PCR test distortion

The most widely used diagnostic test (the PCR test) gives a simple yes/no as to whether someone is infected. But similar PCR tests for other viruses try to peg how contagious a patient might be, by estimating how much of the virus is in the patient’s body currently. So, the challenge coming out of Harvard School of Public Health is why we would be so blinkered as to use only alleged “yes/no” data for everything: diagnosis, public policy, health guidelines, etc.

As Dr. Mina, epidemiologist at the Harvard School of Public Health states, “It is the amount of virus that should dictate the infected patient’s next steps. It’s really irresponsible to forgo the recognition that this is a quantitative issue.”



It’s the cycles

As various leading researchers have pointed out, the PCR test “amplifies” genetic material “in cycles.” The fewer cycles required, the greater the amount of the virus (viral load). The higher the viral load, the greater the likelihood for contagiousness. Currently, doctors are not given the “cycle threshold,” which is the number of amplification cycles needed to “detect” the virus. Yet that is needed to know how infectious patients are for all practical purposes!

The New York Times reports that “three sets of testing data that include cycle thresholds, compiled by officials in Massachusetts, New York and Nevada, demonstrate that up to 90% of people testing positive carried barely any virus.” That means they were pointlessly either quarantined, or contact traced, or had their lives and liberties impinged upon.

Last Thursday, the US reported 45,604 new coronavirus cases. If the rates of contagiousness reported above were to hold, only 4,500 of those cases would qualify as possibly needing to isolate and submit to other intrusions into their lives and movements.

Dr. Mina, among other leading specialists are telling us the cycle threshold currently used is just too high, the limit being utilised is 40 to 37. But tests with thresholds so high may detect not live virus but genetic fragments, leftovers from infections that pose no real current risk. As Dr. Mina puts it, “…akin to finding hair in a room long after a person has left.” This is detritus, lingering evocations of what is not currently there most likely.

Juliet Morrison, virologist at University of California Riverside concurs that any test with a threshold “above” 35 is “too” sensitive to be helpful. She says, and we can join her in the chorus, “I’m shocked that people would think that 40 could represent a positive.” Yes, agreed! But I’m shocked anyone is shocked now after months of fruitless panic mongering when the distorting variable has been there, gleaming in plain view! Dr. Mina (I wonder if he has been muzzled prior or major papers just did not deign to report his counsel) indicates that he recommends we set the figure at 30, or even less. 

This would mean the genetic material re the virus would have to be 100X to 1,000X that of the current standard for the test to return a positive result worth actually acting on or taking as an impetus for any policy!

The Times quotes yet another eminent virologist, Angela Rasmussen of Columbia University, arguing that it is “mind blowing” that people are not recording the C.T. values from all these tests, but just reporting a “positive” and a “negative.” And what are the rest of us supposed to wonder about how much other “smoke” has been “blowing” all this while? As a commentator wrote, “So the facts on the basis of which we knifed our civilisation were not only hysterical, they may just have been non-existent?” Chillingly so.



Further follow up

The FDA confirmed it doesn’t specify cycle threshold ranges to determine who is positive, commercial manufacturers and labs set their own! Really, on what basis? The CDC (Centers for Disease Control) never one to miss an opportunity to miss an opportunity says it is “examining” (oh hallowed day!) the use of cycle threshold measures for “policy decisions.” They said they would have to “collaborate” (be still our beating hearts) with the FDA and device manufacturers to ensure the “measures” can be used properly and everyone knows what they mean. Words truly fail. This is not “breaking news.” It is simply “awakening news,” news we’ve awakened to, despite this being medically blatantly obvious we are being told. 

Digging deeper, the CDC’s own calculations indicate a “live virus” in any sample with a threshold above 33 cycles is excessively difficult to detect, however officials at numerous state labs have gone on record confirming the CDC has not asked them to note any threshold values or to share them with contact-tracing organisations.

We’re being told 30 cycles, 35 maximally, ‘perhaps’ should be the standard.

For example, North Carolina’s state lab uses the Thermo Fisher coronavirus test, which automatically classifies results based on a cutoff of 37 cycles. A spokeswoman for the lab said testers did not have access to the precise numbers.

This amounts to an enormous missed opportunity to learn more about the disease as well. At the request of the NY Times, Wadsworth Center, the state lab of New York, looked at the 794 positive tests they identified in July, based on the threshold given of 40 cycles. Just with a cutoff of 35 cycles, half of those tests would no longer qualify as positive! Limit it to 30 as suggested by Dr. Mina, and 70% would fall off!

Coming to Harvard’s own “back yard,” in Massachusetts, 85-90% of those testing positive in July (with a threshold of 40) would have been deemed negative at the 30 cycles threshold. Quoting Dr. Mina directly, “I would say that none of those people should be contact-traced, not one.” 

Other experts informed of these numbers were stunned. We are stunned too, but perhaps not by the same thing. Director of the Harvard Global Health Institute softens the blow with a folksy opening, “Boy, does it really change the way we need to be thinking about testing.” Yes Doctor, for if this doesn’t, what possibly could 

or would? 

I have continued to be shocked at the fetishism of those believing for a disease with a 99% survivability rate based on US numbers below the age of 70 with comorbidities, that we think there is plague-like imperative to test everyone anyway. Now we find we’re not even testing the people we should be testing either!



Late breaking sanity?

Scott Becker, Executive Director of the Association of Public Health Laboratories says he is “worried” by the number of people with positive results who aren’t infectious. Ahem…you don’t say! Why? “Because it’s so high.” His remedy? He will meet with Dr. Mina to “discuss” the issue. This is actual reporting, not satire. Or rather it is actual reporting ‘and’ it is satire!

The FDA tried to suggest less sensitive tests may not catch people with initially low viral loads. But test more often, because if of concern, their viral load rises quickly. PCR tests as a frontline diagnostic tool when 20% or more of people are testing positive in parts of the US, clearly not afflicted, clearly not translating to hospital admissions or ICU needs, demands that PCR tests as a diagnostic tool (for which they were never created) be seriously questioned.

Experts continue to confirm that people infected with the virus are most infectious from a day or two before symptoms are evident (hence actually “pre-symptomatic not “asymptomatic”), until about five days later. Dr. Mina points out that with current testing rates, you don’t have much chance of really capturing someone in that window.

So if highly sensitive tests (which still range all over the map in quality and the number of false positives thrown up) had some place at the start of the pandemic, today cheap, fast, abundant tests that are less sensitive are likely more needed, as they will certainly catch the really transmissible people, including superspreaders. Dr. Mina puts it with laconic emphasis, “That alone would drive epidemics practically to zero.” 



RNA interference and fake COVID deaths

Another thing we apparently don’t test for is RNA interference (RNAi) which is a primary defence mechanism against COVID and may explain the similarity of outcomes, lockdown or no lockdown, policy A or policy B, except perhaps of letting more immunity develop. 

Severity of lockdown as per a recent analysis in The Economist had no positive correlation to the number of excess deaths “ascribed” to COVID-19 in numerous countries, in fact, on the contrary. In fact, a recent Swedish study of “COVID deaths” outside hospitals found only 15% were as a direct result of the virus as opposed to other clearly contributing factors. So, let’s filter this recent news and apply it prudently along with these other emerging insights.

And to top this all off, there is the following “Breaking News”. COVID deaths we have known were problematic. If a patient had several “comorbidities” (cancers, pneumonia, heart disease), and the cause of death could well have been from these contributing factors, the consensus was to downplay these confounding factors and assign the death to the “novel” coronavirus which has yet to be clinically isolated and even proven as a new pathogen in science!

However, those darlings of obfuscation, the CDC this last week “quietly” updated (verifiable on their website of course) the COVID number to officially record…wait for it…drumroll please…only 6% of all the 153,504 deaths recorded in the US (as of 15 August 2020) actually died from COVID, so 9,210 deaths. The other 94% had two or three other serious illnesses, overwhelming majority of very advanced years; 90% in nursing homes!

Add to that the fact the RT-qPCR tests register “existing” human DNA as a marker for the virus, hence the number of false positives as earlier alluded to; and that there is no independent verification of the existence of a distinctive isolated virus to date outside these tests (which makes a vaccine more debatable and dubious), and the tests currently being used cannot even discriminate between the various corona virus types, at times showing a ‘positive’ for someone with the common cold.

The mainstream media, having leeched and gorged themselves on the spectacle, do not report that the PCR test is not looking for the entire sequence of the COVID-19 virus which has never been determined, but only a nucleate common to all coronaviruses. That is why Professor Kary Mullis, inventor of this test, and who won a Nobel Prize in chemistry in 1993 himself said it is not a diagnostic tool and is in his words “inappropriate to detect a viral infection.” 

It’s dizzying. We tagged deaths that came from a slew of other causes, and even those who are to have died “from” COVID-19 could from symptoms have died from anything that causes respiratory problems, high fever and a cough. And then we started using low cost tests not fit for purpose, as per the inventor of the tests, and used all this as the basis of a growing orthodoxy of panic and economic and social suicide rather than demand the virus be at least isolated and verified and contagiousness as Dr. Mina suggests be what we seek to identify and focus on. Could madness incarnate be much different?

If we can make our peace with Dr. Mina’s recommendation, this also would have breathtaking implication for tourism, and I urge Sri Lanka to be at the forefront of this exploration, along with Harvard, as we can then welcome people to this island paradise, which has done so blessedly well to date, and is increasingly back to viable economic life, and could bolster that, without PCR “blinkers.” We can thereby address the genuinely contagious and safeguard them appropriately, while welcoming the many additional others to sooner and more readily savour Sri Lanka’s many gifts: for tourist, longer term traveller and businessperson alike.

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