After the nth time of "proofing" this post (which I normally do not do), I am wondering whether I should re-address a question I asked about six years ago on the blog: how many angels can dance on the head of a pin?
This is a two-part series. This is the first part. The second part is here.
Original Post
Note: in a long note like this there will be typograpohical and content errors. Almost 99% of it is "factual," but I've thrown in an occasional snarky comment. Tread carefully.
"Positive" or "negative" Covid-19 results: apparently the US has set "40 cycles or more" to detect any trace of the virus as the standard.
From the "Coyote Blog," this comment sent to me by a reader:
Studies have found
that 90% of the positive covid results required 40 or more cycles to
detect any trace of the virus. Most virologist would consider a person
to be negative at any cycle count above 30 because at those levels the
viral count would be so low that the person could not even be considered
infectious (remember these are not linear, 30 cycles is a
multiplication of 2^30, 40 cylces 2^40).
[If the reader provided me a link to that comment, I missed it; otherwise I would have posted it.]
So that took me down a rabbit hole at 1:30 a.m. and I'm typing this at 2:40 a.m. and it will probably be posted at 3:40 a.m.
The reader commented and asked:
If
memory serves me correctly, the example was if you could get somebody
to agree to double your money every day for a month, you'd start out
with a penny and end up with over $10 million bucks.
So,
if many of the COVID tests really have to run 40 or more cycles to
detect any virus - I think that's one part in a trillion... Right?
Is that medically reasonable?
I've
groused a lot about false positives - and who know what's afoot there.
But, this is the first I've heard of how small the needle was in such a
huge haystack.
Now, I know that anthrax is lethal in infinitesimal amounts - and so was the Japanese subway poison - Sarin?
But, if the COVID test number is true (and IF I can still do a little math) - then what in the world is going on?
Or was that comment just totally bogus?
So, the rabbit hole took me to a dozen links which I will post below. Knowing the reader, she has already done the same. LOL.
By the way, before we get started, this is something akin to asking what "number" is the correct number of determining whether one is guilty of a DUI or is "drunk": 0.4; 0.8; 1.0; 1.2; or 1.4? Different jurisdictions use different criteria. But before I digress even more, let's get back to what the reader asked.
1. The comment was not bogus; was completely accurate; and entirely relevant.
2.. Covid-19 tests are reported back to the physician / patient as binary, "positive / negative" and the physician does not receive the sensitivity or the number of cycles used to determine whether the sample was "positive" or "negative."
3. We can discuss why "that number" (the number of cycles used) is not provided at a later time but the quick answer: way too complicated for both the patient and the average over-worked physician. Providing that number would help the clinician but would greatly complicate things for the patient.
4. Yes, the "standard" in the US (except for rapid diagnosis) appears to be 40 cycles. The fewer cycles used, the faster the turnaround time, but the "less accurate" or the "less sensitive."
5. The number of cycles, where n = number of cycles, = 2^n. Therefore, 2^40 = one trillion (google will do this for you in a nanosecond).
a. 2^2 = 4
b. 2^10 = 1,024
c. 2^20 = 1,048,576 or 1.0458576 million
d. 2^40 = 1.0995116 trillion
6. The reader asks whether "one trillion" is too sensitive to mean anything? If you are "infectious" at 2^20, are you still infectious at 2^40?
7. It turns out that
THE NYT has asked that very question; the article is behind a paywall but I was able to access it. It was the first hit I found when asking this very question which means a lot of folks have asked this very same question. Interestingly,
The NYT suggests the criteria for 40 cycles is way too sensitive and a testing cycle of 37 might be more appropriate. The article was dated August 29, 2020 -- or in other words, very, very recently which suggests to me the mainstream media is getting ready to advocate moving the goalposts. This will be way too complicated for Joe Biden to understand but it won't be important. By the time he is asked to sign off on this, Kamala will be acting president.
8. Looking at a dozen or so articles going down the rabbit hole, it appears that anyone with any common sense would suggest 40 cycles is way too sensitive. That many cycles probably causes a lot of false positives. Not only "false positives" in terms of true false positives, but also false positives in the sense that yes, the person truly has Covid-19 particles in his/her blood but the amount is so trivial as to be clinically unimportant.
9. Looking at those dozen or so articles it was hard to come up with a consensus, but some experts suggested cycles as low as 30; most seemed to suggest that 35 to 37 would be "adequate" but still probably too high.
10. For me, the obvious question to ask, is what is the "standard" for other diseases? That's very,very tough to find. I googled "positive/negative" or "infectious status" for HIV and PCR. The best I could find with limited time was a study of HIV on newborn infants, and their cut-off was 30. A "positive rate" with a cycle of 30 meant the infant was not infectious. Below 30 cycles, a "positive" rate meant the infant was infectious or "had the disease." Above 30 cycles, irrelevant. I am not articulating that correctly. You can read the article for your own interpretation, but for me the bottom line in 20 seconds of scanning that article was that in one study testing HIV in high-risk infants, the researchers considered 30 cycles as the "right number of cycles."
11. Bottom line: if your test result takes more than a couple days to return, they were testing out to as many cycles as 40 to determine if "positive" or "negative." If you "tested positive," it may have required as many cycles as 40 to get to "positive." And yes, 2^4 = 1.0995116 trillion according to google which will return the result in 0.46 seconds.
12. If you get your "rapid" result back in a couple of hours, the "n" was probably 30 or less. In my mind, less sensitive but more meaningful, and you will note the NFL, White House, and others must be using rapid testing when they are testing on a daily basis and reporting that same day. "Rapid testing" has a lot of advantages, and not necessarily being "rapid" as the only advantage. If I want to go back to work, I would want the testing lab to use the least sensitive test out there, and that means fewer cycles, and that means faster turnaround time. If Tampa Bay wants Tom Brady to play, they will recommend using a "rapid test," I would assume. A "negative" is a "negative" is a "negative." No one is going to ask “how many cycles?”
13. From there, one can can begin another whole discussion on how many cycles are needed; why "40" was chosen for the US; what number of cycles are being used in China, Russia, and Mozambique; whether we need to change the number of cycles; if we change the number of cycles will that be seen as "moving the goalposts"; will changing the number of cycles be akin to comparing apples to oranges, i.e., 40 cycles vs 30 cycles, calling into question numbers released under the Trump administration vs numbers released under a Biden administration; and, best of all, had Dr Faust mandated testing up to only 30 cycles, would there have even been a pandemic declared at all? I believe the definition of a pandemic is based on the number of cases, not the number of deaths.
Here are some of the sites I visited through asking various questions over at google. I have not checked to see if any of these links are broken.
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PCR: A Bit Of History
From wiki:
A 1971 paper in the Journal of Molecular Biology by Kjell Kleppe and co-workers in the laboratory of H. Gobind Khorana first described a method of using an enzymatic assay to replicate a short DNA template with primers in vitro.
However, this early manifestation of the basic PCR principle did not receive much attention at the time and the invention of the polymerase chain reaction in 1983 is generally credited to Kary Mullis.
When Mullis developed the PCR in 1983, he was working in Emeryville, California for Cetus Corporation, one of the first biotechnology companies, where he was responsible for synthesizing short chains of DNA.
Mullis has written that he conceived the idea for PCR while cruising along the Pacific Coast Highway one night in his car.[
He was playing in his mind with a new way of analyzing changes (mutations) in DNA when he realized that he had instead invented a method of amplifying any DNA region through repeated cycles of duplication driven by DNA polymerase.
In Scientific American, Mullis summarized the procedure: "Beginning with a single molecule of the genetic material DNA, the PCR can generate 100 billion similar molecules in an afternoon. The reaction is easy to execute. It requires no more than a test tube, a few simple reagents, and a source of heat."
DNA fingerprinting was first used for paternity testing in 1988.
Mullis was awarded the Nobel Prize in Chemistry in 1993 for his invention, seven years after he and his colleagues at Cetus first put his proposal to practice.
Mullis's 1985 paper with R. K. Saiki and H. A. Erlich, “Enzymatic Amplification of β-globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia”— the polymerase chain reaction invention (PCR) – was honored by a Citation for Chemical Breakthrough Award from the Division of History of Chemistry of the American Chemical Society in 2017.
