Moon of Alabama Brecht quote
October 13, 2020

Professor Chossudovsky Is Wrong - Here Is How PCR Tests Work

The website Global Research provides at times interesting reading. It is edited by Michael Chossudovsky, an emeritus professor for economics. Unfortunately he at times writes about issues that are beyond his horizon.

In a recent piece, The Covid-19 Numbers Game: The “Second Wave” is Based on Fake Statistics, he falsely claims that the tests which are globally used to detect SARS-CoV-2 infections also react to other viruses and thereby deliver false results.

The method of the currently used SARS-CoV-2 test is based on the reverse transcription polymerase chain reaction (RT-PCR). The polymerase chain reaction can create millions of copies of RNA or DNA snippets fed into it:

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail.
...
Thermal cycling exposes reactants to repeated cycles of heating and cooling to permit different temperature-dependent reactions – specifically, DNA melting and enzyme-driven DNA replication. PCR employs two main reagents – primers (which are short single strand DNA fragments known as oligonucleotides that are a complementary sequence to the target DNA region) and a DNA polymerase.

A clinical probe is taken from a human who may have the virus. In a preparation phase the probe is chemically cleaned and the outer hulls of viruses in it get destroyed. What is left includes the genetic material of the virus.

The genes of the SARS-CpV-2 are an RNA sequence with roughly 30,000 nucleotides. It is like a book with 30,000 characters on how to build the virus. It is unique for this  virus. The researchers who developed the SARS-CoV-2 RT-PCR test have selected several unique snippets of about 100 nucleotides long out of the much longer string. Complementary oligonucleotides of the same length will then get synthesized. These are the primers for all following PCR tests.

The cleaned sample (10 to 200 µL), the primers and the polymerase are fed into a machine. Repeated cycles of heating and cooling will each multiply the number of RNA snippets in the sample. Luminescent markers are added to get an automatically readable result. Typically some 20-25 cycles are needed to detect the virus RNA snippets of an acute infection. When more cycles (typically up to 40) are used even a minimal amount of a specific virus RNA snippet can be detected. The process is highly automated.

Chossudovsky has not understood how the above process works. Specifically he has not understood that the selection of the oligonucleotides for the primer is very specific to the type of virus the test is supposed to detect.

Thus he is wrong when he writes:

According to Dr. Pascal Sacré, “these tests detect viral particles, genetic sequences, not the whole virus”

What this means is that the PCR test cannot detect or identify SARS-CoV-2. What it detects are fragments, which suggests that a standard “PCR positive” cannot be equated to a so-called Covid-19 Positive.

The PCR test will pick up fragments of several viruses including corona viruses as well as influenza (flu viruses A and B)

While SARS-2 which causes Covid-19 is considered to be similar to SARS-CoV-1, it has similar symptoms to seasonal influenza (Viruses A and B). Moreover, some of its milder symptoms are similar to those of the common cold corona viruses. According to the CDC: “Sometimes, respiratory secretions are tested to figure out which specific germ is causing your symptoms. If you are found to be infected with a common coronavirus (229E, NL63, OC43, and HKU1), that does not mean you are infected with the 2019 novel coronavirus.”

According to the CDC there are “seven [human] coronaviruses that can infect people” the first four of which (alpha, beta) are associated with the common cold.
...
In the above context, what this means is that a PCR test will pick up fragments of corona as well as influenza viruses. It will not be able to identify individual viruses including SARS-2.

“Fragments of viruses positive” does not mean “SARS-2 positive” (or Covid-19 Positive). The PCR test may pick up fragments of influenza viruses (A, B) as well as common cold beta coronaviruses (e.g. OC43, HKU1).

This highlighted passages are as wrong as one can possibly get it wrong. The RT-PCR tests for SARS-CoV-2 DO NOT detect other types of viruses.

We know this because the folks who developed the test the WHO recommends to use have written about their development process:

We downloaded all complete and partial (if > 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences.

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The selected oligonucleotide assays, each specific for a certain snippet of the SARS-CoV-2 virus RNA, were then tested for their sensitivity and chemical stability.

They were also tested for cross-reactivity with other viruses:

Cell culture supernatants containing all endemic human coronaviruses (HCoV)‑229E, ‑NL63, ‑OC43 and ‑HKU1 as well as MERS-CoV were tested in duplicate in all three assays (Table 2). [..] Additional undiluted (but not quantified) cell culture supernatants were tested as summarised in Table 2. These were additionally mixed into negative human sputum samples. None of the tested viruses or virus preparations showed reactivity with any assay.

In total 297 clinical samples with 23 different human virus types in them were tested. The newly developed assays developed to find only SARS-CoV-2 reacted with none of those.


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The PCR test for SARS-CoV-2 has a high specificity. It can not detect other types of viruses.

There are additional safety procedures to avoid false tests.

Each test run of typically 90 to 120 samples will include one quality control sample with a known quantity of the SARS-CoV-2 virus RNA. It will also include one quality control sample that is guaranteed to contain no virus RNA. At the end of each run the results of both quality assurance samples will be compared with the expected value. If there is any mismatch the whole run it will be repeated with fresh sample extracts.

When the laboratory machine runs the SARS-CoV-2 PCR test it also will also note the number of cycles it needed for each sample to first detect a reaction. That will typically be in the 20-30 cycles range. If a detection is only made towards the end of the 40 cycle program the machine will note this and alert its operator. Tests which only show positivity above 35 cycles will usually get repeated as such a low reactivity may point to a potential sample contamination.

Where a coronavirus test can go wrong is at the point of sample taking. The swab that is used may not have picked up enough gunk to catch a significant number of viruses. The PCR test will then show the person as negative even when it has caught SARS-CoV-2. There can also be bureaucratic errors where the sample is attributed to the wrong person. The test protocols are designed to prevent this and such cases are rare.

When a person gets infected with SARS-CoV-2 and starts to reproduce the virus its numbers explode to billions of copies per milliliter. When the immune system starts to  defeat the virus the number will go down. Debris of dead virus may still be in the body four to five weeks after the infection onset even when the person is no longer infectious. The graphic below shows which test reacts at which stage of an infection.


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A person that is tested PCR-positive for SARS-CoV-2 will have been infected with the virus. There is no other way to pick up the RNA snippets the PCR test is looking for. But that person may not have developed COVID-19 symptoms and may no longer be infectious. We do not know this for sure. Tests to find out if a person still spreads viable viruses take a several days and require a lot of manual labor in high security laboratories. These can not be done for everyone.

To recap:

  • The PCR test for SARS-CoV-2 is highly specific for that virus and does not detect any other ones.
  • A positive PCR tests demonstrates that the person has or has had the virus.
  • We have no practical way to tell if that person, even when it shows no symptoms, is still infectious and spreading the disease.

The only way to prevent new infections coming from a PCR-positive person is to isolate that person. After 10 days the immune system of most people will have defeated the virus. (That a significant number of people are still ill at that point is the consequence of an exaggerated immune reaction to the virus, not of the virus itself.)

It is sad that an otherwise useful site like Global Research is spreading such false information about the Coronavirus pandemic. Chossudovsky should stick to writing about social issues. He obviously lacks the basic hard science knowledge that is necessary to understand how PCR tests work.

Spreading such unqualified statements during a pandemic like Chossudovsky's piece does is highly irresponsible.

That is the reason why I delete comments at this site with spread similar nonsense.

Posted by b on October 13, 2020 at 19:34 UTC | Permalink

Comments
« previous page

Where I live they must be putting something on the swabs that give the false negatives for the fake China virus because 2 % die after the false result.

Anyways I have to go out and buy my lottery tickets because the prize is so high that I think it is a good investment.

I don't bother with the social distancing stuff because my trusted news source tells me only 0.5 % of my age group would die from the virus.

Once I realized opposing mask wearing was promoting freedom and being forced to wear a mask to be on television behind the President was promoting freedom everything became easier to understand.

Posted by: Randy | Oct 14 2020 16:07 utc | 101

Posted by: vk | Oct 14 2020 15:31 utc | 100

You say: "Even if your source is genuine, it doesn't change the fact that technologies evolve. PCR tests are now effective in detecting viruses."

I'd be interested in seeing your source(s) for this claim.

Posted by: Rick | Oct 14 2020 16:18 utc | 102

@ Posted by: Unlocktheeconomynow | Oct 14 2020 15:45 utc | 101

And here, ladies and gentlemen, is the true face of liberalism. That's what all this paranoia and conspiracy theories are about: the petty class interests of the petite-bourgeoisie. You know you don't give a fuck about dozens of millions of dead around the world; you know the working class is just a disposable instrument for your own wealth accumulation; you know you're a genocide by ideological conviction; you know you carve for death and destruction in the name of private property; you know that, if you could, you would have John Locke's portraits in every room around the globe.

Get out of your closets, liberals. Reveal your true form!

Posted by: vk | Oct 14 2020 16:19 utc | 103

@ Posted by: Rick | Oct 14 2020 16:18 utc | 106

The post of this blog is literally explaining why PCR tests do work and you're asking me for the evidence?

Posted by: vk | Oct 14 2020 16:21 utc | 104

>Unfortunately he [Professor Chossudovsky]at times writes about issues that are beyond his horizon.<

That's the nice way of putting - the professor is a clown.

Posted by: xeno | Oct 14 2020 16:24 utc | 105

@deschutesmaple 76

he has lost much of his credibility taking such an asinine position. He used to have some good articles about 9-11

If you wait long enough, an otherwise smart person will eventually fall on their ass. Chomsky made some howlers about 911 too, when he sided with the 'official' narrative.

Posted by: hooper | Oct 14 2020 16:35 utc | 106

vk 16:21 "The post of this blog is literally explaining why PCR tests do work and you're asking me for the evidence?'

And there are Professors and Academics as citedmout there explaining very clearly and concisely why they don't.

b built a strawman to tear down knowing full where that their are researchers/PHD's. particularly at the Oxford School for Evidence Bases Medicine, who have very clearly explained the problems with the PCR tests
See link provided,again, while reading through the site further-


CEBM and Oxford University:
The Centre for Evidence-Based Medicine develops, promotes and disseminates better evidence for healthcare.


https://www.cebm.net/covid-19/pcr-positives-what-do-they-mean/

Does a PCR “TRUE POSITIVE” mean INFECTIVITY OR VIRULENCE?
What does viral culture tell about PCR positives?

A PCR test might find the virus it was looking for. This results in a PCR positive, but a crucial question remains: is this virus active, i.e. infectious, or virulent? The PCR alone cannot answer this question. The CEBM explains why culturing the virus is needed to answer this question

PCR true positives versus infectivity and virulence
Does a PCR positive mean TRUE POSITIVE if the gene fragments targeted in the PCR are unique to the virus and the PCR is VERY ROBUST?

There is speculation as to whether the PCR can indeed find the virus from a person’s sample or maybe the PCR is not sensitive enough and might give positive when other viruses are present. Some PCR manufacturers tell us there is “cross contamination” and “non-specific” interference with a list of viruses and other in their instructions manuals[3, 4].

Conclusion: A TRUE POSITIVE in PCR does not always mean that the person presents any danger to society. The virus cannot be transmitted when cell culture shows that the virus is not infective.

Can successive tests on the same person give contradictory results?
That a PCR test gives positive or negative depends on how the experiment is conducted. Furthermore, since it is not know whether and how PCR positives correlates to infectivity and how it is that this correlation must be interpreted, the interpretation of a PCR POSITIVE is inconclusive


xeno "Unfortunately he [Professor Chossudovsky]at times writes about issues that are beyond his horizon."

Same as B does... repeatedly. But somehow he's not " a clown"?

Posted by: R Rose | Oct 14 2020 16:37 utc | 107

@ 70 b.... i think the reason a lot of newbies come on these covid threads is someone is keeping an eye out from a different site and want to bombard you with covid madness when you write on covid... the other observation is that a number of regulars don't post on the covid threads...

@ old hippie... thanks for the example...

Posted by: james | Oct 14 2020 16:39 utc | 108

b, rather than delete comments that you think are wrong, perhaps it would be more useful to engage in a rational, reasoned challenge of the competing ideas. There is too much censorship around these days - try not to create more of it.

Posted by: Anon | Oct 14 2020 16:43 utc | 109

b, it is good you acknowledge that PCR tests can and do yield a +ve result when they detect a fragment of the target virus, even if the virus is not "live" or active. You make a good point that if someone has a virus fragment, then they must be or have been infected. Are we sure about this? I would like to search the literature to see whether it is possible for inactive fragments of coronaviruses to enter someone's system, and if so what the typical percentage can be.

Posted by: Anon | Oct 14 2020 16:49 utc | 110

We interrupted the broadcast on "how good are the Sister of the Assumption, that they make us so many PCR" to announce a last minute news ... on-topic, of course, regarding the Covid-19...

According to the newspaper "The Sun" up to 35 crew members of the HMS "Vengeance" (Vanguard Class) have tested positive for # COVID__19, including the on-board doctor.

Megaphone
The SSBN is in Kings Bay, Georgia for the maintenance of its SLBM "Trindent"

https://twitter.com/REjercitos/status/1316276694802739201

What could go wrong?

Imagine that instead of Georgia they would be in the Persian Gulf of the South China Sea, and some espcialist, suffering from "Covid-19 brain fog" starts a military nuclear incident over there....Not so misplaced after we have witnessed The Donald dancing YMCA on the stage after just 10 days of testing positive and falling symptomatically ill..

Posted by: H.Schmatz | Oct 14 2020 16:51 utc | 111

My previous post made me think of something. If an inactive fragment of SARS-CoV-2 enters someone's system, can it cause the immune system to produce SARS-CoV-2 antibodies? Or does the immune system only respond to a full, active SARS-CoV-2 virus?

Posted by: Anon | Oct 14 2020 16:52 utc | 112

Another news which could be related to Covid-19 but really it is not...it is not a joke...but I find it not only paradogic, but even funny that the Nigerian Anti-Theft Squad has as acronym SARS, when in the West, the International Orgnaized Theft Squad is widely benefitting from a SARS-Cov pandemic of obscure origins...

The Nigerian Special Anti-Theft Squad (SARS) has been disbanded by the government after a wave of protests sparked by the death of a man and repeated allegations of abuse by officers.

https://twitter.com/Political_Room/status/1316408428961488897

Vivir para ver...

Posted by: H.Schmatz | Oct 14 2020 17:00 utc | 113

@116 Anon, isn't that what vaccines (specifically, subunit vaccines) do?

Posted by: Cana | Oct 14 2020 17:03 utc | 114

Thank you, b. I rate this post as a similar diligence to the recent post on a newspaper of note, the New York Times. This is a virus of note, and because it is still an ongoing threat, it is good to be aware of and advised of what information is true and what isn't. And this is very helpful to know, in particular when different countries are coping better or worse with the virus, which keeps it thereby a threat to all. When underlying instabilities are being hidden by distortions of information, very useful to have it pointed out that this is happening.

Debsisdead, because I have family where you are, I appreciate your posts and your point of view. Your electoral process is proceeding calmly and efficiently. In that, and in the attitude to the virus, like China, you do not have what we face here in the US. I would say though that it is the calm in the eye of the storm. I hope it can gradually enlarge, that calm, to encompass us all.

(I know I am glossing over discomforts and imperfections, plenty of those in any nation that need sorting out, but just in general as the focal point of this thread, it is better there than here.)

Posted by: juliania | Oct 14 2020 17:21 utc | 115

SRB @ 92

I appreciate the reply and understand the math. Try some different numbers. Small office where only 50 or so continue to come in on a part time schedule. Thirty positive tests in four months. Zero of the positives get sick. Normal people lose all confidence in the results. And you won’t get them back.

Another way to look at this. On this blog, or any blog like it, by now, with 200,000 dead in US there should be lots of posts from those who have lost family. Everyone is getting heated and angry, none are responding as they would if family members and multiple family members had passed away. I am from the cohort that went to Vietnam and died. Or 58,000 of us did. We all know those who died. And now I am in the cohort that is supposedly dying of covid. And supposedly four times as many have died. And no one. Last friend of a friend report of a death was in April. The mailman had it, had an easy time of it. Two friends had it bad, both in extreme risk groups and full recovery. One of those friends has a liver transplant and take immunosuppressants. For someone taking Methtrexolate, well yes, you should be cautious. But the rest of us should be doing D, zinc, C and getting sunshine and exercise. And getting on with life.

Posted by: oldhippie | Oct 14 2020 17:49 utc | 116

@cana #6
That PCR tests produce false positives is not in question.
The only question is how many.
The article I linked to, and the quotes excerpted from, are for a spreadsheet showing how different false positive rates would impact perceived increases in infection, as compared to actual positive rates.

Posted by: c1ue | Oct 14 2020 17:58 utc | 117

@vk #19
The article doesn't say anything about policy or not testing.
What it notes is that the very real incidence of false positives can/will skew perceived rates of COVID-19 infection at low actual rates of COVID-19 infection coupled with wide-scale testing.
And the point is: the policy decisions that are made based on infection rates has to take this into account.
So your comment is both irrelevant, off-topic and misinformed.

Posted by: c1ue | Oct 14 2020 18:01 utc | 118

@vk #89
No, PCR tests do not determine if you had the virus.
They determine that there are bits of genetic material present which match the SARS-2 virus.
That's why there are false positives. The tests can fail for many reasons including:
1) Amplification errors. In order to detect the virus, the actual genetic material must be replicated many times. This process isn't perfect and can/will amplify non-SARS-2 genetic material.
2) Past infections. Someone who doesn't have an active infection but still has SAR-2 genetic material floating around, can still get considered infected
3) Handling errors. It is extremely common that mistakes in handling occur - ranging from insufficient cleaning of the testing equipment to handling of material to the outright criminal/wacky. Look up some of the numerous forensic lab misconduct cases to see.

Again: the point is if false positives are real - and I have yet to see any proof that this problem has been fixed - then policy decisions based purely on PCR testing results have to take this possibility into account. This is particularly true for low infection rates, much less so in severe situations.
And where in the world is there a severe situation a la Italy/New York in March 2020?

Posted by: c1ue | Oct 14 2020 18:09 utc | 119

"No, noise comes from off-target molecules."

The noise is non-specific by definition. The reason for the limit placed on number of cycles is because eventually the product, meaning the results of the test, becomes meaningless.

I don't see any way to 'confuse' the test, I get your drift, however the test is not smart enough to be confused or in this example it won't identify a virus. It reacts, that is all. It's an absolute go/nogo outcome in real time. So it is, or it ain't. The potential for tampering emerges from the primers. If one were to place faulty primers in, or mislabel a container, the test would produce outcomes accordingly, and the person or persons conducting the tests would be 100% correct while being misled. This scenario is at least being implied if not explicit.

Posted by: Curmudgeon | Oct 14 2020 18:27 utc | 120

Replying to Anon | Oct 14 2020 16:52 utc | 112

If an inactive fragment of SARS-CoV-2 enters someone's system, can it cause the immune system to produce SARS-CoV-2 antibodies? Or does the immune system only respond to a full, active SARS-CoV-2 virus?

The question is validated by studies. If you're interested, look into the 'COVID toes' studies. I don't have the links handy, but the evidence suggests that people, particularly the young, who are otherwise asymptomatic and test negative for SARS-CoV-2 experience an inflammatory response associated with COVID-19. The condition is described as similar to chilblains.

Posted by: Curmudgeon | Oct 14 2020 18:52 utc | 121

b. The end block quote command appears to be malfunctioning. The text following the block quote remains in block quote, it has happened twice to my comments on this thread.

Posted by: Curmudgeon | Oct 14 2020 18:57 utc | 122

"No, noise comes from off-target molecules."

The noise is non-specific by definition. The reason for the limit placed on number of cycles is because eventually the product, meaning the results of the test, becomes meaningless. Curmudgeon | Oct 14 2020 18:27 utc | 120

Statisticians define noise as "random component", but in biology very little is purely random. The background is created by DNA of other viruses, bacteria and mucosal cells of the host. Amplification is non-specific, perhaps you can purify the DNA sample a bit, say, removing pieces which are obviously non-viral, but this step was not mentioned. Amplification is needed to get a sufficient number of molecules to detect. The molecules float in liquid, you do not grab them one by one to see if they hybridize with primers (bind to them), so you need to increase their number, but only up to a point.

Posted by: Piotr Berman | Oct 14 2020 19:42 utc | 123

@ Curmudgeon 122

.......and my comments are mysteriously not posting. Interesting.

Posted by: Alpi | Oct 14 2020 19:45 utc | 124

Piotr Berman | Oct 14 2020 19:42 utc | 123

Depends too on the definition of random bringing forward the idea of 'random patterns'. It's an oxymoron. There is another type of cloning than PCR, also not aforementioned on this thread, which does exactly that, removes unwanted material. If I get it right, the observers create antibiotic strains by entering viral genetic material into bacteria providing resistance to antibiotics. When the bacterium are cultured, the unwanted material is killed off by the antibiotic leaving the desired product unharmed. And the methods can be combined to produce other alternate results. This is not to suggest any malign purpose but is merely a point of interest.

Posted by: Curmudgeon | Oct 14 2020 20:14 utc | 125

Posted by: Alpi | Oct 14 2020 1:19 utc | 34
👍

You should know that noticing patterns and thinking independently is both rayzizz and anti #science.
Please report to your nearest HAPPY CAMP for your reeducation.

We WILL NOT tolerate wrongthink and independent thought because that will lead humankind into a future where peace reigns and Malthusian doctrine is not respected and humankind will not be genocided as our families and institutions have planned.
You must understand that thinking is only for Malthusian billionaires and politicians, you are only a useless eater and a parasite that steal food out of our billionaire children mouths and pollute the air us enlightened Malthusians breathe.
/S

Thank you for your exellent use of logic in your comment! It restored a tiny bit of faith in mankind.
God bless you.

Posted by: Per/Norway | Oct 14 2020 20:22 utc | 126

Posted by: b | Oct 14 2020 10:11 utc | 70 I am still wondering who sends the newbies here each and every time I write about Covid issues.

Exactly. Might be worth doing some IP address analysis or maybe track their user names to see if they post under those names anywhere else on the Net and where.

I just did a Google search on my name and found several items I hadn't been aware existed referencing my name, such as this piece at Vulture of Critique from back in 2018: "Richard Steven Hack made the so-called “Twisted Genius” look like an idiot." It refers to comments I made over at Sic Semper Tyrannus arguing against some comments of one of Pat Lang's commentators, "The Twisted Genius", on the DNC "hack". TWG continually argued that the Russians hacked the DNC, and I argued against that.

Then there's a response from Matthew Yglesias to me from back in 2008 when I was posting on his blog. I do remember reading that one.

It's not hard to get a sense of who people are if they post regularly on blogs, whether their own or someone else's. In infosec, hackers can be identified simply from their behavior patterns - even if that attribution is not necessarily correct as to organization or motivation, it enables tracking them. People who express opinions on one subject frequently have similar opinions on other subjects, so their overall philosophical stance isn't hard to determine if they're at all consistent.

There's no question that the majority of pandemic deniers posting here are Trump supporters completely subservient to his opinions while claiming they're somehow "rebels" against "the official narrative." The rest are simply people so consumed with conspiracy theories that everything has to be interpreted through that narrow lens. Some can't realize that there is a difference between a real pandemic and the use of that real pandemic by the rich to further enrich themselves and by the power-seekers to increase their encroachment on civil rights. One doesn't exclude the other. But then most people have no actual concept of logical reasoning or what constitutes evidence. Tack cognitive dissonance on top of that and the situation becomes hopeless.

Posted by: Richard Steven Hack | Oct 14 2020 22:50 utc | 127

Global Health Experts Warn Against Herd Immunity Approach to Covid-19
In an open letter, 80 health experts call the approach ‘a dangerous fallacy unsupported by the scientific evidence


Beyond this, recent outbreaks of Covid-19 have been linked to younger populations, including those who are asymptomatic for the disease. Research has shown that spikes in cases within older populations rise shortly after, indicating that the disease quickly passes between the two groups. Authors of the letter also say that keeping low-risk and high-risk populations isolated from one another is virtually impossible.

Posted by: Richard Steven Hack | Oct 15 2020 0:01 utc | 128

Scientists Confirmed the First Covid-19 Reinfection in the U.S.
A Nevada man who recovered after an April infection tested positive again in May. Here’s what it all means.


Reports of reinfections in Hong Kong, the Netherlands, Belgium, and Ecuador have already been published during the pandemic. Now, a new case study in The Lancet confirms the first reinfection in the United States.

The paper, which was first published as a preprint at the end of August, follows the medical history of one man, a 25-year-old in Washoe County, Nevada, who tested positive for Covid-19 twice: first in mid-April, then again at the end of May. Two negative tests between his infections confirmed that he’d recovered from the initial illness. He had all the expected symptoms the first time around — sore throat, cough, headache, nausea, and diarrhea — and experienced them again during his second infection, together with low blood oxygen and shortness of breath.

While he recovered in self-isolation during his first infection, he had to be hospitalized the second time around. “The second infection,” the authors of the paper write, “was symptomatically more severe than the first.”

Posted by: Richard Steven Hack | Oct 15 2020 0:04 utc | 129

Posted by: Dave Brackett | Oct 14 2020 1:49 utc | 37

"With due diligence, qPCR is solid."

Thanks Dave for your detailed account of what is involved in doing accurate qPCR tests.

Posted by: suzan | Oct 15 2020 0:36 utc | 130

Not wanting to contribute to the testing argument either way, but I found this article, which seems reasonable. The author is @Anna_Minkina, a PhD Candidate in Genome Sciences at the University of Washington in Seattle, where she develops novel genomics technologies.

COVID-19 Testing & The Danger of a Quick Fix Narrative


Simple solutions sell, not just to federal officials, but to us. With the election weeks away, the current administration has a strong incentive to invest in quick fixes which have been sold to the public as panaceas — and we have little time to see them fall short of their promises.

Fast, frequent, and ubiquitous testing would be a game-changer, as Dr. Mina widely proclaims. It is a worthwhile target to aim for, even if we never fully reach it. But striving to get there by eroding public trust in the only reliable test we currently have is short-sighted. And using misleading messaging to unite the public around an untried alternative will only deepen apathy in the long run.

Simple solutions sell.

But simple solutions distract us from coordinating a complex and multifaceted response befitting such a complex and multifaceted problem. The real solution places at least as much emphasis on public trust as it does on “techno-fixes.” It makes use of multiple forms of testing, carefully considering the interplay between sensitivity, frequency, and the integral role of public confidence and buy-in. It invests in contact tracing and promotes consistent, science-backed messaging around mask wearing and social distancing. It keeps us informed about novel treatments & vaccines, without cultivating false hope.

But simple solutions sell.

And so do simple stories.

Posted by: Richard Steven Hack | Oct 15 2020 0:44 utc | 131

U.S. Pandemic-Related Deaths Undercounted, Study Finds
Total could reach 400,000 this year as mental health concerns grow


Total deaths are very consistent from year-to-year, so the over 200,000 Covid-19 deaths this year make an easy-to-see blip in the long-term trend. Thing is, the blip is bigger than that. In the new analysis, deaths between March 1 and August 1 were 20% higher than in the same period in previous years, but only 67% of that excess tally had been officially attributed directly to Covid-19.

“Contrary to skeptics who claim that Covid-19 deaths are fake or that the numbers are much smaller than we hear on the news, our research and many other studies on the same subject show quite the opposite,” says the study’s lead author, Steven Woolf, MD, director emeritus of Virginia Commonwealth University’s Center on Society and Health.

“Some people who never had the virus may have died because of disruptions caused by the pandemic,” Woolf says.”These include people with acute emergencies, chronic diseases like diabetes that were not properly cared for, or emotional crises that led to overdoses or suicides.”

The new findings, detailed October 12 in the Journal of the American Medical Association (JAMA), suggest that more than 400,000 people will die in the United States this year than the recent annual average, even as some causes of deaths, like car crashes, might see declines because people are driving less. Those excess deaths mostly if not entirely be considered pandemic-related, Woolf and colleagues say.

Posted by: Richard Steven Hack | Oct 15 2020 0:47 utc | 132

@ Richard Steven Hack 128

“ There's no question that the majority of pandemic deniers posting here are Trump supporters completely subservient to his opinions while claiming they're somehow "rebels" against "the official narrative.“

Well aren’t you full of yourself. Who knows maybe if I checked your IP address I will come up with b’s address since most of the vitriol you are spreading here is going unscathed while totally legitimate comments get deleted.

A pandemic denier has to be a mindless follower of trump with no independent thought process while the mindless followers of the establishment narrative about the so called pandemic, such as yourself, are total geniuses.. Now I know we are f**ked.

Posted by: Alpi | Oct 15 2020 1:09 utc | 133

Alpi | Oct 15 2020 1:09 utc | 135

I'd take a chill pill, friend. Nothing to see there.

Posted by: Curmudgeon | Oct 15 2020 1:13 utc | 134

Good article on the Great Barrington ensemble- brought to you by courtesy of the Koch Bros.

https://www.wsws.org/en/articles/2020/10/14/revi-014-o14.html

Posted by: bevin | Oct 15 2020 1:33 utc | 135

So alpi@ 135: on the one hand we have Trump, Bolsonaro and Tories everywhere, cheered on by the followers of the Chicago/Austrian economists, and, on the other hand there is the Establishment, where power lies and conventional wisdom is dispensed.
It is a very weird world in which the rebels are seen to be Trump et al. In the real world, where capitalism rules, thee two sides you identify are one: both part of the Establishment, both celebvrating and defending capitalist class rule.

Posted by: bevin | Oct 15 2020 1:40 utc | 136

Posted by: Alpi | Oct 15 2020 1:09 utc | 135

Struck a nerve there, did we?

Posted by: Richard Steven Hack | Oct 15 2020 3:14 utc | 137

As the article above documents, we have good reason to believe that the RT-PCR test reacts positively solely to SARS-CoV-2 RNA fragments.

At the same time, a New York Times review published on August 28 found the following: "In three sets of testing data that include cycle thresholds, compiled by officials in Massachusetts, New York and Nevada, up to 90 percent of people testing positive carried barely any virus." (https://nyti.ms/3i0D0hj)

The Times' story may provide some insight on the odd divergence of rising positive case numbers vs. low hospitalization/death counts. Maybe it's time to take off the masks, end the lockdowns, and treat SARS-CoV-2 as simply another endemic coronavirus that we must live with.

Posted by: Jeff Coleman | Oct 15 2020 7:16 utc | 138

One of the first things you learn in Epidemiology 101 is how a low prevalence disease (5% for Covid-19, let's say) can be associated with a low predictive value positive even with high test sensitivity and specificity (say 96% for each). So, for example, if you have a 1000 people being tested, you get 48 true positives (50*96%) and 2 false negatives (the two together have to equal the 5% prevalence - 50 people). You also have 912 true negatives (950*96%), but that leaves 38 false positives. Now comes the rub-- if you are one of the 1000 people being tested, the probability of your test being positive given you actually are ill (this is called predictive value positive) is calculated thusly: true positives/(true positives+false positives), and in this case is 48/(48+38), or ~56%. Fortunately clinicians can also look at other things, such as whether the person is symptomatic, and whether they have been exposed to a confirmed case. Point is that false positives that depress predictive value positive don't necessarily mean you have a bad test - it's the low prevalence of disease that causes the problem.

By the way, the predictive value negative does not behave in the same way in the low prevalence scenario. It is calculated as follows: true negatives/(true negatives+false negatives): 912/(912+2), or 99.8%. So if you get a negative test, you can be pretty sure you're actually negative.

Part of the problem is that the press does a poor job of explaining the differences between sensitivity (probability of test positive given presence of disease as identified by a gold standard), specificity (probability of test negative given the absence of disease by gold standard), predictive value positive (probability of disease given a positive test) and predictive value negative (probability of absence of disease given a negative test).

Also thanks to Dave Brackett above@37 for explaining mechanisms. It's easy to see how false negatives can occur (swab technique, presymptomatic, etc.) but it was harder to see how false positives can occur (obviously now I see - choice of reagents, etc. but also lab technique).

Posted by: citrine | Oct 15 2020 10:42 utc | 139

Bevin: "Good article on the Great Barrington ensemble- brought to you by courtesy of the Koch Bros. "

Yes, I read the article. Good? Laughable. Garbage.Garbage article unless your idea of "good" is aspersion? Smear. Unverified claims.

And name calling, yes, the name calling. Though those standards seem to be par for the course at MoA. Including from b himself

I love the guy who claims the idea of "consensus view"
Consensus does not equal science and in fact he doesn't claim it does Gregg Gonalves and "they don’t represent anything like a consensus view"

Consensus view = Bandwagon = A general view = popularity contest and nothing more

No proof provided for claims of funding by anyone- Just claimed. Like gossip


Posted by: R Rose | Oct 15 2020 11:20 utc | 140

I personally know four covid fatalities so far.

1st: 84 year old neighbor. Her daughter called, but the old lady wasn't very anal about keeping her cell phone charged and missed the call due to a flat battery. Daughter freaks out and calls rescue services to check on mom, and then insists mom go to the hospital to be checked out anyway. Mom catches covid in the hospital and dies a week later.

2nd: My sister's husband's ex-wife's brother and his wife got the covid from who-knows-where. Real social butterflies who liked to party and hit clubs. Wifey survived while hubby died. That was unnerving as the guy was athletic and over twenty years younger than me.

3rd: Good friend's daughter, who was a mother of four and a nurse in the local trauma center, got the covid at work and kicked the bucket after fighting it a month. Her kids now have the Black American curse of growing up in a single parent household. Some Black families just can't catch a break.

4th: Coworker gave it to her mom (good thing I've been staying away from the office for a while!) and her mom died. Coworker was the sort to wear her mask around her chin, as if it was her chin that was emitting the virus. I did not offer my condolences to the egocentric woman for her murdering her own mother.

OK, so it isn't really a "Bring out your dead!" kind of scene (at least not yet), and two of those who died were probably going to kick off sometime in the next two decades anyway, but I at least have no doubt that the covid is killing for real.

Posted by: William Gruff | Oct 15 2020 14:09 utc | 141

Public authorities In Illinois have admitted that each positive Covid test is a "new case." A close friend tested positive several times, once when he had Covid, several times thereafter when workplace demanded a negative test. Finally had to be sent to a new lab where he tested negative, because the lab he originally used was know to experience extreme sensitivity in its tests.

Posted by: Zakukommander | Oct 15 2020 14:27 utc | 142

@ Posted by: R Rose | Oct 15 2020 11:20 utc | 140

You know what garbage is? Making a declaration of public policy purportedly grounded in science without giving any citations to the science which is claimed (falsely) to be supportive. The declaration lists people, not papers, as though the public should trust authority figures, not the scientific record.

~~~~~

https://truthout.org/articles/white-house-uses-petition-by-fake-doctors-with-prank-names-to-push-herd-immunity/

~~~~~

While I find the vt website hysterical and untursutworthy, they sometimes hit the target as in this instance with this haunting image of Covid-faced president — caution it may give one nightmares:

https://www.veteranstoday.com/2020/10/11/great-barrington-declaration-a-fake-secretly-funded-by-koch-science-denialist/


Posted by: suzan | Oct 15 2020 15:03 utc | 143

Suzan @ 143:

More articles of aspersion? I want facts. I want primary citations.
The link provided by Bevin, and I did read it, was a weasel wording masterpiece.
Have you provided anything of more substance? Not that I read. Just more smear and guilt by association.
I sadly looked at truth out, but, never, ever read veterans today.

Posted by: R Rose | Oct 15 2020 15:42 utc | 144

@citrine #139
The potential issue with false positives is that there are society-wide policy decisions being made on the basis of infection numbers.
This is not normally an issue with a clinician making a diagnosis.

Posted by: c1ue | Oct 15 2020 16:14 utc | 145

On the 'herd immunity' campaign which is run by the corporate right wing:

The proposal is not evidence-based and does not reflect even a minority view in the scientific community. Rather, it appears to be the product of an organized, well-funded political campaign in the US and UK. The UK campaign has been described elsewhere. In the US, the campaign appears to be largely coordinated by two right-wing think tanks — the Hoover Institution and the American Institute for Economic Research — in coordination with the Trump administration. Key elements of this campaign have included:

Appointing the Hoover Institution’s Scott Atlas as an official advisor to the White House Coronavirus Task Force in August. Atlas has long alternated between supporting a herd immunity strategy and denying he supports it. When 100 Stanford infectious disease scientists wrote an open letter denouncing Atlas’s unscientific views, he threatened to sue them.
Coordinating a media blitz whose public face includes three scientists: Jay Bhattacharya (a Stanford professor who is a colleague of Atlas and former fellow at the Hoover Institution), Martin Kulldorff (a statistician at Harvard Medical School), and Sunetra Gupta (an epidemiologist at Oxford). We’ve documented more than 50 interviews, public appearances, and published commentaries advocating the herd immunity strategy from these three individuals alone. The vast majority came after Atlas’s White House appointment on August 10, 2020.
Convening an in-person meeting at the American Institute for Economic Research campus in Great Barrington, Massachusetts with Bhattacharya, Kulldorff, and Gupta. There, the three signed the “Great Barrington Declaration”, which argues for the herd immunity strategy (rebranded as “Focused Protection”). AIER registered the domain gbdeclaration.org, where people can sign the declaration. The Guardian has since reported that many of the signatories (including “Dr. Johnny Bananas”) are obviously fake.
Convening a meeting between the White House Coronavirus Task Force and Bhattacharya, Kulldorff, and Gupta to cap off the Great Barrington Declaration event. In relation to the meeting, Atlas stated, “Their targeted protection of the vulnerable and opening schools and society policy matches the policy of the President and what I have advised”.
Advising state and local politicians, amid rising COVID-19 incidence, to avoid further restrictions aimed at lowering case counts. This has included public meetings with Florida Governor Ron DeSantis, San Diego County Supervisor Jim Desmond, and the Arizona state legislature. DeSantis cited his roundtable discussion as a pretext for not implementing further COVID-19 protections.

Posted by: b | Oct 15 2020 16:48 utc | 146

I'm not going to get into the scientific argument. I do not know and I'm not afraid to admit it. I still have a strong opinion on what's going on. That's based on the sides people are taking and their credibility.

For instance, back in June governments and media stopped reporting on deaths, instead focusing on rising case numbers. Mid July, where I live, a mask law came into effect, even though we had zero cases at the time and cases were extremely low throughout the province. Now case numbers are on the rise and are once again being hyped.

The one thing in common is that every emphasis and decision by governments and the media is intended to create and sustain fear. Perhaps there are no false positives in recent numbers, however you can be certain that if there were they'd be more than happy to use them in order to create more fear.

At this point, I will not trust anything coming from such fearmongers. Just enforcing mask wearing - when they DO NOT protect anyone from the virus - means their credibility is ZERO.

Why the Left has bought into this Covid Cult highlights how far the Left has fallen. Only need to see the hatred for Trump, the only leader not conforming with the official narrative. Right or wrong, at least he creates a discussion. Of course we are not suppose to discuss or to think. Ours is to follow orders.

With the restrictions and outright bans on so many things that give people pleasure, it's like Oliver Cromwell and the Puritans are in charge again. Plus the hysteria we see from the Left reminds me of Salem 1692. The behavior of governments and the media angers me for taking advantage of a health crisis to impose the most extreme responses and violate everyone's civil liberties in the process. Yet the Left's embrace of such insanity is truly mind boggling. I guess after 25 years of trying to scare people with global warming, you finally stumbled upon something frightening and you aren't going to miss your chance to impose your views on all citizens. As the second lockdowns come our way you're back for second helpings of the Jonestown Kool Aid.

There's an easy way to settle this. Come year end, compare the number of deaths to past numbers. The Swedish average for the past 3 decades is in the range of 89,000 - 94,000. By mid August Sweden had 62.000 deaths, on pace for the upper end of the average or slightly above the average. Hardly Black Death numbers. Plus Sweden did not do a lock down and has no mask law! Why are we forced to endure such things?

Sorry I do not see this as a health issue. It's about denying others the freedom of choice. It's about imposing one sacred view on everyone and forcing them to conform.

Posted by: EoinW | Oct 15 2020 16:56 utc | 147

posted by b

"The herd immunity campaign follows a playbook that has been used to protect corporate interests from accountability in the past"

That is a completely non credible stance, since natural acquired immunity would directly takes away from the vaccine manufacturing profiteering

The fake signature thing is such a red herring- I can't believe anyone is falling for it? It's a fallacious argument that distracts from the main issue-

this has got to be a new low

Posted by: R Rose | Oct 15 2020 16:57 utc | 148

For Rose:

Is it a low or is the statement an emotional response to an interruption or disappointment in expectation? Herd immunity is the goal, I don't think anyone can argue against it effectively. The method to achieve the goal is what is under debate.

The 'playbook' implications can be argued either way. We can probably agree that corporate interests play a major role in this scenario. Again the goals are not that different, it's the methods where disagreements arise. Which corporate interests will prevail? How much of the outcome will be determined by which entities who stand to gain the most from a particular outcome?

I've seen some comments here expressing disdain for the author who is apparently not keeping lockstep with 'sticking it to the man' or challenging the mainstream presentation. I think it's to be expected, but personally I have no dog in the fight, no opinion or expectation meant to be satisfied. But there is one exception to the previous statement.

I'm here to learn, and my way is to look for the people who speak or write from a gnostic approach, meaning you and others expressing from a position of knowledge. So while all of the links and citations are of great value, I can get there in other ways then attending these sessions on this blog. My point is merely that I enjoy this format much more than most others, and I'm not the smartest person in the room, which means by some standards regardless of how I might 'feel' about others comments, I'm still in the right place where I have an opportunity to learn from you and others.

Thanks in advance for your consideration. ~Blake

Posted by: Curmudgeon | Oct 15 2020 18:27 utc | 149

Curmudgeon: thanks for responding- "Is it a low or is the statement an emotional response to an interruption or disappointment in expectation?"

It's a low and perhaps that's where the disappointment aspect comes in to play?

I'm shocked at how little recognition there is of standard propaganda or influence tactics. I read the article linked by bevin, one at truth out and b's linked piece. They are in essence the same articles. Three similar versions of the same claims have been posted by 3 commenters. And not one of them realizes the articles contain little substance but lots of manipulative persuasion. From name calling, guilt by association, bandwagon and the smelly red herring, all relying largely on the 'big lie' reinforcement through repetition.


Herd immunity will occur. As it always has. It is the way of life on this planet.


Posted by: R Rose | Oct 15 2020 20:21 utc | 150

Rose:
"Herd immunity will occur. As it always has. It is the way of life on this planet."

Yes, and there will be a cost, but the wheel turns. I get it, but I must've some where along the way developed a callous. I don't mind the propaganda or I would avoid it just as I avoid used car salesmen and snake oil. I notice a lot of people are under a lot of stress. The right wingers, for example, celebrated the apparent 'meltdown' of Nancy Pelosi on CNN in an interview with Wolf Blitzer. As much as I disagree with her, I took no joy from it. No joy from the president's recent bout with the flu either. Can it be possible to be an empath with no feelings of our own? I think maybe likely.

If I were ambitious, I would invent the 'chill pill' and open source it-- so I can relax even if it meant getting up off my lazy ass to help other people. I'm not. I have a bad attitude, the epitome of the selfish gene, I'm junk dna for the collectivists. Good day.

Posted by: Curmudgeon | Oct 15 2020 20:34 utc | 151

"Herd immunity will occur. As it always has. It is the way of death on this planet."

Fixed that for ya!

Posted by: William Gruff | Oct 15 2020 20:34 utc | 152

Billy: yeppers, the wheel turns. :!

Posted by: Curmudgeon | Oct 15 2020 20:38 utc | 153

In reference to the apparent stress, look what happened to Steve Scully of CSPAN. Blunder, lie, justify, repeat.

Curmudgeon's rule:
Can't stand the heat, stay out of the kitchen.

Posted by: Curmudgeon | Oct 15 2020 20:53 utc | 154

Curmudgeon @151: "I notice a lot of people are under a lot of stress."

I think there are certain vantage points from which one can see that the empire is burning. While it is tough to tell from down on the street, there are ivory towers in the empire from which the residents can see the flames around the periphery. Those ivory tower dwellers try to maintain the appearance of normalcy so as to not panic the sheep, and I think that ends up really stressing them out.

Posted by: William Gruff | Oct 15 2020 21:02 utc | 155

Interesting word choice. I appreciate your comments. There's also this, though... they have panicked the herd, (sheep whatever) and what makes it more powerful is the convenience of SARS-COV-2. Stampedes in closed environment makes a meatgrinder. I'm paraphrasing Malcolm Reynolds from the "Firefly" series.

I recently looked up "Mass Psychogenic Illness", commonly referred to as mass hysteria.

perfect storm

Posted by: Curmudgeon | Oct 15 2020 21:17 utc | 156

William Gruff

""Herd immunity will occur. As it always has. It is the way of death on this planet."

You misunderstand- It is the way of life on this planet and death is a part of it. Those that survive carry on. It is the reason you and I and all of us are here. Our ancestors survived. You've fixed nothing.

Posted by: R Rose | Oct 15 2020 21:36 utc | 157

There is a corona committee in Germany from a group of German lawyers and international scientists.

Video: Crimes against Humanity

https://www.youtube.com/watch?v=kr04gHbP5MQ&lc=Ugx6HDDg4SwSVm1U5VB4AaABAg.9EOLwjSVjF79ElIIMPsx69

PS. So far there is no purified sample. Scientists from all over the world were interviewed. Please just keep an eye on this video.

Posted by: BlackBox | Oct 15 2020 21:37 utc | 158

Herd immunity will occur. As it always has
__________________________________________

There is no herd immunity for HIV and other sexually transmitted viruses. Or for Ebola and the original SARS.

Posted by: jinn | Oct 15 2020 21:58 utc | 159

To Jinn: That's likely because the others are not highly transmissible. Good point though, they haven't been all that successful in coming up with effective vaccines.

Posted by: Curmudgeon | Oct 15 2020 22:02 utc | 160

Ebola is highly transmittable, scarily so, you do not want to be anywhere in the vicinity of anyone with Ebola or anywhere they've been or touched or anything from their body without full protective gear, preferably BSL4 (but that might not be available). There are medications and vaccines used against Ebola including from Russia, one of the Ebola vaccinations gained US FDA approval yesterday or some time this last week.

SARS-CoV-2 is a much bigger and more advanced virus than either Ebola or HIV or the 1918 influenza, it is also much sneakier than any of them, it is some of the things we actually do know so far, but we do not know what all the information in SARS-CoV-2 does or how.

Considering the little we do know about it sneaking around the body without much difficulty before striking it would not be surprising it if automatically (it would be chemical) behaves differently when the body reacts with varying intensity according to how much of it has been seen before… so then what about the third time or the fourth or fifth and so on? Impressive for something that is nothing much more than a string of chemicals and generally not considered to be alive.

And yeah "herd immunity" in the current context is only an euphemism for murder, massacre, genocide, we don't know which. The hubris is scary, the whole point of all the effort is to not have to find out how bad it can get but a lot of people simply couldn't care less and thinks humanity will survive anything no matter what without any effort.

Posted by: Sunny Runny Burger | Oct 15 2020 22:57 utc | 161

I had thought otherwise, but is it safe to say it's less transmissible?

Posted by: Curmudgeon | Oct 15 2020 23:02 utc | 162

Yes there is a price to be paid for living. That price is always death. We do our best to put off paying that final installment as long as we can. A cost that we should not be paying is giving up our free societies. In fact it is the ultimate selfish act that we give away what should be the birthright of future generations.

If we were dealing with the Black Death about to wipeout 50% of the population one might have a case for the extreme abuses of power governments are exercising. However we're talking about losing less than 1% and nearly all are at the end of a long life or have serious health issues. That simply doesn't merit the risk of losing our free society forever. Plus the science and numbers do not justify it. Sweden has proven that masks and lockdowns don't do anything.

Posted by: EoinW | Oct 15 2020 23:03 utc | 163

BlackBox | Oct 15 2020 21:37 utc | 158

PS. So far there is no purified sample. Scientists from all over the world were interviewed.

CDC 2019-Novel Coronavirus (2019-nCoV)
Real-Time RT-PCR Diagnostic Panel

For Emergency Use Only

Instructions for Use

Catalog # 2019-nCoVEUA-01
1000 reactions
For In-vitro Diagnostic (IVD) Use
Rx Only

Centers for Disease Control and Prevention
Division of Viral Diseases
1600 Clifton Rd NE
Atlanta GA 30329

@ p39

Performance Characteristics
Analytical Performance:

Limit of Detection (LoD):

LoD studies determine the lowest detectable concentration of 2019-nCoV at which approximately 95% of all (true positive) replicates test positive. The LoD was determined by limiting dilution studies using characterized samples.

The analytical sensitivity of the rRT-PCR assays contained in the CDC 2019 Novel Coronavirus (2019- nCoV) Real-Time RT-PCR Diagnostic Panel were determined in Limit of Detection studies. Since no quantified virus isolates of the 2019-nCoV are currently available, assays designed for detection of the 2019-nCoV RNA were tested with characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and viral transport medium (VTM) to mimic clinical specimen. Samples were extracted using the QIAGEN EZ1 Advanced XL instrument and EZ1 DSP Virus Kit (Cat# 62724) and manually with the QIAGEN DSP Viral RNA Mini Kit (Cat# 61904). Real-Time RT-PCR assays were performed using the ThemoFisher Scientific TaqPath™ 1-Step RT-qPCR Master Mix, CG (Cat# A15299) on the Applied Biosystems™ 7500 Fast Dx Real-Time PCR Instrument according to the CDC 2019-nCoV RealTime RT-PCR Diagnostic Panel instructions for use.

[emphasis added]

Posted by: pogohere | Oct 16 2020 6:49 utc | 164

And here are the latest survival rate estimates from the Center for Disease Control:

Age 0-19 … 99.997%
Age 20-49 … 99.98%
Age 50-69 … 99.5%
Age 70+ … 94.6%

The “science” argument is officially over. An increasing number of doctors and medical experts are breaking ranks and explaining how the current mass hysteria over “cases” (which now includes perfectly healthy people) is essentially meaningless propaganda ...

https://consentfactory.org/2020/10/13/the-covidian-cult/

Posted by: Jim C. | Oct 16 2020 7:48 utc | 165

the only trouble with B's analysis is these tests will in fact yield false positives for other caronaviruses.

sure - google that.
And read this
https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(20)30453-7/fulltext

Now why would that B?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189409/

Posted by: Jim C | Oct 16 2020 7:55 utc | 166

Jim @166
It's not the virus, it's the reaction that's killing us. The virus certainly exists, I don't think that's in contention. It serves as a contributing factor to the 'crisis'. So we get con-theory like 'Plandemic' and such.

That's why I looked up "Mass Psychogenic Illness", commonly referred to as mass hysteria. This is what we're actually looking at now. The campaign concentrates on doing exactly the opposite of what the medical community recommends to defeat mass hysteria. They're throwing fuel on the fire.

Posted by: Curmudgeon | Oct 16 2020 8:07 utc | 167

pogohere | Oct 16 2020 6:49 utc | 164

Also a bit further up the page in your link to the FDA guidance are some bullet comments referring to the efficacy of the test. See p. 37, Limitations cont'd on p. 38. The test does not identify the disease, it only detects presence of viral RNA and it doesn't determine presence of infection. The old way was to diagnose by symptoms. The test is meant to be combined with other analytical tools like CT etc, it is not a diagnosis, and clearly is not a tool for ruling out the virus.

Posted by: Curmudgeon | Oct 16 2020 9:26 utc | 168

In case anyone wonders I did write the previous post; I needed to check the CDC detection kit snafu before replying to Oldhippie.

Oldhippie: I can only sympathize with those in your example, something must have gone wrong and it's impossible for me to say what. I note that it's well after the US CDC recalled their faulty detection kits so at least it shouldn't be from those.

Curmudgeon: as far as I understand they both spread very easily and beyond that I'm not sure which if any could be said to be worse or whether it's a meaningful distinction.

Pogohere: in your emphasis I think the word "quantified" is the crucial one (maybe also with an implied "commercially" stuck into "currently available" to make "currently commercially available").

The way I read it is that they have to simulate it because they can't simply order a sizeable amount of readily available "isolated virus" (ie. pure/nothing but) from someone (nor make that themselves in their own labs).

The virus has been isolated many times in several labs but that doesn't mean they have a way to produce a larger quantity of it in a form that can be readily used for studies or in this case calibration of detection where they need a lot/much more of it for whatever reason (I don't know but suspect "scaling it up" again rears its head, it often does and usually is the difference between having achieved something in a lab and managing to make it into a more "trivial" product or easily available capability).

I could be wrong, someone far more knowledgeable than me would have to confirm the various parts.

About me: I should point out that my use of Methotrexate is "only" to beat back and partially destroy my hyperactive immune system (and by now most MDs will have a good chance at guessing the name of that illness since it's common and not cancer) which might be a good thing as far as SARS-CoV-2 goes. I also happen to have blood type O which might also be a good thing, and like b I'm a chimney stack… Anyway no one knows enough to predict a likely future or what will ultimately matter or not (I'm pulling serious "overtime" anyway: lucky to survive childhood accidents and whatnot lol :D ).

Posted by: Sunny Runny Burger | Oct 16 2020 9:27 utc | 169

Sunny Runny Burger:
I think Ebola is not airborne, you would have to make physical contact and unless STD have changed, I'm not aware of any other way to get it than physical contact. SARS is airborne, a major game-changer. But you're right, it doesn't matter. The reference was to herd immunity. I got a similar take on the available specimens, but in my mind it doesn't change the fact that the standard is simulated. The test is allowed under the emergency use authorization, otherwise it wouldn't be approved until all the i's and j's were aptly dotted.

Posted by: Curmudgeon | Oct 16 2020 10:13 utc | 170

According to the ECDC numbers on the 15th found almost at the bottom of the page (linking their page again but it changes daily) the percentage of those considered dead from COVID among those considered to be infected is currently roughly 2.8%. This does not count excess mortality and does not exclude false positives, (unless my brain has clocked out for the day) both of those would raise the mortality maybe by a lot. In addition this is with at the very least attempts at fighting both the spread and the lethality.

The numbers I'm using are their current best effort, they have plenty of disclaimers.

Because I'm more than capable of messing it up (I like numbers and math but I'm sloppy and awful at calculating and remembering lol) I'll show my "work" XD

(part/whole)×100 = percentage

(1093140÷38581234)×100 = 2.833346388

Check: 38581234×2.833346388% = 1093139.999984828

For only the US: 2,7%

(216872/7916100)×100 = 2,739631889
7916100×2,739631889% = 216871,999965129

Spread it into enough age groups (why not divide them into half years or month or days? :P (sarcasm)) and you can turn that into any percentage of 99.99…9% survival and then why not just as well round it up to get a clean sheet of 100% survival? :D (it becomes dodgy bookkeeping "statistics"…).

Posted by: Sunny Runny Burger | Oct 16 2020 10:23 utc | 171

Ah I only corrected some of the decimal signs and operators in the calculations. Sorry for the mismatch of different mathematical symbols and notation meaning the same thing (it is extremely annoying that mathematics does not use a global standard).

Also I should have written:
"…among those considered to have been infected…"

Posted by: Sunny Runny Burger | Oct 16 2020 10:40 utc | 172

Curmudgeon I agree although with a small caveat that neither is thought to be airborne (transmission) in the infectious sense of the word, at least not to any large degree, and instead both can be spread by (respiratory) droplets (unless deliberately or inadvertently aerosolized by equipment).

The airborne vs. droplet thing seems stupid, messy, and annoying, maybe not useful either. As a typical example the Wikipedia page on Airborne Transmission manages to sort of contradict itself in the first two paragraphs alone but somehow gets to the point that "respiratory droplets" and "airborne transmission" are meant to be two different things.

Posted by: Sunny Runny Burger | Oct 16 2020 11:11 utc | 173

haha, manage to contradict itself, big surprise there, eh? I already been through the fan blades on the airborne transmission thing, so I'll step along. I still insist on keeping my N95 masks in the freezer ICOE. At least there's no disagreement on the STD part.

This doctor said to me, "You never know how much detail people want to know", which I translated to mean "You're splitting hairs, dude." Nice way of putting it.

Posted by: Curmudgeon | Oct 16 2020 16:24 utc | 174

For Sunny Runny Burger:
You might want to take a look at this study (hyperactive immune response)

https://www.sciencedirect.com/science/article/pii/S0896841120301281?via%3Dihub

"Autoimmune and autoinflammatory conditions may be triggered by SARS-CoV-2."

The abstract is eye-opener.

Posted by: Curmudgeon | Oct 16 2020 18:01 utc | 175

WSWS doesn't like the "Great Barrington Declaration":

The Great Barrington Declaration: A manifesto of death

Posted by: Bemildred | Oct 16 2020 18:15 utc | 176

Who is the MORON that wrote this "The researchers who developed the SARS-CoV-2 RT-PCR test have selected several unique snippets of about 100 nucleotides long out of the much longer string. Complementary oligonucleotides of the same length will then get synthesized. These are the primers for all following PCR tests."?!

They are so good that they've even built a primer 100% equal to a part of the Homo sapiens chromosome 8!

Try not to write so many moronic stuff about a chemical reaction that WILL NEVER be a test!

Posted by: voza0db | Oct 16 2020 18:29 utc | 177

The day those guys are socialists is the day I'm Adolf Hitler!

Posted by: voza0db | Oct 16 2020 18:34 utc | 178

@Curmudgeon | Oct 16 2020 18:01 utc | 175

In the remaining 20% of cases, the disease may become severe and/or critical. In most patients of this latter group, there is a phase characterized by the hyperresponsiveness of the immune system.

Well... assuming that the existence of a new infectious viral particle is the agent causing that, it can ONLY CAUSE THAT, on OLD and obsolete human animals. If by any chance the human animal is not OLD than it's just one animal that is in a miserable Health condition.

So... no worries!

Posted by: voza0db | Oct 16 2020 19:44 utc | 179

Yes Prof Choud is wrong ( he does not understand medical or science) BUT NO That is incorrect MOA the PCR can't diagnsoe disages and can't even dtect one whole transmissible "virus".
https://notpublicaddress.wordpress.com/2020/10/07/a-summary-about-the-testing/

Posted by: BDBinc | Oct 17 2020 0:34 utc | 180

The PCR test is totally unsuitable for clinical use. It gives no clue as to the prevalence of the virus. We all carry a vast number of different viruses all the time. It is normal and healthy.

The fact that most of these "cases" are healthy people seems to have escaped the writer. Until now, the word "case" was only used for sick people. Its use currently is pure unadulterated propaganda.

Posted by: Alfred (Cairns) | Oct 17 2020 4:32 utc | 181

voza0db @179

I think the assumption is premature. We've a lot to learn about autoimmune disease. The virus may be incidental rather than the cause since most people don't react to it. It's just another random piece of RNA floating around. Obsolete... I'm thinking about that. The mRNA vaccine is a potential 'cure' for obsolescence. The way I read it, the vaccine is an update to the immune system. Bill Gates must be so proud.

Posted by: Curmudgeon | Oct 17 2020 5:57 utc | 182

Ah Moon, how about you stick to wars because the fact is well known the tests do not diagnose anything at all.

Posted by: Marilyn Shepherd | Oct 17 2020 6:50 utc | 183

@ Curmudgeon | Oct 17 2020 5:57 utc | 182

Yep... Billy G is proud alright!

Posted by: voza0db | Oct 17 2020 10:59 utc | 184

@ Marilyn Shepherd | Oct 17 2020 6:50 utc | 183

Indeed Marilyn... And the funny part is that THEY even say it, but I'm sure the author of this nonsense article doesn't understand the basics!

The lack of a clear-cut “gold-standard” is a challenge for evaluating covid-19 tests; pragmatically, clinical adjudication may be the best available “gold standard,”...
source

Basically what they are saying (but no one cares) is that the chemical reaction PCR IS NOT A TEST and is only good for sell a make a nice few billions of PROFIT!

In the end we're just wasting resources...

Posted by: voza0db | Oct 17 2020 11:05 utc | 185

to Anne @82
you are RIGHT - not only are a lot of A1C tests not being properly interpreted, but the newfangled oral drugs being marketed for diabetes are not well-understood, and most doctors don't know that. elderly people with diabetes are often dangerously low-blood-sugar, sometimes not even diagnosed at death.

but on the subject of Chossudovsky, why throw the baby out with the bath water? why is this such a big deal? so what?

Posted by: k | Oct 17 2020 15:00 utc | 186

Alpi@34:
The style of your writing (all form, no substance), together with the fact you were able to jump on my post quite quickly to, is very strongly indicative you are trained an paid to surveil this site.

You make no points, at all.

Just the general, nonspecific talking points you were provided

Good luck with that - if the posters on this site were not critical thinkers, I'd say you could have a winning strategy.

- Shyaku

Posted by: Shyaku | Oct 18 2020 1:14 utc | 187

Chossodusky may indeed be wrong on the specifics, but false positives from PCR tests were, it seemed, of sufficient concern for the WHO and CDC to propose specific recommendations for each of the pre-Covid19, post-2000 pan/epidemics including secondary tests for asymptomatic positive cases - a stipulation not made for Covid19 - make of that what you will. y

Yes the tests may be 100% specific, but positive tests may result from cross-contamination / lax practices too - a possibility in such rapidly expanding (often out-sourced) circumstances. This piece highlights some of the issues and links to previous CDC guidelines.


https://www.medrxiv.org/content/10.1101/2020.04.26.20080911v3.full.pdf?fbclid=IwAR18zF1Zwye1zMbbwAiGq9kpWUBasbsmI3AKOadjRmGGr1_5ybb9e8oariY

Posted by: Adrian D. | Oct 19 2020 11:31 utc | 188

I enclose selected Limitations of the PCR Test as stated by CDC :

"
• Performance of the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel has only been established in upper and lower respiratory specimens (such as nasopharyngeal or oropharyngeal swabs, sputum, lower respiratory tract aspirates, bronchoalveolar lavage, and nasopharyngeal wash/aspirate or nasal aspirate).
• Negative results do not preclude 2019-nCoV infection and should not be used as the sole basis for treatment or other patient management decisions. Optimum specimen types and timing for peak viral levels during infections caused by 2019-nCoV have not been determined. Collection of multiple specimens (types and time points) from the same patient may be necessary to detect the virus.
• A false-negative result may occur if a specimen is improperly collected, transported or handled. False-negative results may also occur if amplification inhibitors are present in the specimen or if inadequate numbers of organisms are present in the specimen.
• Positive and negative predictive values are highly dependent on prevalence. False-negative test results are more likely when prevalence of disease is high. False-positive test results are more likely when prevalence is moderate to low.
• Do not use any reagent past the expiration date.
• If the virus mutates in the rRT-PCR target region, 2019-nCoV may not be detected or may be detected less predictably. Inhibitors or other types of interference may produce a false-negative result. An interference study evaluating the effect of common cold medications was not performed.
• Test performance can be affected because the epidemiology and clinical spectrum of infection caused by 2019-nCoV is not fully known. For example, clinicians and laboratories may not know

38 CDC-006-00019, Revision: 05 CDC/DDID/NCIRD/ Division of Viral Diseases Effective: 07/13/2020
the optimum types of specimens to collect, and, during the course of infection, when these specimens are most likely to contain levels of viral RNA that can be readily detected.
• DETECTION OF VIRAL RNA MAY NOT INDICATE THE PRESENCE OF INFECTIOUS VIRUS OR THAT 2019 - nCov IS THE CAUSATIVE AGENT FOR CLINICAL SYMPTOMS.
• THE PERFORMANCE OF THIS TEST HAS NOT BEEN ESTABLISHED FOR MONITORING TREATMENT OF 2019 nCOV INFECTION
.
• THIS TEST CANNOT RULE OUT DISEASES CAUSED BY OTHER BACTERIAL OR VIRAL PATHOGENS


Performance Characteristics
Analytical Performance:
Limit of Detection (LoD):
LoD studies determine the lowest detectable concentration of 2019-nCoV at which approximately 95% of all (true positive) replicates test positive. The LoD was determined by limiting dilution studies using characterized samples.

The analytical sensitivity of the rRT-PCR assays contained in the CDC 2019 Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel were determined in Limit of Detection studies. SINCE NO QUANTIFIED VIRUS ISOLATES OF THE 2019 - n COV ARE CURRENTLY AVAILABLE assays designed for detection of the 2019-nCoV RNA were tested with characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of known titer (RNA copies/μL) spiked into a diluent consisting of a suspension of human A549 cells and viral transport medium (VTM) TO MIMIC CLINICAL SPECIMEM "

This means what is tested is a HYPOTHETIC IMAGINED VIRUS which so far has never been isolated ..The RNA could be from anything else ...

THE INCRIMINATING SENTENCES WRITTEN IN BOLD ..by ME .. a MEDICAL DOCTOR
THE PCR TEST IS NOT SUITABLE to confirm or reject a diagnosis of COV 19 Infection The PCR Test ..admittted by CDC .. can NOT diagnose anything with certainty....


Posted by: Ole C G Olesen | Oct 20 2020 1:50 utc | 189

Scanning through the comments it sure appears that the more scientific informed commenters tend to be critical towards PCR tests (see Brackett's post e.g.) bc some actually know what they are talking about from their practical work.

What made me made de-bookmark your site is this: "@all - I have deleted about 20 comments on this thread that made obviously false assertions...".

P.S: I made a donation to your site a couple of years ago, no regrets, but chose to do some comments here and there only recently as "Johannes" when I found that you've lost your mind over C19. Have no relationship with Chossudowsky whatsoever (a friend of mine was invited as a speaker to a MH 17 truth finding mission as a speaker on Chossudowsky's proposal). My latest - censored by you - post has alluded to the fact, that PCR tests are not suitable for screening for which they are used, however, like for calculating the "new infection rate" (Neuinfektinsrate). As to why and how this could be "obviously false" is up to you, I have some education in medical statistics.

I am aware that this post won't survive the censor's scissors but I feel it was necessary to stick it to you with this final note. In case you are interested to have small chitchat with a German co-national - yes, I am German - just send me your Email and will provide all my contact data.

Posted by: Johannes | Oct 22 2020 9:47 utc | 190

Scanning through the comments it sure appears that the more scientific informed commenters tend to be critical towards PCR tests (see Brackett's post e.g.) bc some actually know what they are talking about from their practical work.
____________________________________________________

I think you need to read that post again. It was a detailed explanation of how the PCR test should be designed so that it will be "solid". By solid I assume he means reliable.

Posted by: jinn | Oct 22 2020 12:53 utc | 191

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