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Some considerations on the retraction paper for the Corman-Drosten PCR test

With a lot of fuss, 22 ‘experts’ have requested the retraction of the first scientific article that describes a PCR test for the coronavirus. According to this club, led by molecular biologist and creationist Pieter Borger, a lot is wrong with it. The test was designed, however, by internationally leading scientists such as Christian Drosten and Marion Koopmans. So to show that it is no good you will have to come up with some pretty good arguments, but that is rather disappointing in this case.

Borger on Twitter: “We are ready! Retraction request indicating all design errors of the RT-PCR test can now be sent to Eurosurveillance. 20 PCR experts worldwide participated! A monster job, but with the potential to kill the monster that grips the world!”

The attention-grabbing for their action, which had been going on on social media for some time before the actual submission of their ‘retraction paper’, has been successful to the extent that the Russian propaganda channel RT has picked it up and Member of Parliament Wybren van Haga (for the far-right party Forum for Democracy of Thierry Baudet) has asked questions in Parliament on the matter. The fundamentalist Christian newspaper Reformatorisch Dagblad, in which Borger regularly published creationist pieces, also paid attention to it, but not in a way he had anticipated: “PCR test survives a flood of criticism“. According to Borger, the journalist had set him up and had passed the science journalists of the paper.

The criticism of the ‘Corman-Drosten paper‘ (Victor Corman is the first author of the article) is quite technical in nature and for someone who has no expertise in the field of PCR, it is often difficult to assess its value. I certainly do not have that knowledge, so I will be modest here. Borger, however, presents his club of 22 as experts without hesitation (see his tweet above), whereas this is clearly only true for at most a few of them. One signatory, the Dutch malicious neurologist Jan Bonte, admits on Twitter:

Bonte using his pseudonym: “@BorgerPieter I am not a PCR expert and I never will be. That is not a bad thing at all. But isn’t this the same thing you said? #PCR test”

At the end of this article, I will discuss some other people from the list, as I did on Twitter. Some (mostly anonymous) tweeps argued that I only tweet such ad hominems only because I anxiously want to avoid having a look at the content of the criticism by Borger et al. This is demonstrably false, but a blog such as this one lends itself better for this purpose than threads on Twitter.

Review report Corman-Drosten et al. Eurosurveillance 2020

The retraction paper (for which they have set up their own website) contains 10 points of criticism, ‘major scientific flaws’ in their words. These range from wobbly primers and problems with annealing temperatures to the lack of a prescribed breaking point for the number of cycles. It would go too far to explain in detail here how such an RT-qPCR test works, just read it on Wikipedia and read, for example, an interesting thread by the Australian virologist Ian Mackay on Twitter in which he explains how to carry out the procedure in practice.

Much of the criticism boils down to the fact that the primers and probes proposed in the Corman-Drosten article are not well chosen. Precisely those elements should recognize and multiply (parts) of the coronavirus RNA while ignoring RNA from other sources. According to Borger, the test is ‘completely non-specific’:

“The Covid test is completely non-specific. The beds may as well be full of influenza pneumonia. This is normal for this time of year. You can call it Covid, but then you have to test it specifically, @MinPress”

The idea that patients who are now in hospitals and ICUs with Covid-19 would actually have flu is somewhat peculiar, given the fact that flu does not circulate at all at the moment (in the Netherlands at least) as can be seen in the NIVEL surveillance. I doubt that Borger really means that the Covid test is so non-specific that it can also turn out positive when someone is infected with influenza only.

In an earlier article on LinkedIn, Borger complained that the Corman-Drosten test would also be positive with SARS-CoV (the SARS virus that appeared in 2002/2003) and some other (bat) coronaviruses. He could not explain to me at the time why this would pose a problem. On the contrary, the test was specially designed to be positive for SARS-CoV as well, because material from that virus was easily available to laboratories and could therefore be used as a positive control. This feature of the test does not give false positives because that virus has not been found in humans since 2003, and neither have those bat viruses of course. Drosten explained this clearly in the media earlier this year:

Drosten on NDR, 18 March 2020: “It is true, but this is of course completely misleading information, purely theoretically this test would react against the old SARS corona virus. But that has not been present in humans for 16 years. And in theory, this test would also react against a whole range of bat corona viruses, but they do not exist in humans either.”

Other risks for false positives?

One of the primers would also exactly match a bacterium, Pantoea agglomerans. It could be found in people with a malfunctioning immune system. Is that something to worry about? I don’t think so. If you try to figure out in what circumstances this bacterium could pose a problem, you’ll soon discover that it’s a bacterium that occurs in plants. If, for example, you prick yourself on an infected plant, you could get a local infection. With a malfunctioning immune system, such an infection can get out of hand and even lead to sepsis. However, this seldom happens. And before you find the bacteria in your nose or throat, it is probably already pretty serious with the person in question [*]; such a person will not go for a corona test but straight into the hospital.

Figure 3 from the retraction paper

Another problem: some primers might stick partly on each other. This is theoretically undesirable, but does it cause problems in practice? If I read the following paragraph in the article by Corman and Drosten et al, it seems to me that they have tested this and ruled it out as a problem:

From the article by Corman et al, Eurosurveillance (2020)

Anyway, as has already been said, I am not an expert in this area. What I do think to understand is that all the issues that are raised come down to stating that the specificity of the Corman-Drosten test is not that great. That would imply that you would find a lot of false positives. However, that is not the case, see for example a blog by the earlier mentioned Mackay: The “false-positive PCR” problem is not a problem.
An important aspect of the ‘retraction report’ is the lack of any experimental evidence that would substantiate that the theoretical problems put forward actually do cause false positives in practice.

‘Unique fingerprint’ – Borgers creationism seeping through?

Also in the retraction report is Borger’s ‘find’ that SARS-CoV-2 is a weakened version of SARS-CoV. He wrote this down in an article in the American Journal of Biomedical Science & Research in the spring of this year. The title of the journal may sound impressive, but it turns out to be a predatory journal. Fun fact: around the same time as the journal published Borger’s article, they also accepted an article that was so obviously fake that it could not pass any serious peer review.

“Well, I have not heard anything yet, @MarionKoopmans. Nevertheless, I was the first to discover the two genetic fingerprints in SARS-CoV2 that also appear in SARS-CoV1 and which confirm that SARS = COVID.

Borger thinks he was the first to see that the RNA of the current coronavirus contains a series of codons (set of 3 base pairs encoding for a protein) almost identical to the corresponding series in the 2003 SARS virus, which would be unique. For Borger, it is the proof (together with his mistaken assumption that SARS and Covid-19 can both be treated well with chloroquine) that these are actually the same viruses and diseases. The current coronavirus would be a weakened variant of SARS-CoV, less lethal by now, but easier to spread.

In SARS-CoV the protein series is KTFPTEPKKDKKTDEAQ. Now such a series is somewhat variable anyway, the individual proteins can be coded by several codons, Lysine (K) for example by AAA and AAG. Borger quotes a Science article from 2003, which states that this series is unique for SARS-CoV. However, it is clear that this should be read as ‘we haven’t found it anywhere else’. Anyone who now searches the databases for that series will find that it has been found in coronaviruses of various bat species and also in civets. As a result, Borger’s story is already largely shattered, but there is also research that shows that the evolutionary developments that led to the two viruses from a common predecessor started to diverge quite a long time ago. Published in Nature, so we may attach a little more weight to that than to Borger’s publication in such a ‘you-pay-we-publish’ magazine.

I think Borger’s idea fitted a little too nicely into his version of creationism to let it pass. I’m not going to elaborate on this, but if the reader wants to know more about it, I can warmly recommend the extensive review by Bart Klink of Borger’s book Terug naar de oorsprong, of hoe de nieuwe biologie het tijdperk van Darwin beëindigt – translated as Darwin Revisited – which also deals with Borger’s view on RNA viruses. It is however in Dutch: De wetenschappelijke dwaalwegen van een creationistisch bioloog. (The scientific aberrations of a creationist biologist)

The list of signatories

I have already talked enough about Borger, but who are his 21 allies? The list ‘leaked out’ early. The website shouldn’t have been made public until Monday, but someone shared a link before, after which the website administrator and co-signer, 3D-artist Bobby Malhotra, hastily put a password on the pages. Just a little too late to prevent that someone stored it in web archives. When I shared screenshots of them, Malhotra even accused me of having photoshopped them and threatened to hack my computer in barely concealed terms. Such a fine gentleman.

Another person who was closely involved writing the report is Prof. Ulrike Kämmerer, who had already stirred controversy in Germany about the PCR test, but who, for example, also promotes nonsensical diets for cancer. Those who are mentioned more specifically as experts are Dr Michael Yeadon and Kevin McKernan. The first had an important job at Pfizer (and wrongly says that the pandemic is already over) and McKernan is someone who has been involved in the development of machines for DNA sequencing. He probably knows best of the club what he is talking about, but just like Borger and Malhotra, he is rather rude on Twitter against Koopmans and Drosten among others.

Then we have Thomas Binder, a Swiss cardiologist, who put himself in the limelight last year with conspiracy theories about the poison gas attack in Douma. About corona, he also maintains that there might be a connection between Covid-19 and 5G. Earlier this year he was arrested and put in a psychiatric institution for some time.

And among the Italian signatories, we find Dr. Stefano Scoglio. A homoeopath, with a PhD in philosophy, who believes he was nominated for the Nobel Prize in Medicine and is one of those types who continue to claim that the virus has never been isolated.

Please add your own findings on these guys or others from the list in the comments below. I think there is still plenty of interesting stuff to find out about them!

Conclusion

What do they actually intend to achieve with their criticism of the test? Why should it be withdrawn at all if the primers chosen are not optimal? After all, it has not been presented as the most optimal test, but as a test that was designed quickly, but could still be very useful at the beginning of the pandemic. And there are now other tests, with other primers.
They somehow suggest that all the measures taken to limit the spread of the coronavirus actually depend on this PCR test, the first to receive official scientific recognition and to be embraced by the WHO. If this piece of the machinery of the fight against coronavirus can be removed, all the grounds for these measures would disappear, they seem to think. That is nonsense, of course. The sick who have to be admitted do not suddenly have another disease without a PCR test. And without a PCR test, you would probably have to go into quarantine much more often and for much longer in the event of suspicion of infectivity. Because then we would again have to rely on virus cultures that do not work as well and certainly take much longer.

On Twitter, others (including Koopmans) have already voiced criticism, discussing all or parts of the ‘retraction paper’. And once again: with this post, I am not trying at all
to deal with that report exhaustively. There are others who are much more qualified than I am, for example, the editorial board of Eurosurveillance, which will probably formulate a firm response.


This is a rather quick and rough translation of the original article in Dutch on Kloptdatwel.nl
(Image: thiagolazarino |Pixabay)


[*] update 3 December 2020: perhaps I am putting this a little too strongly. There are studies that find the bacterium in the oral cavity and the tonsils of a small percentage of healthy people. However, the presence of the bacterium is not enough to turn this PCR test positive, more is needed. The person who suggested it as a possible design problem, McKernan, also indicated on Twitter that he does not really expect this to cause false positives. So it is more nitpicking about the design and that the authors did not discuss this hypothetical problem in the article.


Also read Frank Visser’s view on the matter in the 20th part of his serie The Corona Conspiracy: PCR-Gate: A Storm in a Petri Dish?

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18 thoughts to “Some considerations on the retraction paper for the Corman-Drosten PCR test”

  1. I am not a medical scientist so i will refrain from making technical comments about the Drosten Corman paper or the challenge to it by the team of scientists. However all of you attacking the scientists asking for the retraction seem to gloss over the highly unusual speed – 24 hours(!) – between submission and publication time of the paper by Eurosurveilance. And the equally lightning fast speed from its publication to when the WHO endorsed it as the standard test to be used for mass testing for covid.
    One would think that considering the important role the PRC test would be playing during the pandemic there might have been the normal peer review process before publishing? Or that the WHO might have the Drosten Corman paper analyzed by experts before endorsing the PCR test to be used by countries around the world.
    The “wham bam thank you mame” rocket speed with which it was all done from submission to WHO endorsement and with little or no review seems suspicious.
    Who funded the research behind the Drosten Corman PCR paper? Who has funded previous research by Drosten and Corman? And who funds Eurosurveilance ?
    We know Big Pharma has its dollar thumb on the WHO as shown by the WHO letting consultants from pharma drug industry redraft the WHO definition of “pandemic” in 2009 mere weeks before the outbreak of H1N1 with the result that H1N1was able to qualify as a pandemic which it would not have by the previous WHO pandemic criteria. By having H1N1 qualify as a pandemic Big Pharma made 3/4 trillion dollars from H1N1 vaccine shots – the vast majority never being used and earning the WHO a damming Council of Europe
    investigation.
    Follow the money trail as it would not surprise me at all if that the hyper accelerated timeline from paper submission to WHO endorsement was lubricated by Big Pharma dollars. It is just what Big Pharma does – and does very well too.

    1. Answers to all the questions you ask can be found with a few mouseclicks. The peer review process for the Corman Drosten paper was streamlined, the article was announced, reviewers were asked to be ready so that there would be no delays. All understandable to get the maximal profit from this test which could be essential in getting a grip on the spread of the new virus as early as possible. Also, everybody is allowed to use this primer set without paying license fees or something like that.

  2. One of the authors of the review of Borger et al. (2020) is Marjolein Doesburg-van Kleffens. The section “Author’s Affiliations” reveals that Doesburg-van Kleffens has used “Maasziekenhuis Pantein, Beugen, the Netherlands” as affiliation for this review. The review does not contain information that one or more of the authors and/or one or more of their institutes (affiliations) do not agree with any of the findings in Borger at al. (2020). This implies that the Maasziekenhuis Pantein endorses all the views about the PRC test which are listed in Borger et al. (2020). That’s towards my opinion a highly remarkable point of view for this hospital. See https://www.maasziekenhuispantein.nl/ for backgrounds about this hospital (only in Dutch).

  3. This getting a bit silly. As I wrote in my post, only a couple of the signees can boast some or expert knowledge of PCR (at least McKernan and Borger). One of them, Bonte, openly admits he didn’t contribute a single character to the report and fully relies on Borger for the PCR stuff.

    A: I did say ‘some’ of their backgrounds…. About J. Bonte, I agree if he hasn’t contributed, he shouldn’t be on the list.

    When you write that Drosten as faked his credentials and even that he isn’t a professor, you are totally out of line. You’ve fallen for the defamatory tricks of his opponents. How you can even think that he fakes being a professor while he is listed as such by his employer is beyond my understanding.

    A: I cannot tell you too much now.

    That Borger challenges Koopmans for a debate shouldn’t surprise, that’s common trich for creationists. If one accepts they will shout that scientists take them seriously (not as a threat to common sense though) and that their fantasies thus equal science.

    A: Emotional response, irrelevant what you ‘think’ would happen. With crucial debates like these, rules should be established to control the debate pure scientifically. I can almost feel your hidden frustration typing the sentences.

    If my opinion on this ‘retraction paper’ hasn’t become clear from this post, then let me state that to me it is utterly unconvincing. The authors might have pointed out some theoretical issues, a better PCR-test is conceivable (and in use!), but they failed to show that these potential problems do cause problems in practice as they have not shown any experimental evidence. So, to call these potential issues ‘major scientific flaws’ is laughable.

    A: Still nothing of value to be this convinced, especially as a science writer. But I understand your position.

  4. Ad Hominem, wait for the results and draw your conclusion then. Unprofessional article to say the least.

    1. It’s not Ad Hominem in the sense of a logical fallacy. The authors of the ‘retraction paper’ portray themselves as experts, so it is more than fair to check their backgrounds to see whether that claim makes sense.

      1. Well I have tracked some of their backgrounds, these are not men/women that are poorly established. On the technical basis, they outweigh M. Koopmans en C. Drosten, this is not a argument from authority. C. Drosten has been caught faking his credentials, his isn’t a Prof. (will be used against him in a lawsuit). P. Borger, has also made a formal request, challenging M. Koopmans to a professional/open debate regarding PCR. Now that to me shows competence and confidence, that is what science is all about.

        Your previous message: “(often using inappropriate language)?”
        Well I have been following the bunch of you, both sides use inappropriate language, let’s not point fingers. I understand the matter is important and emotion can’t be dismissed. But seeing your style of critique; which is based on emotion rather than objective rationality, is the reason I’m critiquing ‘you’ in the first pace. Since you’re main articles contain science, keep it at science.

        What is your personal statement on the RT-paper anyway? Do you claim that a team of scientists falsely found 10 methodological errors and all of them are wrong? For what? They are taking it up against powerful institutions, this isn’t a dance for fame. The authors of the Corman/Drosten-paper haven’t made a single definitive argument. Which does raise some eyebrows don’t you agree Pepijn? Please enlighten me.

        1. This getting a bit silly. As I wrote in my post, only a couple of the signees can boast some or expert knowledge of PCR (at least McKernan and Borger). One of them, Bonte, openly admits he didn’t contribute a single character to the report and fully relies on Borger for the PCR stuff.

          When you write that Drosten as faked his credentials and even that he isn’t a professor, you are totally out of line. You’ve fallen for the defamatory tricks of his opponents. How you can even think that he fakes being a professor while he is listed as such by his employer is beyond my understanding.

          That Borger challenges Koopmans for a debate shouldn’t surprise, that’s common trich for creationists. If one accepts they will shout that scientists take them seriously (not as a threat to common sense though) and that their fantasies thus equal science.

          If my opinion on this ‘retraction paper’ hasn’t become clear from this post, then let me state that to me it is utterly unconvincing. The authors might have pointed out some theoretical issues, a better PCR-test is conceivable (and in use!), but they failed to show that these potential problems do cause problems in practice as they have not shown any experimental evidence. So, to call these potential issues ‘major scientific flaws’ is laughable.

  5. So all is well with the PCR test? Also a strange conclusion that would be: Ct hardly worth mentioning? Gross manipulation to get to these vaccines does not exist? Just follow what happened in Sweden and we can see all is just like any other corono-viruses albeit a bit more serious for some. Even the CDC wrote that only 6% die of COVID-19 alone and the rest is old with, on average, 2.6 co-morbidities. Deaths overall for the year are no different. No lockdowns meant the situation would have been like Sweden: now near zero deaths for months, while the rest has to suffer this vaccine drive and economic collapse far worse than this flu-like illness.
    Authors and medics are often bought, but not Borger or Yeadon (experts is written in brackets as if this author here is the real one (yeah, like the fact checkers paid by Bill Gates). Cui bono, who profits, is what matters.

    1. This particular PCR-test is just what it is, a remarkably well-performing test considering the haste in which it was developed and the lack of actual SARS-CoV-2 samples to test it against at the time. There are now numerous other primer sets in use, some of which perform better than the ones originally proposed int the Corman-Drosten paper.

      The rest of your comments I consider off-topic on this post, so I will not address the issues you raise there.

      1. Greetings and thanks for the very interesting article.
        I need to say that while reading the Borger review, most of the thoughts I had were very similar to yours.

        Upon researching the other 21 signees I was delighted to find Fabio Franchi, a fellow Italian. He is an anti-vaxxer and Covid negationist which frequently ends up in the news for controversies.

        Anyways, I wanted to ask if you had any documentation on the new primer sets in use and any proof of their better performance. Currently debating it with a friend but I can’t seem to find any hard evidence of it.

        Happy new year and best regards!

        1. I do not know which primer sets are commonly in use at the moment. There are now many commercial kits and I don’t if there is something like a registry for the primers that those use. I think the WHO only mentions the original Charité primers and several others like the ones used in China and the ones developed by CDC.

  6. This article hasn’t said anything, instead of criticizing the researchers in question regarding the RT-paper, I would suggest you stay objective in this matter. The reason being that Euro Surveillance hasn’t made an official statement; RT-paper.

    M. Koopmans, stated publicly on radio that the PCR was not able to detect viral infection nor
    contagiousness. C. Drosten hasn’t made any rational argument either, he played Ad Hominem, by stating “Terrible. The authors’ expertise is like that of a second month piano student criticizing a concert pianist for using black keys. This cannot continue like this”. This hasn’t to do anything with science and is disrespectful by nature. Drosten sounds as a man that is under stress, which is questionable.

    1. Don’t you think it is a bit strange to suggest that we should all wait what the journal has to say about this ‘retraction paper’ while the authors constantly challenge the authors of the Carman-Drosten paper to comment on it via Social Media (often using inappropriate language)?

      On the radio, Koopmans didn’t tell anything that isn’t already widely known amongst people who took the effort to look into how PCR works and what you can do with it. It can detect viral infection, you are just not 100% whether it is still an active infection or whether you see just the remnants of a recent infection. And the question of contagiousness poses somewhat of an extra problem on top of that. Nothing new here.
      And for Drosten, you’re now just cherry-picking one tweet. He’s been informing the public since the beginning of this crisis and doing more research on PCR-tests which Borger cum suis totally ignore.

  7. From Eurosurveillance:

    We have recently received correspondence regarding a paper published this year, questioning both the content and the editorial procedures used to evaluate the article prior to publication. We can assure our readers and authors that we take comments relating to scientific content, the processing of articles and editorial transparency seriously.

  8. He wrote this down in an article in the American Journal of Biomedical Science & Research in the spring of this year. The title of the journal may sound impressive, but it turns out to be a predatory journal.

    This illustrates the important point that the customers of predatory journals are not just (a) gullible researchers who believe the spam invitations they receive, and submit their genuine papers, and (b) bad researchers who submit junk papers because they need to pump up their CVs. There are also (c) malicious denialists, promoting a political agenda, stove-piping their press-releases through journals that they know are predatory in order to have them taken seriously by the media.

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