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.
Update 4 February 2021: Eurosurveillance rejects the request for retraction.
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:
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 [archived copy]) 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 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:
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.
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:
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.
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 Microbiology, 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!
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.
[*] 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?
Update 4/2/2021: Eurosurveillance rejects the request for retraction. The response addresses the rapid peer review and states following the advice from five independent experts, that were consulted:
The consulted experts confirmed that the Corman et al. article was scientifically adequate for its purpose and for the limited data and material available at this early stage in the COVID-19 pandemic. Any laboratory deciding to use the primers and protocol suggested in this article would ascertain the assay for its fitness for purpose and compliance with local quality and accreditation requirements; this is what has happened worldwide since the publication of the article. With more data and evolving knowledge, laboratories have since further improved the initial method, as per usual practice.
Added on 9 February 2021
Two of the authors of the ‘retraction paper’, Kevin McKernan and Bobby Malhotra, gave very misleading information on the Corman-Drosten protocol to Naomi Wolf in an interview that she published on YouTube on 24 January 2021. Here some fragments with my commentary:
A far more detailed analysis can be found in Frank Visser’s most recent contribution part of his series titled ‘The Corona Conspiracy’: Part 24: PCR-Gate 2: When Lockdown Skeptics Pose as Expert Scientists.