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RT-PCR Test to Detect SARS-CoV-2 Reveals 10 Major Scientific Flaws at the Molecular and Methodological Level: Consequences for False Positive Results
By Pieter Borger, Bobby Rajesh Malhotra, and et al.
Global Research, December 16, 2020
Corman-Drosten Review Report 27 November 2020
Url of this article:
https://www.globalresearch.ca/external-peer-review-rt-pcr-test-detect-sars-cov-2-reveals-10-major-scientific-flaws-molecular-methodological-level-consequences-false-positive-results/5730889

Abstract

In the publication entitled “Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR” (Eurosurveillance 25(8) 2020) the authors present a diagnostic workflow and RT-qPCR protocol for detection and diagnostics of 2019-nCoV (now known as SARS-CoV-2), which they claim to be validated, as well as being a robust diagnostic methodology for use in public-health laboratory settings.

In light of all the consequences resulting from this very publication for societies worldwide, a group of independent researchers performed a point-by-point review of the aforesaid publication in which 1) all components of the presented test design were cross checked, 2) the RT-qPCR protocol-recommendations were assessed w.r.t. good laboratory practice, and 3) parameters examined against relevant scientific literature covering the field.

The published RT-qPCR protocol for detection and diagnostics of 2019-nCoV and the manuscript suffer from numerous technical and scientific errors, including insufficient primer design, a problematic and insufficient RT-qPCR protocol, and the absence of an accurate test validation. Neither the presented test nor the manuscript itself fulfils the requirements for an acceptable scientific publication. Further, serious conflicts of interest of the authors are not mentioned. Finally, the very short timescale between submission and acceptance of the publication (24 hours) signifies that a systematic peer review process was either not performed here, or of problematic poor quality.  We provide compelling evidence of several scientific inadequacies, errors and flaws.

Considering the scientific and methodological blemishes presented here, we are confident that the editorial board of Eurosurveillance has no other choice but to retract the publication.

Concise Review Report

This paper will show numerous serious flaws in the Corman-Drosten paper, the significance of which has led to worldwide misdiagnosis of infections attributed to SARS-CoV-2 and associated with the disease COVID-19. We are confronted with stringent lockdowns which have destroyed many people’s lives and livelihoods, limited access to education and these imposed restrictions by governments around the world are a direct attack on people’s basic rights and their personal freedoms, resulting in collateral damage for entire economies on a global scale.

There are ten fatal problems with the Corman-Drosten paper which we will outline and explain in greater detail in the following sections.

The first and major issue is that the novel Coronavirus SARS-CoV-2 (in the publication named 2019-nCoV and in February 2020 named SARS-CoV-2 by an international consortium of virus experts) is based on in silico (theoretical) sequences, supplied by a laboratory in China [1], because at the time neither control material of infectious (“live”) or inactivated SARS-CoV-2 nor isolated genomic RNA of the virus was available to the authors. To date no validation has been performed by the authorship based on isolated SARS-CoV-2 viruses or full length RNA thereof. According to Corman et al.:

“We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.” [1]

The focus here should be placed upon the two stated aims: a) development and b) deployment of a diagnostic test for use in public health laboratory settings. These aims are not achievable without having any actual virus material available (e.g. for determining the infectious viral load). In any case, only a protocol with maximal accuracy can be the mandatory and primary goal in any scenario-outcome of this magnitude. Critical viral load determination is mandatory information, and it is in Christian Drosten’s group responsibility to perform these experiments and provide the crucial data.

Nevertheless these in silico sequences were used to develop a RT-PCR test methodology to identify the aforesaid virus. This model was based on the assumption that the novel virus is very similar to SARS-CoV from 2003 as both are beta-coronaviruses.

The PCR test was therefore designed using the genomic sequence of SARS-CoV as a control material for the Sarbeco component; we know this from our personal email-communication with [2] one of the co-authors of the Corman-Drosten paper. This method to model SARS-CoV-2 was described in the Corman-Drosten paper as follows:

the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology.”

The Reverse Transcription-Polymerase Chain Reaction (RT-PCR) is an important biomolecular technology to rapidly detect rare RNA fragments, which are known in advance. In the first step, RNA molecules present in the sample are reverse transcribed to yield cDNA. The cDNA is then amplified in the polymerase chain reaction using a specific primer pair and a thermostable DNA polymerase enzyme. The technology is highly sensitive and its detection limit is theoretically 1 molecule of cDNA. The specificity of the PCR is highly influenced by biomolecular design errors.

What is important when designing an RT-PCR Test and the quantitative RT-qPCR test described in the Corman-Drosten publication?

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Summary Catalogue of Errors Found in the Paper

The Corman-Drosten paper contains the following specific errors:

1. There exists no specified reason to use these extremely high concentrations of primers in this protocol. The described concentrations lead to increased nonspecific bindings and PCR product amplifications, making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

2. Six unspecified wobbly positions will introduce an enormous variability in the real world laboratory implementations of this test; the confusing nonspecific description in the Corman-Drosten paper is not suitable as a Standard Operational Protocol making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

3. The test cannot discriminate between the whole virus and viral fragments. Therefore, the test cannot be used as a diagnostic for intact (infectious) viruses, making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus and make inferences about the presence of an infection.

4. A difference of 10° C with respect to the annealing temperature Tm for primer pair1 (RdRp_SARSr_F and RdRp_SARSr_R) also makes the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

5. A severe error is the omission of a Ct value at which a sample is considered positive and negative. This Ct value is also not found in follow-up submissions making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

6. The PCR products have not been validated at the molecular level. This fact makes the protocol useless as a specific diagnostic tool to identify the SARS-CoV-2 virus.

7. The PCR test contains neither a unique positive control to evaluate its specificity for SARS-CoV-2 nor a negative control to exclude the presence of other coronaviruses, making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

8. The test design in the Corman-Drosten paper is so vague and flawed that one can go in dozens of different directions; nothing is standardized and there is no SOP. This highly questions the scientific validity of the test and makes it unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

9. Most likely, the Corman-Drosten paper was not peer-reviewed making the test unsuitable as a specific diagnostic tool to identify the SARS-CoV-2 virus.

10. We find severe conflicts of interest for at least four authors, in addition to the fact that two of the authors of the Corman-Drosten paper (Christian Drosten and Chantal Reusken) are members of the editorial board of Eurosurveillance. A conflict of interest was added on July 29 2020 (Olfert Landt is CEO of TIB-Molbiol; Marco Kaiser is senior researcher at GenExpress and serves as scientific advisor for TIB-Molbiol), that was not declared in the original version (and still is missing in the PubMed version); TIB-Molbiol is the company which was “the first” to produce PCR kits (Light Mix) based on the protocol published in the Corman-Drosten manuscript, and according to their own words, they distributed these PCR-test kits before the publication was even submitted [20]; further, Victor Corman & Christian Drosten failed to mention their second affiliation: the commercial test laboratory “Labor Berlin”. Both are responsible for the virus diagnostics there [21] and the company operates in the realm of real time PCR-testing.

In light of our re-examination of the test protocol to identify SARS-CoV-2 described in the Corman-Drosten paper we have identified concerning errors and inherent fallacies which render the SARS-CoV-2 PCR test useless.

Conclusion

The decision as to which test protocols are published and made widely available lies squarely in the hands of Eurosurveillance. A decision to recognise the errors apparent in the Corman-Drosten paper has the benefit to greatly minimise human cost and suffering going forward.

Is it not in the best interest of Eurosurveillance to retract this paper? Our conclusion is clear. In the face of all the tremendous PCR-protocol design flaws and errors described here, we conclude: There is not much of a choice left in the framework of scientific integrity and responsibility.

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Authors

1) Dr. Pieter Borger (MSc, PhD), Molecular Genetics, W+W Research Associate, Lörrach, Germany 

2) Rajesh Kumar Malhotra (Artist Alias: Bobby Rajesh Malhotra), Former 3D Artist / Scientific Visualizations at CeMM – Center for Molecular Medicine of the Austrian Academy of Sciences (2019-2020), University for Applied Arts – Department for Digital Arts Vienna, Austria

3) Dr. Michael Yeadon BSs(Hons) Biochem Tox U Surrey, PhD Pharmacology U Surrey. Managing Director, Yeadon Consulting Ltd, former Pfizer Chief Scientist, United Kingdom 

4) Dr. Clare Craig MA, (Cantab) BM, BCh (Oxon), FRCPath, United Kingdom

5) Kevin McKernan, BS Emory University, Chief Scientific Officer, founder Medical Genomics, engineered the sequencing pipeline at WIBR/MIT for the Human Genome Project, Invented and developed the SOLiD sequencer, awarded patents related to PCR, DNA Isolation and Sequencing, USA

6) Prof. Dr. Klaus Steger, Department of Urology, Pediatric Urology and Andrology, Molecular Andrology, Biomedical Research Center of the Justus Liebig University, Giessen, Germany

7) Dr. Paul McSheehy (BSc, PhD), Biochemist & Industry Pharmacologist, Loerrach, Germany

8) Dr. Lidiya Angelova, MSc in Biology, PhD in Microbiology, Former researcher at the National Institute of Allergy and Infectious Diseases (NIAID), Maryland, USA

9) Dr. Fabio Franchi, Former Dirigente Medico (M.D) in an Infectious Disease Ward, specialized in “Infectious Diseases” and “Hygiene and Preventive Medicine”, Società Scientifica per il Principio di Precauzione (SSPP), Italy

10) Dr. med. Thomas Binder, Internist and Cardiologist (FMH), Switzerland

11) Prof. Dr. med. Henrik Ullrich, specialist Diagnostic Radiology, Chief Medical Doctor at the Center for Radiology of Collm Oschatz-Hospital, Germany

12) Prof. Dr. Makoto Ohashi, Professor emeritus, PhD in Microbiology and Immunology, Tokushima University, Japan

13) Dr. Stefano Scoglio, B.Sc. Ph.D., Microbiologist, Nutritionist, Italy

14) Dr. Marjolein Doesburg-van Kleffens (MSc, PhD), specialist in Laboratory Medicine (clinical chemistry), Maasziekenhuis Pantein, Beugen, The Netherlands

15) Dr. Dorothea Gilbert (MSc, PhD), PhD Environmental Chemistry and Toxicology. DGI Consulting Services, Oslo, Norway

16) Dr. Rainer J. Klement, PhD. Department of Radiation Oncology, Leopoldina Hospital Schweinfurt, Germany

17) Dr. Ruth Schruefer, PhD, human genetics/ immunology, Munich, Germany, 

18) Dra. Berber W. Pieksma, General Practitioner, The Netherlands

19) Dr. med. Jan Bonte (GJ), Consultant Neurologist, The Netherlands

20) Dr. Bruno H. Dalle Carbonare (Molecular biologist), IP specialist, BDC Basel, Switzerland

21) Dr. Kevin P. Corbett, MSc Nursing (Kings College London) PhD (London South Bank) Social Sciences (Science & Technology Studies) London, England, United Kingdom

22) Prof. Dr. Ulrike Kämmerer, specialist in Virology / Immunology / Human Biology / Cell Biology, University Hospital Würzburg, Germany

Notes

[1] Corman Victor M, Landt Olfert, Kaiser Marco, Molenkamp Richard, Meijer Adam, Chu Daniel KW, Bleicker Tobias, Brünink Sebastian, Schneider Julia, Schmidt Marie Luisa, Mulders Daphne GJC, Haagmans Bart L, van der Veer Bas, van den Brink Sharon, Wijsman Lisa, Goderski Gabriel, Romette Jean-Louis, Ellis Joanna, Zambon Maria, Peiris Malik, Goossens Herman, Reusken Chantal, Koopmans Marion PG, Drosten Christian. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):pii=2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045

[2] Email communication between Dr. Peter Borger & Dr. Adam Meijer: Supplementary Material

[3] Jafaar et al., Correlation Between 3790 Quantitative Polymerase Chain Reaction–Positives Samples and Positive Cell Cultures, Including 1941 Severe Acute Respiratory Syndrome Coronavirus 2 Isolates. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1491/5912603

[4] BBC, January 21st 2020: https://www.bbc.com/news/world-asia-china-51185836;
Archive: https://archive.is/0qRmZ

[5] Google Analytics – COVID19-deaths worldwide: https://bit.ly/3fndemJ
Archive: https://archive.is/PpqEE

[6] Laboratory testing for COVID-19 Emergency Response Technical Centre, NIVD under
China CDC March 15th, 2020: http://www.chinacdc.cn/en/COVID19/202003/P020200323390321297894.pdf

[7] Real-Time PCR Handbook Life Technologies: https://www.thermofisher.com/content/dam/LifeTech/global/Forms/PDF/real-time-pcr-
handbook.pdf

Nolan T, Huggett J, Sanchez E.Good practice guide for the application of quantitative PCR (qPCR) First Edition 2013

[8] Trestan Pillonel et al, Letter to the editor: SARS-CoV-2 detection by real-time RT-PCR: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268274/

[9] Kurkela, Satu, and David WG Brown. “Molecular-diagnostic techniques.” Medicine 38.10
(2009): 535-540.

[10] Wolfel et al., Virological assessment of hospitalized patients with COVID-2019
https://www.nature.com/articles/s41586-020-2196-x

[11] Thermofischer Primer Dimer Web Tool: https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/multiple-primer-analyzer.html

Supplementary Material

[12] Primer-BLAST, NCBI – National Center for Biotechnology Information: https://www.ncbi.nlm.nih.gov/tools/primer-blast/

[13] Marra MA, Steven JMJ, Caroline RA, Robert AH, Angela BW et al. (2003) Science. The
Genome sequence of the SARS-associated coronavirus. Science 300(5624): 1399-1404.

[14] Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete
genome: https://www.ncbi.nlm.nih.gov/nuccore/MN908947

[15] Borger P. A SARS-like Coronavirus was expected but nothing was done to be prepared. Am J Biomed Sci Res 2020. https://biomedgrid.com/pdf/AJBSR.MS.ID.001312.pdf
https://www.researchgate.net/publication/341120750_A_SARS-
like_Coronavirus_was_Expected_but_nothing_was_done_to_be_Prepared
;

Archive: https://archive.is/i76Hu

[16] Eurosurveillance paper evaluation / review process: https://www.eurosurveillance.org/evaluation

[17] Official recommendation of the Corman-Drosten protocol & manuscript by the WHO,published on January 13th 2020 as version 1.0 of the document:
https://www.who.int/docs/default-source/coronaviruse/wuhan-virus-assay-
v1991527e5122341d99287a1b17c111902.pdf
; archive: https://bit.ly/3m3jXVH

[18] Official WHO-recommendation for the Corman / Drosten RT-qPCR-protocol, which
directly derives from the Eurosurveillance-publication, document-version 2-1, published on
17th January 2020: https://www.who.int/docs/default-source/coronaviruse/protocol-v2-
1.pdf?sfvrsn=a9ef618c_2

[19] Eurosurveillance Editorial Board, 2020: https://www.eurosurveillance.org/upload/site-
assets/imgs/2020-09-Editorial%20Board%20PDF.pdf
;

Archive: https://bit.ly/2TqXBjX

[20] Instructions For Use LightMix SarbecoV E-gene plus EAV Control, TIB-Molbiol & Roche
Molecular Solutions, January 11th 2020: https://www.roche-as.es/lm_pdf/MDx_40-0776_96_Sarbeco-E-
gene_V200204_09164154001 (1).pdf

Archive, timestamp – January 11th 2020: https://archive.is/Vulo5;
Archive: https://bit.ly/3fm9bXH

[21] Christian Drosten & Victor Corman, responsible for viral diagnostics at Labor Berlin:
https://www.laborberlin.com/fachbereiche/virologie/
Archive: https://archive.is/CDEUG

[22] Tom Jefferson, Elizabeth Spencer, Jon Brassey, Carl Heneghan Viral cultures for COVID-
19 infectivity assessment. Systematic review. Systematic review doi:
https://doi.org/10.1101/2020.08.04.20167932 https://www.medrxiv.org/content/10.1101/2020.08.04.20167932v4

[23] Kim et al.,The Architecture of SARS-CoV-2 Transcriptome:
https://www.sciencedirect.com/science/article/pii/S0092867420304062

[24] ECDC reply to Dr. Peter Borger, 18th November 2020:
Supplementary Material

[25] Prof. Dr. Ulrike Kämmerer & team, survey & Primer-BLAST table:
Supplementary Material

Disclaimer: The contents of this article are of sole responsibility of the author(s). The Centre for Research on Globalization will not be responsible for any inaccurate or incorrect statement in this article.