Major Shortcomings of the First Who-Recommended RT-QPCR to 'Detect' SARS-CoV-2 and to 'Diagnose' COVID-19. NGS Provides Evidence that Successive Waves of SARS-CoV-2 Variants Lack Genomic Relationship

Abstract

Introduction: For the first time in medical history, the result of a laboratory assay, here RT-qPCR, was used as the sole criterion to diagnose a disease, namely Covid-19, without any rating of clinical symptoms and to justify the implementation of population-wide non-pharmaceutical interventions during virus season.

Objectives: (1) To summarize concerns raised within the scientific community on the first WHO-recommended RT-qPCR protocol to detect SARS-CoV-2 sequences; (2) To genomically characterize individual SARS-CoV-2 strains circulating in the Czech Republic from autumn 2020 to spring 2021 applying next generation sequencing; (3) To re-initiate the currently missing scientific dialogue and return to reason and evidence-based medicine.

Results: Neglected principles of good scientific practice resulted not only in the publication of the WHO-recommended Charité RT-qPCR protocol, but also in multiple health-related problems. On the one hand, unnecessary quarantine of false positive-tested, but healthy individuals, as well as lockdowns and atrocious collateral damage on societies and economies worldwide due to a high number of false-positive 'PCR-cases.' On the other hand, some chain of infection caused by false negative-tested, but symptomatic individuals lead to real Covid-19 clusters. Based on the genomic mutation profile of SARS-CoV-2, we were able to demonstrate that the three individual waves culminating from autumn 2020 to spring 2021 were successive, but lacked direct genomic relationship between each other. This became obvious with the omicron variant, which did not reveal direct evolutionary connection to any of the previous SARS-CoV-2 variants.

Conclusions: Both our own results and data from available literature confirmed that validation of any PCR-based diagnostic test by sequencing is mandatory, not only during the initial phase of establishment, but also on a regular basis during the following time. To prevent future misconduct, science needs a reality check and must re-initiate the scientific dialogue and liberate itself from political influence and dogma.

Funding Information: RL has been funded by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 883441, project STAMINA (Demonstration of intelligent decision support for pandemic crisis prediction and management within and across European borders). All other authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

Declaration of Interests: RL, Erasmus MC and BioCoS, has signed a joint ownership agreement related to SARS-CoV-2 detection methods. All other authors declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work.

Ethics Approval Statement: Samples for routine molecular diagnostics were taken upon informed consent and due to governmental legal directive in regards to the Covid-19 pandemic testing strategy, issued and archived by the referring Clinics. Anonymized samples were processed in accordance with the Declaration of Helsinki.

Keywords: Charité protocol, COVID-19, next generation sequencing (NGS), RT-qPCR, SARS-CoV-2, scientific misconduct