A RT-qPCR test targeting the conserved 5´-UTR of SARS-CoV-2 overcomes major shortcomings of the first WHO-recommended RT-qPCR test

For the first time in medical history, the result of a laboratory assay (RT-qPCR) was used as the sole criterion to diagnose a disease (Covid-19) without any rating of clinical symptoms and to justify the implementation of population-wide non-pharmaceutical interventions during virus season. The aim of this study is (1) to evaluate a robust RT-qPCR test that overcomes major 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 NGS and (3) to re-initiate the currently missing scientific dialogue and return to reason and evidence-based medicine. We present a RT-qPCR test designed for the detection of all SARS-CoV-2 variants known so far.  Based on the genomic mutation profile, we demonstrate that the three individual waves culminating from autumn 2020 to spring 2021 in the Czech Republic 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. In addition, we provide evidence that neglected principles of good scientific practice resulted not only in the publication of the WHO-recommended Charité RT-qPCR protocol, but also in health-related problems. Unnecessary quarantine of false positive-tested, 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.” Further, some chain of infection caused by false negative-tested, symptomatic individuals lead to real Covid-19 clusters. Both our results and literature data confirm that validation of any PCR-based diagnostic test by sequencing is mandatory on a regular basis. To prevent future misconduct, science needs a reality check and must re-initiate the scientific dialogue and liberate itself from political influence and dogma.