RT-PCR Test Targeting the Conserved 5'-UTR of SARS-CoV-2 Overcomes Shortcomings of the First WHO-Recommended RT-PCR Test

Abstract

For the first time in medical history, a laboratory assay (RT-PCR) was used as the sole criterion to diagnose a disease (COVID-19) and to define infectivity of a virus (SARS-CoV-2) without rating clinical symptoms and proof of replication-competent virus to justify implementing population-wide, untested interventions. The aims here are (1) to evaluate a robust quantitative RT-PCR (RT-qPCR) protocol that overcomes major concerns raised within the scientific community on the first WHO-recommended RT-qPCR protocol for SARS-CoV-2 sequences, (2) to characterize individual SARS-CoV-2 strains circulating in the Czech Republic from autumn 2020 to spring 2021 applying next generation sequencing and (3) to re-initiate 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 without producing false-positives. Based on the genomic mutation profile, we demonstrate that the three individual waves (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 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.” Otherwise, infectious symptomatic individuals were given a false sense of security by false-negative test results, which could lead to 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.