Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic.

Reverse-transcription quantitative PCR (RT-qPCR) is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). We analysed 1927 samples collected in a local public hospital during the autumn 2020 peak of the pandemic in the Czech Republic. The tests were performed using the Seegene Allplex 2019-nCov assay, which simultaneously detects three SARS-CoV-2 genes. In all samples analysed, 44.5 % were negative for all three genes, and 37.6 % were undoubtedly positive, with all three viral genes being amplified. A high degree of correlation between values among the genes confirmed the internal consistency of testing. Most of the positive samples were detected between the 15th and 35th cycles. We also registered a small number of samples with only one (13.2 %) or two (4.7 %) amplified genes, which may have originated from either freshly infected or already recovering patients. In addition, we did not detect any potentially false-positive samples from low-prevalence settings. Our results document that PCR testing represents a reliable and robust method for routine diagnostic detection of SARS-CoV-2.