Application of Metagenomic Next-Generation Sequencing (mNGS) and real-time RT-PCR Using different nasopharyngeal swabs in Diagnosing SARS-CoV-2 Omicron

Abstract

Abstract Background: The Omicron variant, which main types was BA5.2and BF.7 in China, in December 2022 to January 2023 leaded to off-target of the S and N genes, and the kits used were not adequately and independently evaluated when these agents are studied and developed. To ensure the accuracy of coronavirus test results, performance verification of commercial Real-Time quantitative PCR (RT-qPCR) was required. Objective: We performed a clinical evaluation for two Real Time SARS-CoV-2 assay, and to verify them based on different detection reagents and different clinical specimens. Methods: We performed clinical evaluations of two existing Chinese SARS-CoV-2 RT-qPCR kits COVID-19 nucleic acid detection kits (e-Diagnostic Biomedical, Wuhan, China) and 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, Shanghai, China) using BSD ( Bondson) (Guangzhou Bondson Biotechnology Co. Ltd.;batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens. Results: The coincidence rate for Fosun and e-Diagnostic kits were individually 95% and 100%. Verified that the detection limit for Fosun and e-Diagnostic kits was 300copies/mL. All were below the detection limit for Fosun reagent was 300copies/mL. e-Diagnostic was 500copies/mL. Fosun had the largest CV for ORF1ab and N gene at the the detection limit concentration(4.80%,3.49%), while e-Diagnostic had the smaller (0.93%,1.10%). Negative results were tested in cross-reactivity. During the verification of clinical samples, sequencing analyses had shown that Fosun single gene miss rate was relatively high, especially ORF1ab, followed by N gene miss rate. we survey that all N genes were detected in clinical specimens, ,ORFab dropout (i.e., a negative/low result) occurred in (10.8%) of 225 Omicron variant. Conclusions: Our results endorse the use of these two commercial kits for the diagnosis of SARS-CoV-2 in China, as their clinical performance has been fully validated by a large number of clinically confirmed cases.