SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay

Hilti, Dominique; Wehrli, Faina; Roditscheff, Anna; Risch, Martin; Risch, Lorenz; Egli, Adrian; Bodmer, Thomas; Wohlwend, Nadia

doi:10.3390/pathogens12121383

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Hilti, D., Wehrli, F., Roditscheff, A., Risch, M., Risch, L., Egli, A., Bodmer, T., & Wohlwend, N. (2023). SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay. Pathogens, 12(12), 1383. https://doi.org/10.3390/pathogens12121383

Abstract

At the end of 2021, we observed an increase in N-gene target failures (NGTF) with the TaqPathTM COVID-19 CE-IVD RT-PCR Kit from Thermo Fisher Scientific (TaqPath). We subsequently used whole-genome sequencing (Oxford Nanopore Technology) to identify potential issues with N-gene PCR efficacy. Among 168,101 positive samples with a cycle threshold (CT) value <30 from August 2021 to May 2022, 194 specimens without N-gene amplification by PCR were identified (0.12%). Most NGTF samples originated from a wave of infection attributable to the