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Case Reports
. 2020 Oct;25(39):2001650.
doi: 10.2807/1560-7917.ES.2020.25.39.2001650.

SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene

Katharina Ziegler  1   2 , Philipp Steininger  1 , Renate Ziegler  2 , Jörg Steinmann  2 , Klaus Korn  1 , Armin Ensser  1
Affiliations
Case Reports

SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene

Katharina Ziegler et al. Euro Surveill. 2020 Oct.

Abstract

We found that a single nucleotide polymorphism (SNP) in the nucleoprotein gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a patient interfered with detection in a widely used commercial assay. Some 0.2% of the isolates in the EpiCoV database contain this SNP. Although SARS-CoV-2 was still detected by the other probe in the assay, this underlines the necessity of targeting two independent essential regions of a pathogen for reliable detection.

Keywords: SARS-CoV-2; diagnostic quantitative RT-PCR, single nucleotide polymorphism.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Mutations in the nucleoprotein gene of a SARS-CoV-2 patient virus and strategy to reveal the mutation responsible for loss of detection in the Xpert Xpress SARS-CoV-2 assay, Germany, July 2020
Figure 2
Figure 2
Number of SARS-CoV-2 sequences in the GISAID database and frequency of the C29200T SNP, by month of isolation, December 2019–August 2020 (n = 104,242)
See this image and copyright information in PMC

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