TABLE 1.

Summary of RT-PCR results for two clinical samples with suspected N gene diagnostic escape and N gene mutations detected

Assay and target region or sample name	Cycle threshold value		N gene mutationsa
	SNDE1	SNDE2
Xpert Xpress SARS-CoV-2 assay  (Cepheid, USA)
E gene	12.9	13.3
N gene	Not detected	Not detected
cobas SARS-CoV-2 test on cobas  6800 system (Roche Diagnostics,  Switzerland)
E gene	15.66	Not doneb
ORF1ab	15.46	Not doneb
RealStar SARS-CoV-2 RT-PCR kit v1.0  (altona Diagnostics GmbH,  Germany)
E gene	12.01	12.37
S gene	11.62	11.83
SNDE1			PANGO lineage (11): AY.23.1 (sublineage B.1.617.2); SNPs: A28461G, G28881T, G28916T, G29195T, G29402T; deletions/insertions: none in N gene (genome positions 28274–29533); amino acid substitutions: D63G, R203M, G215C, A308S, D377Y
SNDE2			PANGO lineage (11): AY.23.1 (sublineage B.1.617.2); SNPs: A28461G, G28881T, G28916T, G29195T, G29402T; deletions/insertions: none in N gene (genome positions 28274–29533); amino acid substitutions: D63G, R203M, G215C, A308S, D377Y

^aCompared to the reference sequence (GenBank accession number NC_045512). SNP, single-nucleotide polymorphism.

^bThere was insufficient remnant for sample SNDE2 for the Roche cobas SARS-CoV-2 test to be performed.