A recurrent mutation at position 1 26,340 of SARS-CoV-2 is associated with failure of the E-gene qRT-PCR utilized in a commercial dual-target diagnostic assay

Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
pandemic requires accurate laboratory testing to identify infected individuals, while also
clearing essential staff to continue work. At the current time a number of qRT-PCR assays
have been developed to identify SARS-CoV-2, targeting multiple positions in the viral
genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of
transmission chains it is prudent to monitor circulating viruses for variants that might
compromise these assays. Here we report the identification of a C-to-U transition at
position 26,340 of the SARS-CoV-2 genome which is associated with failure of the cobas®
SARS-CoV-2 E-gene qRT-PCR in eight patients. As the cobas® SARS-CoV-2 assay
targets two positions in the genome, the individuals carrying this variant were still called as
SARS-CoV-2 positive. Whole genome sequencing of SARS-CoV-2 showed all to carry
closely related viruses. Examination of viral genomes deposited on GISAID showed this
mutation has arisen independently at least four times. This work highlights the necessity of
monitoring SARS-CoV-2 for the emergence of SNPs which might adversely affect RT
PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.