SARS-CoV-2 E gene variant alters analytical sensitivity characteristics of viral detection using a commercial RT-PCR assay.

Diagnostic assays for detecting SARS-CoV-2 are essential for patient management, infection prevention, and the public health response for COVID-19. The efficacy and reliability of these assays are of paramount importance in both tracking and controlling spread of the virus. Real-time RT-PCR assays rely on a fixed genetic sequence for primers and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Herein, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results.