Endemic SARS-CoV-2 Polymorphisms Can Cause a Higher Diagnostic Target Failure Rate than Estimated by Aggregate Global Sequencing Data

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to mutate during the ongoing COVID-19 pandemic, and some of the nucleotide polymorphisms may result in diagnostic detection failures. Documented polymorphisms resulting in partial failure of diagnostic assays include g.26340C>T resulting in E gene target failure on the Roche (Indianapolis, IN) cobas 6800/8800 assay (1), g.21765_21770 deletion resulting in S gene target failure (SGTF) on the Thermo Fisher (Carlsbad, CA) TaqPath assay that is associated with the B.1.1.7 and other lineages (2, 3), and g.29200C>W resulting in N gene target failure (NGTF) on the Cepheid Xpert assays (4, 5).