Endemic SARS-CoV-2 Polymorphisms Can Cause a Higher Diagnostic Target Failure Rate than Estimated by Aggregate Global Sequencing Data
Daniel D. Rhoads, David Plunkett, Joy Nakitandwe, Andrew Dempsey, Zheng Jin Tu, Gary W. Procop, David Bosler, Brian P. Rubin, Michael J. Loeffelholz, Jay E. Brock
Abstract
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).