Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR
Manu Vanaerschot, Sabrina A Mann, James T. Webber, Jack Kamm, Sidney M. Bell, John Bell, Si Noon Hong, Minh Phương Nguyễn, Lienna Y. Chan, Karan Bhatt, Michelle Tan, Angela M. Detweiler, Alex Espinosa, Wesley Wu, Joshua Batson, David Dynerman, Debra A. Wadford, Andreas S. Puschnik, Norma Neff, Vida Ahyong, Steve Miller, Patrick Ayscue, Cristina M. Tato, Simon Paul, Amy Kistler, Joseph L. DeRisi, Emily Crawford
Abstract
Since 7 April 2020, our coronavirus disease 2019 (COVID-19) diagnostic laboratory (CLIAHUB) has received samples from multiple counties in California. Our reverse transcriptase PCR (RT-PCR) protocol (1) employs N-gene (NIID_2019-nCov_N_F2/R2ver3/P2 [Japan]) (2) and E-gene (E_Sarbeco_F/R/P1 [Germany]) (3) simplex assays. In July 2020, we identified 40+ samples from Madera County with poor N-gene assay performance relative to the E-gene assay.