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

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.…

Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay

“…This study is the first to undertake sequencing of the Xpert amplicons to confirm the mutations responsible for the failure of the N gene RT-qPCR targets in the GeneXpert system; both mutations identified in this study have previously been reported ( 8 – 10 ). As the primers and probe sequences used by the Xpert assay are not publicly available, the amplified products of the Xpert assay were sequenced to identify the targets.…”

“…Analysis of these sequences using the GISAID database showed them to be closely related to sequences isolated in Colorado, USA. Rhoads et al ( 9 ) and Leelawong et al ( 8 ) also identified the C29197T mutation in cases from Ohio and New York, respectively. The C29197T mutation accounts for approximately 0.01% of all sequences uploaded to the GISAID EpiCoV database as of June 2021.…”

“…At present, three mutations have been identified in the N gene that likely result in N gene target detection failures in the Xpert assay; C29197T ( 8 , 9 ), C29200T ( 10 ), and C29200A ( 7 ). All three mutations affect the poly C region within the probe binding region of the U.S. CDC 2019_nCoV_N2 target, indicating that mutations in this region may be associated with poor probe performance.…”

“…In this report, we describe two independent single-point mutations in the N gene of SARS-CoV-2 that adversely affect the amplification of the N2 target in the Xpert assay. The first mutation, C29200T ( 10 ), was found in eight patients, and the second, C29197T ( 8 , 9 ), was found in five patients. Sequencing of the Xpert amplicons confirmed the location of both mutations to be within the amplified region of the Xpert N gene target.…”

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance

“…Further, data from the UK have led to an estimated 61% higher hazard of death associated with B.1.1.7 infections compared to non-B.1.1.7 infections ( 14 ). While generally not present in the currently recognized VOCs, a synonymous mutation in the N gene of SARS-CoV-2 leading to detection failure of that target in a popular commercial assay was found in 18% of sequenced samples in a region in California ( 15 ). These findings highlight the need for the timely detection of these variants for their management.…”