SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay

Steven C. Holland, Ajeet Bains, Larinda A. Holland, Matthew F. Smith, Regan A. Sullins, Nicholas J. Mellor, Alexis W. Thomas, Nathaniel Johnson, Vel Murugan, Efrem S. Lim

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRTPCR diagnostic assays. We investigated four polymorphisms circulating in the SARS-CoV-2 Delta lineage that result in N gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutations were detected from the SARS-CoV-2 genome sequences that matched with the diagnostic assay results of saliva specimens. Full length N genes from the samples displaying NGTF were cloned into plasmids and assayed using three SARS-CoV-2 qRT-PCR assays. These constructs resulted in reduced sensitivity to the TaqPath COVID-19 Combo Kit compared to the controls (mean Ct differences of 3.06, 7.70, 12.46, and 14.12), but were detected equivalently on the TaqPath COVID-19 Fast PCR Combo 2.0 or CDC 2019_nCoV_N2 assays. This work highlights the importance of genomic sequencing to monitor circulating mutations and provide guidance in improving diagnostic assays.

Original languageEnglish (US)
Article number1316
JournalViruses
Volume14
Issue number6
DOIs
StatePublished - Jun 2022

Keywords

  • COVID-19
  • N gene dropout
  • SARS-CoV-2
  • delta variant
  • qRT-PCR

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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