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Article

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

1
Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
2
Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
3
School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Judd F. Hultquist, Ramón Lorenzo-Redondo and Egon Anderson Ozer
Viruses 2022, 14(6), 1316; https://doi.org/10.3390/v14061316
Received: 26 April 2022 / Revised: 10 June 2022 / Accepted: 14 June 2022 / Published: 16 June 2022
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRT-PCR 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. View Full-Text
Keywords: SARS-CoV-2; COVID-19; delta variant; N gene dropout; qRT-PCR SARS-CoV-2; COVID-19; delta variant; N gene dropout; qRT-PCR
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MDPI and ACS Style

Holland, S.C.; Bains, A.; Holland, L.A.; Smith, M.F.; Sullins, R.A.; Mellor, N.J.; Thomas, A.W.; Johnson, N.; Murugan, V.; Lim, E.S. SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay. Viruses 2022, 14, 1316. https://doi.org/10.3390/v14061316

AMA Style

Holland SC, Bains A, Holland LA, Smith MF, Sullins RA, Mellor NJ, Thomas AW, Johnson N, Murugan V, Lim ES. SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay. Viruses. 2022; 14(6):1316. https://doi.org/10.3390/v14061316

Chicago/Turabian Style

Holland, Steven C., Ajeet Bains, LaRinda A. Holland, Matthew F. Smith, Regan A. Sullins, Nicholas J. Mellor, Alexis W. Thomas, Nathaniel Johnson, Vel Murugan, and Efrem S. Lim. 2022. "SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay" Viruses 14, no. 6: 1316. https://doi.org/10.3390/v14061316

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