SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay
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 <i>N</i> gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutatio...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/6/1316 |
| _version_ | 1797481328896114688 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Steven C. Holland |
| collection | DOAJ |
| description | 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 <i>N</i> 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 <i>N</i> 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 C<sub>t</sub> 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. |
| first_indexed | 2024-03-09T22:12:58Z |
| format | Article |
| id | doaj.art-1cfaf753e9f84c58a84062e107cb5bf4 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T22:12:58Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-1cfaf753e9f84c58a84062e107cb5bf42023-11-23T19:27:19ZengMDPI AGViruses1999-49152022-06-01146131610.3390/v14061316SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic AssaySteven C. Holland0Ajeet Bains1LaRinda A. Holland2Matthew F. Smith3Regan A. Sullins4Nicholas J. Mellor5Alexis W. Thomas6Nathaniel Johnson7Vel Murugan8Efrem S. Lim9Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USACenter for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USAAs 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 <i>N</i> 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 <i>N</i> 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 C<sub>t</sub> 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.https://www.mdpi.com/1999-4915/14/6/1316SARS-CoV-2COVID-19delta variantN gene dropoutqRT-PCR |
| spellingShingle | 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 SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay Viruses SARS-CoV-2 COVID-19 delta variant N gene dropout qRT-PCR |
| title | SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay |
| title_full | SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay |
| title_fullStr | SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay |
| title_full_unstemmed | SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay |
| title_short | SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay |
| title_sort | sars cov 2 delta variant n gene mutations reduce sensitivity to the taqpath covid 19 multiplex molecular diagnostic assay |
| topic | SARS-CoV-2 COVID-19 delta variant N gene dropout qRT-PCR |
| url | https://www.mdpi.com/1999-4915/14/6/1316 |
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