Article ; Online: SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay.
2021 Volume 27, Issue 9, Page(s) 1353.e1–1353.e5
Abstract: ... dropout or Ct value shift compared with the S or RdRp gene.: Methods: VOC B.1.1.7 and non-B.1.1.7 SARS ... quantitative real-time PCR (qRT-PCR) assay can identify SARS-CoV-2 B.1.1.7 lineage samples by a specific N gene ... corresponding to D3 or 3L variants.: Discussion: An N gene dropout or Ct value shift is shown for B.1.1.7 ...
| Abstract | Objectives: Detection and surveillance of SARS-CoV-2 is of eminent importance, particularly due to the rapid emergence of variants of concern (VOCs). In this study we evaluated if a commercially available quantitative real-time PCR (qRT-PCR) assay can identify SARS-CoV-2 B.1.1.7 lineage samples by a specific N gene dropout or Ct value shift compared with the S or RdRp gene. Methods: VOC B.1.1.7 and non-B.1.1.7 SARS-CoV-2-positive patient samples were identified via whole-genome sequencing and variant-specific PCR. Confirmed B.1.1.7 (n = 48) and non-B.1.1.7 samples (n = 58) were analysed using the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay for presence of SARS-CoV-2 S, RdRp and N genes. The N gene coding sequence of SARS-CoV-2 with and without the D3L mutation (specific for B.1.1.7) was cloned into pCR™II-TOPO™ vectors to validate polymorphism-dependent N gene dropout with the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay. Results: All studied B.1.1.7-positive patient samples showed significantly higher Ct values in qRT-PCR (Δ6-10, N gene dropout on Ct values > 29) of N gene than the corresponding values of S (p ≤ 0.0001) and RdRp (p ≤ 0.0001) genes. The assay reliably discriminated B.1.1.7 and non-B.1.1.7 positive samples (area under the curve = 1) in a receiver operating characteristic curve analysis. Identical Ct value shifts (Δ7-10) were detected in reverse genetic experiments, using isolated plasmids containing N gene coding sequences corresponding to D3 or 3L variants. Discussion: An N gene dropout or Ct value shift is shown for B.1.1.7-positive samples in the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay. This approach can be used as a rapid tool for B.1.1.7 detection in single assay high throughput diagnostics. |
|---|---|
| MeSH term(s) | COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing ; Coronavirus Nucleocapsid Proteins/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Multiplex Polymerase Chain Reaction ; Mutation ; ROC Curve ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Sensitivity and Specificity ; Whole Genome Sequencing/methods |
| Chemical Substances | Coronavirus Nucleocapsid Proteins |
| Language | English |
| Publishing date | 2021-05-24 |
| Publishing country | England |
| Document type | Journal Article |
| ZDB-ID | 1328418-6 |
| ISSN | 1469-0691 ; 1470-9465 ; 1198-743X |
| ISSN (online) | 1469-0691 |
| ISSN | 1470-9465 ; 1198-743X |
| DOI | 10.1016/j.cmi.2021.05.025 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
More links
Kategorien
In stock of ZB MED Cologne/Königswinter
| Zs.A 4541: Show issues | Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG) |
|||
| Zs.MO 284: Show issues |
Order via subito
This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.