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 widely used commercial multiplex PCR assay

  1. P Wollschlaeger
  2. N Gerlitz
  3. D Todt
  4. S Pfaender
  5. T Bollinger
  6. A Sing
  7. A Dangel
  8. N Ackermann
  9. K Korn
  10. A Ensser
  11. E Steinmann
  12. M Buhl
  13. J Steinmann
1 evaluations Published on
Read the full article Related papers
This article on Sciety

Abstract

Objectives

Increased importance in detection and surveillance of SARS-CoV-2 has been demonstrated due to the emergence of variants of concern (VOCs). In this study we evaluated if a commercially available real-time SARS-CoV-2 PCR assay can identify B.1.1.7 lineage samples by a specific N gene dropout or Ct value shift compared to the S or RdRP gene.

Methods

Patients samples with confirmed B.1.1.7 variant by whole-genome sequencing and variant-specific PCR (n=48) and non-B.1.1.7 samples (n=53) were tested by the Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay for presence of S, RdRP and N gene of SARS CoV-2. The N gene coding sequence of SARS-CoV-2 with and without D3L mutation (specific for B.1.1.7) were cloned into pCR®-TOPO vectors and Allplex™ SARS-CoV-2/FluA/FluB/RSV™ PCR assay was performed.

Results

All studied B.1.1.7 patient samples showed significantly higher Ct values (Δ 6-10, N-gene dropout on Ct values >29) in the N gene compared to the respective values of S and RdRP gene. Receiver operating characteristic (ROC) curve analysis resulted in 100% sensitivity and specificity for ΔCt N/RdRP and ΔCt N/S. As a result of the reversed genetic experiments we found also the shift in Ct values for the 3L variant N-gene.

Conclusions

N gene dropout or Ct value shift is specific for B.1.1.7 positive samples using 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.

Related articles

Related articles are currently not available for this article.