Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay

Stephanie Popping; Richard Molenkamp; Joachim D. Weigel; Pim G.N.J. Mutsaers; Jolanda C. Voermans; Sander van Boheemen; Marc C. Shamier; Reina S. Sikkema; David F. Nieuwenhuijse; Bas B. Oude Munnink; Marion P.G. Koopmans; Jeroen J.A. van Kampen

doi:10.1016/j.jviromet.2021.114397

Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay

Stephanie Popping^*, Richard Molenkamp, Joachim D. Weigel, Pim G.N.J. Mutsaers, Jolanda C. Voermans, Sander van Boheemen, Marc C. Shamier, Reina S. Sikkema, David F. Nieuwenhuijse, Bas B. Oude Munnink, Marion P.G. Koopmans, Jeroen J.A. van Kampen

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

8 Citations (Scopus)

Abstract

Here we describe a SARS-CoV-2 variant with diminished amplification of the ORF ORF1ab target in the Cobas® dual-target SARS-CoV-2 assay resulting in a discrepancy of Ct-values (Ct-value 20.7 for the E-gene and Ct-value 30.2 for ORF1ab). Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). This case highlights the importance of surveillance of genomic regions used in molecular diagnostics and the importance of the public release of target regions used to update commercial and in-house developed SARS-CoV-2 PCR tests. This work underpins the importance of using dual-targets in molecular diagnostic assays to limit the change of false-negative results due to primer and/or probe mismatches.

Original language	English
Article number	114397
Journal	Journal of Virological Methods
Volume	300
DOIs	https://doi.org/10.1016/j.jviromet.2021.114397
Publication status	Published - Feb 2022

Bibliographical note

Funding Information:
SP: received financial support from Gilead Sciences outside of the submitted work.

Funding Information:
Sequencing was funded by ZonMW (grant agreement no: 10150062010005 ).

Publisher Copyright:
© 2021

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10.1016/j.jviromet.2021.114397

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634734/

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Popping, S., Molenkamp, R., Weigel, J. D., Mutsaers, P. G. N. J., Voermans, J. C., van Boheemen, S., Shamier, M. C., Sikkema, R. S., Nieuwenhuijse, D. F., Oude Munnink, B. B., Koopmans, M. P. G., & van Kampen, J. J. A. (2022). Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay. Journal of Virological Methods, 300, Article 114397. https://doi.org/10.1016/j.jviromet.2021.114397

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title = "Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay",

abstract = "Here we describe a SARS-CoV-2 variant with diminished amplification of the ORF ORF1ab target in the Cobas{\textregistered} dual-target SARS-CoV-2 assay resulting in a discrepancy of Ct-values (Ct-value 20.7 for the E-gene and Ct-value 30.2 for ORF1ab). Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). This case highlights the importance of surveillance of genomic regions used in molecular diagnostics and the importance of the public release of target regions used to update commercial and in-house developed SARS-CoV-2 PCR tests. This work underpins the importance of using dual-targets in molecular diagnostic assays to limit the change of false-negative results due to primer and/or probe mismatches.",

author = "Stephanie Popping and Richard Molenkamp and Weigel, {Joachim D.} and Mutsaers, {Pim G.N.J.} and Voermans, {Jolanda C.} and {van Boheemen}, Sander and Shamier, {Marc C.} and Sikkema, {Reina S.} and Nieuwenhuijse, {David F.} and {Oude Munnink}, {Bas B.} and Koopmans, {Marion P.G.} and {van Kampen}, {Jeroen J.A.}",

note = "Funding Information: SP: received financial support from Gilead Sciences outside of the submitted work. Funding Information: Sequencing was funded by ZonMW (grant agreement no: 10150062010005 ). Publisher Copyright: {\textcopyright} 2021",

year = "2022",

month = feb,

doi = "10.1016/j.jviromet.2021.114397",

language = "English",

volume = "300",

journal = "Journal of Virological Methods",

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Popping, S , Molenkamp, R , Weigel, JD , Mutsaers, PGNJ , Voermans, JC , van Boheemen, S, Shamier, MC, Sikkema, RS , Nieuwenhuijse, DF , Oude Munnink, BB, Koopmans, MPG & van Kampen, JJA 2022, 'Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay', Journal of Virological Methods, vol. 300, 114397. https://doi.org/10.1016/j.jviromet.2021.114397

TY - JOUR

T1 - Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay

AU - Popping, Stephanie

AU - Molenkamp, Richard

AU - Weigel, Joachim D.

AU - Mutsaers, Pim G.N.J.

AU - Voermans, Jolanda C.

AU - van Boheemen, Sander

AU - Shamier, Marc C.

AU - Sikkema, Reina S.

AU - Nieuwenhuijse, David F.

AU - Oude Munnink, Bas B.

AU - Koopmans, Marion P.G.

AU - van Kampen, Jeroen J.A.

N1 - Funding Information: SP: received financial support from Gilead Sciences outside of the submitted work. Funding Information: Sequencing was funded by ZonMW (grant agreement no: 10150062010005 ). Publisher Copyright: © 2021

PY - 2022/2

Y1 - 2022/2

N2 - Here we describe a SARS-CoV-2 variant with diminished amplification of the ORF ORF1ab target in the Cobas® dual-target SARS-CoV-2 assay resulting in a discrepancy of Ct-values (Ct-value 20.7 for the E-gene and Ct-value 30.2 for ORF1ab). Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). This case highlights the importance of surveillance of genomic regions used in molecular diagnostics and the importance of the public release of target regions used to update commercial and in-house developed SARS-CoV-2 PCR tests. This work underpins the importance of using dual-targets in molecular diagnostic assays to limit the change of false-negative results due to primer and/or probe mismatches.

AB - Here we describe a SARS-CoV-2 variant with diminished amplification of the ORF ORF1ab target in the Cobas® dual-target SARS-CoV-2 assay resulting in a discrepancy of Ct-values (Ct-value 20.7 for the E-gene and Ct-value 30.2 for ORF1ab). Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). This case highlights the importance of surveillance of genomic regions used in molecular diagnostics and the importance of the public release of target regions used to update commercial and in-house developed SARS-CoV-2 PCR tests. This work underpins the importance of using dual-targets in molecular diagnostic assays to limit the change of false-negative results due to primer and/or probe mismatches.

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DO - 10.1016/j.jviromet.2021.114397

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VL - 300

JO - Journal of Virological Methods

JF - Journal of Virological Methods

M1 - 114397

ER -

Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay

Abstract

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