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

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: C11...

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Autores principales: Popping, Stephanie, Molenkamp, Richard, Weigel, Joachim D., Mutsaers, Pim G.N.J., Voermans, Jolanda C., van Boheemen, Sander, Shamier, Marc C., Sikkema, Reina S., Nieuwenhuijse, David F., Oude Munnink, Bas B., Koopmans, Marion P.G., van Kampen, Jeroen J.A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier B.V. 2022
Materias:
Short Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634734/
https://www.ncbi.nlm.nih.gov/pubmed/34863783
http://dx.doi.org/10.1016/j.jviromet.2021.114397
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author Popping, Stephanie
Molenkamp, Richard
Weigel, Joachim D.
Mutsaers, Pim G.N.J.
Voermans, Jolanda C.
van Boheemen, Sander
Shamier, Marc C.
Sikkema, Reina S.
Nieuwenhuijse, David F.
Oude Munnink, Bas B.
Koopmans, Marion P.G.
van Kampen, Jeroen J.A.
author_facet Popping, Stephanie
Molenkamp, Richard
Weigel, Joachim D.
Mutsaers, Pim G.N.J.
Voermans, Jolanda C.
van Boheemen, Sander
Shamier, Marc C.
Sikkema, Reina S.
Nieuwenhuijse, David F.
Oude Munnink, Bas B.
Koopmans, Marion P.G.
van Kampen, Jeroen J.A.
author_sort Popping, Stephanie
collection PubMed
description 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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spelling pubmed-86347342021-12-01 Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay Popping, Stephanie Molenkamp, Richard Weigel, Joachim D. Mutsaers, Pim G.N.J. Voermans, Jolanda C. van Boheemen, Sander Shamier, Marc C. Sikkema, Reina S. Nieuwenhuijse, David F. Oude Munnink, Bas B. Koopmans, Marion P.G. van Kampen, Jeroen J.A. J Virol Methods Short Communication 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. Published by Elsevier B.V. 2022-02 2021-12-01 /pmc/articles/PMC8634734/ /pubmed/34863783 http://dx.doi.org/10.1016/j.jviromet.2021.114397 Text en © 2021 Published by Elsevier B.V. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Short Communication
Popping, Stephanie
Molenkamp, Richard
Weigel, Joachim D.
Mutsaers, Pim G.N.J.
Voermans, Jolanda C.
van Boheemen, Sander
Shamier, Marc C.
Sikkema, Reina S.
Nieuwenhuijse, David F.
Oude Munnink, Bas B.
Koopmans, Marion P.G.
van Kampen, Jeroen J.A.
Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title_full Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title_fullStr Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title_full_unstemmed Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title_short Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay
title_sort diminished amplification of sars-cov-2 orf1ab in a commercial dual-target qrt-pcr diagnostic assay
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634734/
https://www.ncbi.nlm.nih.gov/pubmed/34863783
http://dx.doi.org/10.1016/j.jviromet.2021.114397
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