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.
UR - http://www.scopus.com/inward/record.url?scp=85120705190&partnerID=8YFLogxK
U2 - 10.1016/j.jviromet.2021.114397
DO - 10.1016/j.jviromet.2021.114397
M3 - Article
AN - SCOPUS:85120705190
SN - 0166-0934
VL - 300
JO - Journal of Virological Methods
JF - Journal of Virological Methods
M1 - 114397
ER -