Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays

Abstract Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in si...

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Bibliographic Details
Published in:bioRxiv 2021-01
Main Authors: Nakabayashi, Takeru, Kawasaki, Yuki, Murashima, Koichiro, Omi, Kazuya, Yuhara, Satoshi
Format: Article
Language:English
Subjects:
Coronaviruses
Infectious diseases
Mutation
Polymerase chain reaction
Sensitivity analysis
Severe acute respiratory syndrome coronavirus 2
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Summary:Abstract Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays. Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2021.01.19.426622