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bioRxiv · 10.1101/2021.01.19.426622

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

Nakabayashi, T.·Kawasaki, Y.·Murashima, K.·Omi, K.·Yuhara, S.
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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.

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Nakabayashi, T., Kawasaki, Y., Murashima, K., Omi, K., Yuhara, S.. 2021-01-20. Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays. https://doi.org/10.1101/2021.01.19.426622

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