PT  - JOURNAL ARTICLE
AU  - Takeru Nakabayashi
AU  - Yuki Kawasaki
AU  - Koichiro Murashima
AU  - Kazuya Omi
AU  - Satoshi Yuhara
TI  - Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays
AID  - 10.1101/2021.01.19.426622
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.19.426622
4099  - http://biorxiv.org/content/early/2021/01/20/2021.01.19.426622.short
4100  - http://biorxiv.org/content/early/2021/01/20/2021.01.19.426622.full
AB  - 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 StatementThe authors have declared no competing interest.