Trends of Mismatches in Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan for Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2

• Published in: Japanese Journal of Infectious Diseases Vol. 76; no. 3; pp. 204 - 206
• Main Authors: Shirato, Kazuya, Ujike, Makoto, Kawase, Miyuki
• Format: Journal Article
• Language: English
• Published: Japan National Institute of Infectious Diseases 31.05.2023; Japan Science and Technology Agency
• Subjects: Animals; Assaying; Avian flu; Communicable Diseases; coronavirus disease 2019 (COVID-19); Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 Testing; Infectious diseases; Japan - epidemiology; Nucleotides; omicron; Polymerase chain reaction; Real time; real-time RT-PCR; Respiratory diseases; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Trends; Viral diseases; Japan; omicron; real-time RT-PCR; coronavirus disease 2019 (COVID-19); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
• ISSN: 1344-6304; 1884-2836; 1884-2836
• DOI: 10.7883/yoken.JJID.2022.556

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2021 and gradually overtook the Delta variant, which was the predominant variant at that time. The Omicron variant has been consecutively replaced by related sublineages. The real-time RT-PCR assays developed by the National Institute of Infectious Diseases (NIID), Japan (i.e., the NIID-N2 and NIID-S2 assays) are the reference assays that have been used in Japan since the outbreak of SARS-CoV-2. To evaluate the applicability of the NIID assays for the Omicron variants, trends in the prevalence of nucleotide mismatches in the primer/probe sequences were traced using sequences registered in the Global Initiative on Sharing Avian Influenza Data database. Approximately 99% of the deposited Omicron variant sequences did not have any mismatches in the NIID assay primer/probes from January to August 2022. This indicates that the NIID assays have been able to detect the changing SARS-CoV-2 Omicron variants.