tetano
Editor, Senior Moderator
Jpn J Infect Dis
. 2022 Dec 28.
doi: 10.7883/yoken.JJID.2022.556. Online ahead of print.
Trends of mismatches in real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan for Omicron variants of severe acute respiratory syndrome coronavirus 2
Kazuya Shirato[SUP] 1 [/SUP], Makoto Ujike[SUP] 2 [/SUP], Miyuki Kawase[SUP] 1 [/SUP]
Affiliations
Abstract
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, 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.
Keywords: Omicron; coronavirus disease 2019 (COVID-19); real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
. 2022 Dec 28.
doi: 10.7883/yoken.JJID.2022.556. Online ahead of print.
Trends of mismatches in real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan for Omicron variants of severe acute respiratory syndrome coronavirus 2
Kazuya Shirato[SUP] 1 [/SUP], Makoto Ujike[SUP] 2 [/SUP], Miyuki Kawase[SUP] 1 [/SUP]
Affiliations
- PMID: 36575025
- DOI: 10.7883/yoken.JJID.2022.556
Abstract
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, 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.
Keywords: Omicron; coronavirus disease 2019 (COVID-19); real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).