Author: Shirato, Kazuya; Tomita, Yuriko; Katoh, Hiroshi; Yamada, Souichi; Fukushi, Shuetsu; Matsuyama, Shutoku; Takeda, Makoto
Title: Performance evaluation of real-time RT-PCR assays for detection of severe acute respiratory syndrome coronavirus-2 developed by the National Institute of Infectious Diseases, Japan. Cord-id: k2os0px4 Document date: 2021_2_26
ID: k2os0px4
Snippet: Soon after the December 2019 outbreak of coronavirus disease 2019 in Wuhan, China, a protocol for real-time RT-PCR assay detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) was established by the National Institute of Infectious Diseases (NIID) in Japan. The protocol used Charité's nucleocapsid (Sarbeco-N) and NIID's nucleocapsid (NIID-N2) assays. During the following months, SARS-CoV-2 spread causing a global pandemic, and a variety of SARS-CoV-2 sequences were registered t
Document: Soon after the December 2019 outbreak of coronavirus disease 2019 in Wuhan, China, a protocol for real-time RT-PCR assay detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) was established by the National Institute of Infectious Diseases (NIID) in Japan. The protocol used Charité's nucleocapsid (Sarbeco-N) and NIID's nucleocapsid (NIID-N2) assays. During the following months, SARS-CoV-2 spread causing a global pandemic, and a variety of SARS-CoV-2 sequences were registered to public databases, such as the Global Initiative on Sharing All Influenza Data (GISAID). In this study, we evaluated the newly developed S2 assay (NIID-S2) to replace the Sarbeco-N assay and the performance of NIID-N2 and NIID-S2 assays, referring mismatches in the primer/probe targeted region. We found the analytical sensitivity and specificity of the NIID-S2 set were comparable to the NIID-N2 assay, and the detection rate for clinical specimens was identical to that of the NIID-N2 assay. Furthermore, among available sequences (approximately 192,000), the NIID-N2 and NIID-S2 sets had 2.6% and 1.2% mismatched sequences, respectively, although most of these mismatches did not affect the amplification efficiency, with the exception of the 3' end of the NIID-N2 forward primer. These findings indicate that the previously developed NIID-N2 assay remains suitable for the detection SARS-CoV-2 with support of the newly developed NIID-S2 set.
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