tetano
Editor, Senior Moderator
Jpn J Infect Dis
. 2021 Jun 30.
doi: 10.7883/yoken.JJID.2021.213. Online ahead of print.
Less frequent sequence mismatches in variants of concern (VOCs) of SARS-CoV-2 in the real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan
Kazuya Shirato[SUP] 1 [/SUP], Shutoku Matsuyama[SUP] 1 2 [/SUP], Makoto Takeda[SUP] 1 [/SUP]
Affiliations
Abstract
Various variants of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) began emerging worldwide from the end of 2020 to the beginning of 2021. The variants GRY/VOC202012/01 (B1.1.7), GH/N501Y.V2 (B1.351), and GR/N501Y.V3 (P1) are characterized by N to Y amino acid substitution at position 501 in the S protein. The variant containing L to R substitution at position 452 in the S protein G/L452R.V3 (B1.617) was endemic to India. The heightened concern regarding these variants is related to their increased viral infectivity. Information about nucleotide mismatch(es) on the primer/probe sequence is important for maintaining good performance of real-time PCR assays. In this study, real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan (NIID-N2 and NIID-S2 assays), were reviewed to analyze nucleotide mismatches of variants in primer/probe sequences. The frequency of mismatched sequences in three variants (GRY/VOC202012/01, GH/N501Y.V2, and GR/N501Y.V3) was lower than that in all SARS-CoV-2 sequences. The mismatch, that G to C substitution at nucleotide 8 in reverse primer of S2 set, elevated to about 16.3% in G/L452R.V3, however the substitution did not affect the analytical sensitivity of assay. Therefore, the study indicates that the NIID-N2 and NIID-S2 sets detect VOCs of SARS-CoV-2 with reliable efficiency.
Keywords: Coronavirus Diseases 2019 (COVID-19); real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); variant of concern (VOC).
. 2021 Jun 30.
doi: 10.7883/yoken.JJID.2021.213. Online ahead of print.
Less frequent sequence mismatches in variants of concern (VOCs) of SARS-CoV-2 in the real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan
Kazuya Shirato[SUP] 1 [/SUP], Shutoku Matsuyama[SUP] 1 2 [/SUP], Makoto Takeda[SUP] 1 [/SUP]
Affiliations
- PMID: 34193667
- DOI: 10.7883/yoken.JJID.2021.213
Abstract
Various variants of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) began emerging worldwide from the end of 2020 to the beginning of 2021. The variants GRY/VOC202012/01 (B1.1.7), GH/N501Y.V2 (B1.351), and GR/N501Y.V3 (P1) are characterized by N to Y amino acid substitution at position 501 in the S protein. The variant containing L to R substitution at position 452 in the S protein G/L452R.V3 (B1.617) was endemic to India. The heightened concern regarding these variants is related to their increased viral infectivity. Information about nucleotide mismatch(es) on the primer/probe sequence is important for maintaining good performance of real-time PCR assays. In this study, real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan (NIID-N2 and NIID-S2 assays), were reviewed to analyze nucleotide mismatches of variants in primer/probe sequences. The frequency of mismatched sequences in three variants (GRY/VOC202012/01, GH/N501Y.V2, and GR/N501Y.V3) was lower than that in all SARS-CoV-2 sequences. The mismatch, that G to C substitution at nucleotide 8 in reverse primer of S2 set, elevated to about 16.3% in G/L452R.V3, however the substitution did not affect the analytical sensitivity of assay. Therefore, the study indicates that the NIID-N2 and NIID-S2 sets detect VOCs of SARS-CoV-2 with reliable efficiency.
Keywords: Coronavirus Diseases 2019 (COVID-19); real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); variant of concern (VOC).