Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants  

作　　者：Rou-Jian Lu Li Zhao Bao-Ying Huang Fei Ye Wen-Ling Wang Wen-Jie Tan 

机构地区：[1]Key Laboratory of Biosafety,National Health and Family Planning Commission,National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing 102206,China

出　　处：《Chinese Medical Journal》2021年第17期2048-2053,共6页中华医学杂志（英文版）

基　　金：This work was supported by grants from the National Key Research and Development Program of China(Nos.2016YFD0500301,2021YFC0863300,and 2020YFC0840900).

摘　　要：Background:With the ongoing worldwide coronavirus disease 2019(COVID-19)pandemic,an increasing number of viral variants are being identified,which poses a challenge for nucleic acid-based diagnostic tests.Rapid tests,such as real-time reverse transcription-polymerase chain reaction(rRT-PCR),play an important role in monitoring COVID-19 infection and controlling its spread.However,the changes in the genotypes of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants may result in decreased sensitivity of the rRT-PCR assay and it is necessary to monitor the mutations in primers and probes of SARSCoV-2 detection over time.Methods:We developed two rRT-PCR assays to detect the RNA-dependent RNA polymerase(RdRp)and nucleocapsid(N)genes of SARS-CoV-2.We evaluated these assays together with our previously published assays targeting the ORF1ab and N genes for the detection and confirmation of SARS-CoV-2 and its variants of concern(VOCs).In addition,we also developed two rRT-PCR assays(S484K and S501Y)targeting the spike gene,which when combined with the open reading frames(ORF)1ab assay,respectively,to form duplex rRT-PCR assays,were able to detect SARS-CoV-2 VOCs(lineages B.1.351 and B.1.1.7).Results:Using a SARS-CoV-2 stock with predetermined genomic copies as a standard,the detection limit of both assays targeting RdRp and N was five copies/reaction.Furthermore,no cross-reactions with six others human CoVs(229E,OC43,NL63,HKU1,severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus)were observed using these assays.In addition,the S484K and S501Y assays were combined with the ORF1ab assay,respectively.Conclusions:Four rRT-PCR assays(RdRp,N,S484K,and S501Y)were used to detect SARS-CoV-2 variants,and these assays were shown to be effective in screening for multiple virus strains.

关 键 词：COVID-19 SARS-CoV-2 RT-PCR assay Variants of concern RNA polymerase NUCLEOCAPSID SARS-CoV-2 B.1.351 SARS-CoV-2 B.1.1.7 SARS-CoV-220A S484K variant 

分 类 号：R511.9[医药卫生—内科学] R440[医药卫生—临床医学]