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Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2.
Li, Jianguo; Gao, Zefeng; Chen, Jing; Cheng, Ruiling; Niu, Jiahui; Zhang, Jialei; Yang, You; Yuan, Ximei; Xia, Juan; Mao, Guoli; Liu, Hulong; Dong, Yongkang; Wu, Changxin.
  • Li J; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
  • Gao Z; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
  • Chen J; Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan, China.
  • Cheng R; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
  • Niu J; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
  • Zhang J; College of Life Sciences, Shanxi University, Taiyuan, China.
  • Yang Y; College of Life Sciences, Shanxi University, Taiyuan, China.
  • Yuan X; College of Life Sciences, Shanxi University, Taiyuan, China.
  • Xia J; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
  • Mao G; Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China.
  • Liu H; Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China.
  • Dong Y; Administrative Office, the Fourth People's Hospital of Taiyuan, Taiyuan, China.
  • Wu C; Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
Front Cell Infect Microbiol ; 12: 953027, 2022.
Article in English | MEDLINE | ID: covidwho-2022658
ABSTRACT
Quick differentiation of the circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmission. However, the widely used gene sequencing method is time-consuming and costly when facing the viral recombinant variants, because partial or whole genome sequencing is required. Allele-specific real time RT-PCR (qRT-PCR) represents a quick and cost-effective method in SNP genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 3 multiplex allele-specific qRT-PCR assays targeting 12 key differential mutations for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2). Two parallel multiplex qRT-PCR reactions were designed to separately target the protype allele and the mutated allele of the four mutations in each allele-specific qRT-PCR assay. The variation of Cp values (ΔCp) between the two multiplex qRT-PCR reactions was applied for mutation determination. The developed multiplex allele-specific qRT-PCR assays exhibited outstanding analytical sensitivities (with limits of detection [LoDs] of 2.97-27.43 copies per reaction), wide linear detection ranges (107-100 copies per reaction), good amplification efficiencies (82% to 95%), good reproducibility (Coefficient of Variations (CVs) < 5% in both intra-assay and inter-assay tests) and clinical performances (99.5%-100% consistency with Sanger sequencing). The developed multiplex allele-specific qRT-PCR assays in this study provide an alternative tool for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2).
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Front Cell Infect Microbiol Year: 2022 Document Type: Article Affiliation country: Fcimb.2022.953027

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Front Cell Infect Microbiol Year: 2022 Document Type: Article Affiliation country: Fcimb.2022.953027