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CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.
Liang, Yuanhao; Lin, Hongqing; Zou, Lirong; Zhao, Jianhui; Li, Baisheng; Wang, Haiying; Lu, Jing; Sun, Jiufeng; Yang, Xingfen; Deng, Xiaoling; Tang, Shixing.
  • Liang Y; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
  • Lin H; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
  • Zou L; Guangdong Provincial Institute of Public Health, Guangdong Center for Diseases Control and Prevention, Guangzhou, China.
  • Zhao J; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
  • Li B; Guangdong Provincial Institute of Public Health, Guangdong Center for Diseases Control and Prevention, Guangzhou, China.
  • Wang H; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
  • Lu J; Guangdong Provincial Institute of Public Health, Guangdong Center for Diseases Control and Prevention, Guangzhou, China.
  • Sun J; Guangdong Provincial Institute of Public Health, Guangdong Center for Diseases Control and Prevention, Guangzhou, China.
  • Yang X; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
  • Deng X; Guangdong Provincial Institute of Public Health, Guangdong Center for Diseases Control and Prevention, Guangzhou, China.
  • Tang S; Department of Epidemiology, School of Public Health, Southern Medical Universitygrid.284723.8, Guangzhou, China.
Microbiol Spectr ; 9(3): e0101721, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1522923
ABSTRACT
A big challenge for the control of COVID-19 pandemic is the emergence of variants of concern (VOCs) or variants of interest (VOIs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may be more transmissible and/or more virulent and could escape immunity obtained through infection or vaccination. A simple and rapid test for SARS-CoV-2 variants is an unmet need and is of great public health importance. In this study, we designed and analytically validated a CRISPR-Cas12a system for direct detection of SARS-CoV-2 VOCs. We further evaluated the combination of ordinary reverse transcription-PCR (RT-PCR) and CRISPR-Cas12a to improve the detection sensitivity and developed a universal system by introducing a protospacer adjacent motif (PAM) near the target mutation sites through PCR primer design to detect mutations without PAM. Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2. In addition, the open reading frame 8 (ORF8) mutations (T/C substitution at nt28144 and the corresponding change of amino acid L/S) could differentiate L and S lineages of SARS-CoV-2. The low limit of detection could reach 10 copies/reaction. Our assay successfully distinguished 4 SARS-CoV-2 strains of wild type and alpha (B.1.1.7), beta (B.1.351), and delta (B.1.617.2) variants. By testing 32 SARS-CoV-2-positive clinical samples infected with the wild type (n = 5) and alpha (n = 11), beta (n = 8), and delta variants (n = 8), the concordance between our assay and sequencing was 100%. The CRISPR-based approach is rapid and robust and can be adapted for screening the emerging mutations and immediately implemented in laboratories already performing nucleic acid amplification tests or in resource-limited settings. IMPORTANCE We described CRISPR-Cas12-based multiplex allele-specific assay for rapid SARS-CoV-2 variant genotyping. The new system has the potential to be quickly developed, continuously updated, and easily implemented for screening of SARS-CoV-2 variants in resource-limited settings. This approach can be adapted for emerging mutations and implemented in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests using existing resources and extracted nucleic acid.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: CRISPR-Cas Systems / COVID-19 Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study / Screening study Limits: Humans Language: English Journal: Microbiol Spectr Year: 2021 Document Type: Article Affiliation country: Spectrum.01017-21

Full text: Available Collection: International databases Database: MEDLINE Main subject: CRISPR-Cas Systems / COVID-19 Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study / Screening study Limits: Humans Language: English Journal: Microbiol Spectr Year: 2021 Document Type: Article Affiliation country: Spectrum.01017-21