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COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.
Fasching, Clare L; Servellita, Venice; McKay, Bridget; Nagesh, Vaishnavi; Broughton, James P; Sotomayor-Gonzalez, Alicia; Wang, Baolin; Brazer, Noah; Reyes, Kevin; Streithorst, Jessica; Deraney, Rachel N; Stanfield, Emma; Hendriks, Carley G; Fung, Becky; Miller, Steve; Ching, Jesus; Chen, Janice S; Chiu, Charles Y.
  • Fasching CL; Mammoth Biosciences, Inc., Brisbane, California, USA.
  • Servellita V; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • McKay B; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Nagesh V; Mammoth Biosciences, Inc., Brisbane, California, USA.
  • Broughton JP; Mammoth Biosciences, Inc., Brisbane, California, USA.
  • Sotomayor-Gonzalez A; Mammoth Biosciences, Inc., Brisbane, California, USA.
  • Wang B; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • Brazer N; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Reyes K; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • Streithorst J; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Deraney RN; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • Stanfield E; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Hendriks CG; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • Fung B; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Miller S; Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.
  • Ching J; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Chen JS; Mammoth Biosciences, Inc., Brisbane, California, USA.
  • Chiu CY; Mammoth Biosciences, Inc., Brisbane, California, USA.
J Clin Microbiol ; 60(7): e0026122, 2022 07 20.
Article in English | MEDLINE | ID: covidwho-1909573
ABSTRACT
Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we present the development and validation of a rapid COVID-19 variant DETECTR assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations, at least one of which is found in nearly all major variants. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 261 clinical samples yielded a SNP concordance of 97.3% and agreement of 98.9% (258 of 261) for SARS-CoV-2 lineage classification, using SARS-CoV-2 whole-genome sequencing and/or real-time RT-PCR as test comparators. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR as a faster and simpler diagnostic method compared with sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.
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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: J Clin Microbiol Year: 2022 Document Type: Article Affiliation country: Jcm.00261-22

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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: J Clin Microbiol Year: 2022 Document Type: Article Affiliation country: Jcm.00261-22