Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

Cell. 2021 Jan 21;184(2):323-333.e9. doi: 10.1016/j.cell.2020.12.001. Epub 2020 Dec 4.


The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.

Keywords: COVID-19; CRISPR Dx; CRISPR-Cas13; SARS-CoV-2; mobile phone microscopy; point-of-care diagnostics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • COVID-19 Nucleic Acid Testing / economics
  • COVID-19 Nucleic Acid Testing / instrumentation
  • COVID-19 Nucleic Acid Testing / methods*
  • CRISPR-Cas Systems
  • Cell Line
  • Cell Phone / instrumentation*
  • Coronavirus Nucleocapsid Proteins / genetics
  • Humans
  • Nasopharynx / virology
  • Optical Imaging / instrumentation
  • Optical Imaging / methods*
  • Phosphoproteins / genetics
  • Point-of-Care Testing
  • RNA Interference
  • RNA, Viral / analysis*
  • RNA, Viral / genetics
  • Sensitivity and Specificity
  • Viral Load / economics
  • Viral Load / instrumentation
  • Viral Load / methods*


  • Coronavirus Nucleocapsid Proteins
  • Phosphoproteins
  • RNA, Viral
  • nucleocapsid phosphoprotein, SARS-CoV-2