Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2

Nat Commun. 2020 Nov 20;11(1):5921. doi: 10.1038/s41467-020-19097-x.


The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

Publication types

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

MeSH terms

  • Betacoronavirus / isolation & purification*
  • Biological Assay
  • COVID-19
  • CRISPR-Associated Proteins / metabolism*
  • Coronavirus Infections / diagnosis
  • Coronavirus Infections / virology
  • Fluorescence
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Pandemics
  • Pneumonia, Viral / diagnosis
  • Pneumonia, Viral / virology
  • SARS-CoV-2


  • CRISPR-Associated Proteins