1. Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2
- Author
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Sameed Siddiqui, Bronwyn MacInnis, Chloe K. Boehm, Cameron Myhrvold, Robin Gross, Tinna-Solveig F. Kosoko-Thoroddsen, Molly Kemball, Alexandra C. Stanton, Jon Arizti-Sanz, Katie Caviness, Bennett M. Shaw, Loni Wronka, Jacob E. Lemieux, Catherine A. Freije, Pardis C. Sabeti, Nicholas H. Bergman, Brittany A. Petros, Lisa E. Hensley, and Gordon Adams
- Subjects
Coronavirus disease 2019 (COVID-19) ,business.industry ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,CRISPR-Associated Proteins ,Pneumonia, Viral ,COVID-19 ,Smartphone application ,Virology ,Viral Inactivation ,Article ,Fluorescence ,Betacoronavirus ,Molecular Diagnostic Techniques ,Medicine ,Humans ,Biological Assay ,business ,Coronavirus Infections ,Disease transmission ,Pandemics - Abstract
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.
- Published
- 2020