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


Jon Arizti-Sanz*, Catherine A Freije*, Alexandra C Stanton, Chloe K Boehm, Brittany A Petros, Sameed Siddiqui, Bennett M Shaw, Gordon Adams, Tinna-Solveig F Kosoko-Thoroddsen, Molly E Kemball, Jessica N Uwanibe, Jacob E Lemieux, Fehintola V Ajobasile, Philomena E Eromon, Robin Gross, Loni Wronka, Katie Caviness, Lisa E Hensley, Nicholas H Bergman, Bronwyn L MacInnis, Christian T Happi, Pardis C Sabeti*, and Cameron Myhrvold*†. 2020. “Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2.” Nature Communications, 11. Publisher's Version


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.


Last updated on 12/01/2020