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

Arizti-Sanz, Jon; Freije, Catherine A.; Stanton, Alexandra C.; Petros, Brittany A.; Boehm, Chloe K.; Siddiqui, Sameed; Shaw, Bennett M.; Adams, Gordon; Kosoko-Thoroddsen, Tinna-Solveig F.; Kemball, Molly E.; Uwanibe, Jessica N.; Ajogbasile, Fehintola V.; Eromon, Philomena E.; Gross, Robin; Wronka, Loni; Caviness, Katie; Hensley, Lisa E.; Bergman, Nicholas H.; MacInnis, Bronwyn L.; Happi, Christian T.; Lemieux, Jacob E.; Sabeti, Pardis C.; Myhrvold, Cameron

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.