Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay

Anahtar, Melis N; Shaw, Bennett M; Slater, Damien; Byrne, Elizabeth H; Botti-Lodovico, Yolanda; Adams, Gordon; Schaffner, Stephen F; Eversley, Jacqueline; McGrath, Graham E G; Gogakos, Tasos; Lennerz, Jochen; Marble, Hetal Desai; Ritterhouse, Lauren L; Batten, Julie M; Georgantas, N Zeke; Pellerin, Rebecca; Signorelli, Sylvia; Thierauf, Julia; Kemball, Molly; Happi, Christian; Grant, Donald S; Ndiaye, Daouda; Siddle, Katherine J; Mehta, Samar B; Harris, Jason B; Ryan, Edward T; Pierce, Virginia M; LaRocque, Regina C; Lemieux, Jacob E; Sabeti, Pardis C; Rosenberg, Eric S; Branda, John A; Turbett, Sarah E

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.