Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

Velu, Priya; Craney, Arryn; Ruggiero, Phyllis; Sipley, John; Cong, Lin; Hissong, Erika M.; Loda, Massimo; Westblade, Lars F.; Cushing, Melissa; Rennert, Hanna

An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital (NYPH) system following the emergency use authorization (EUA) issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=174) using newly designed dual-target rRT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting SARS-CoV-2 in upper respiratory (URT) and lower respiratory tract (LRT) specimens. Accuracy testing demonstrated excellent assay agreement between expected and observed values and comparable diagnostic performance to reference tests. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 URT specimens from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Here we demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarize clinical data from early in the epidemic in New York City.