Testing
Nasopharyngeal swabs, nasal aspirates, tracheal aspirates, and bronchoalveolar lavage (BAL) samples were tested for detection of SARS-CoV-2 in Clinical Microbiology Laboratory at CHCO. The molecular assays performed included the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel, Abbott RealTime  SARS-CoV-2 assay (Abbott Laboratories, Chicago, IL), the Simplexa® COVID-19 Direct assay (DiaSorin Molecular LLC, Cypress, CA), the BioFire®Respiratory Panel 2.1 (BioFire Diagnostics, Salt Lake City, UT), and the Xpert® Xpress SARS-CoV-2/Flu/RSV assay (Cepheid, Sunnyvale, CA). Testing was completed per manufacturer instructions as outlined in the respective Emergency Use Authorization Instructions for use12-15. Residual specimens from a subset of study subjects with persistently positive SARS-CoV-2 were re-tested using the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel. Reported CT values were calculated by taking the mean of the CT values for the N1 and N2 viral gene targets. For samples in which SARS-CoV-2 was not detected, a CT value of 40 was assigned.