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New Test: Coronavirus 2019 (COVID-19) Nucleic Acid Detection Tests
The Microbiology Division will switch our current STAT testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B, and respiratory syncytial virus (RSV) to the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV assay. The previous Xpert Flu/RSV and Xpert SARS-CoV-2 stand-alone assays are no longer being manufactured. This change will affect the STAT SARS-CoV-2 testing, BUT NOT THE ROUTINE testing. This test has been authorized by the Food and Drug Administration (FDA) under an Emergency Use Authorization (EUA).

Effective date: Oct. 27, 2020

Methodology and reporting:
The Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV test is a rapid, multiplexed real-time reverse transcription polymerase chain reaction (RT-PCR) test intended for the simultaneous qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV viral RNA in either nasopharyngeal swab, nasal swab or nasal wash/aspirate specimens collected from individuals suspected of respiratory viral infection consistent with Coronavirus disease 2019 (COVID-19). The new assay detects but does not differentiate between the N2 and E gene targets for SARS-CoV-2. The presence of other coronaviruses in the B lineage, Betacoronavirus genus, including SARS-CoV-1 may cause a false positive result. However, none of these other coronaviruses is known to currently circulate in the human population. 

The limit of detection for the SARS-CoV-2 target is 131 copies/ml.

Important consideration:
Due to the limited supply of reagents, this test will only be available in Epic for symptomatic patients in the Emergency Department and inpatient settings, asymptomatic pre-procedural patients within 24h of their procedure, or labor & delivery patients.

Specimen requirements:

Collect: Preferred: Nasopharyngeal swab in viral transport media (VTM) or universal transport media (UTM). Alternative specimen types: nasal swab or nasal wash/aspirate.
Stability: Ambient: 24h; Refrigerated: 7 days; Frozen: 1 month. 
Minimum volume: 1 swab in VTM or UTM.
Turnaround time (TAT): 2 hours

Test code: SCFR

Rejection criteria: 
Specimens that exceed stated stability, unlabeled/mislabeled/mismatched specimens, specimens submitted in leaking containers, swabs with wooden shafts, dry swabs not in transport media, non-sterile containers, bloody samples.

A summary of all tests offered by our laboratory services can be found here:


Cassiana Bittencourt, MD                         
Division of Clinical Microbiology

Edwin S. Monuki, MD, PhD
Department of Pathology & Laboratory Medicine
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