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Coronavirus 2019 (COVID-19) Nucleic Acid Detection Tests
Effective immediately, the Medical Microbiology Division will be testing nasopharyngeal specimens collected from individuals with suspected COVID-19 infection on two different platforms. Specimens will be tested for the presence of SARS-CoV-2 RNA using the automated ePlex or Abbott m2000 platforms. The ePlex uses reverse transcription and polymerase chain reaction (RT-PCR) coupled with exonuclease digestion and electrochemical detection. The Abbott m2000 uses real-time reverse transcription and polymerase chain reaction (rRT-PCR). Both tests have been validated by the Microbiology Laboratory for the detection of SARS-CoV-2 RNA. A table describing their differences is provided below.

Effective date: March 24, 2020

Important Considerations:          
  • For ambulatory patients, please follow the pathway for approving COVID-19 testing by calling the Patient Access Center 949-824-8600 or 714-456-7002.
  • For inpatients, please follow the same approval pathway via EPIC instructions; the currently designated physicians to page are as follows:
    • Monday-Sunday 7 a.m. - 7 p.m.: Lanny Hsieh or Miki Watanabe
    • Monday-Sunday 7 p.m. - 7 a.m.: Donald Forthal or TBD
  • For occupational health patients, please contact 714-456-8300.
  • For simplicity and conservation, one specimen is sufficient and recommended for both COVID-19 and influenza/RSV testing if both tests are requested.
  • The rapid ePlex SARS-CoV-2 test should only be considered when fast turnaround time is required and requires approval of the designated clinical team due to limited reagent availability.
  • Clinical accuracy and predictive values of SARS-CoV-2 testing have not been systematically evaluated.
  • A few published studies suggest that viral loads are highest early during the disease course (3-6 days after symptom onset)1-4
  • A “Not Detected” (negative) result does not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. This result should be combined with clinical observations, patient history, and epidemiological information.
  • Due to the risk of SARS-CoV-2 propagation for laboratory personnel, all orders for viral cultures (code: CULVRS) from respiratory sources will be sent to our reference laboratory, ARUP.
Abbott m2000 GenMark ePlex
Methodology rRT-PCR against two SARS-CoV-2 target genes RT-PCR against one SARS-CoV-2 target gene coupled with exonuclease digestion and electrochemical detection
Lower limit of detection (LoD) 100 copies/mL 105 copies/mL
(From vendor; official LoD may change pending potential resubmission to the FDA)
TAT 24 hours after receipt in the Microbiology Laboratory 3 hours after receipt in the Microbiology Laboratory
STAT Not available Upon approval AND dependent on reagent availability
Runs Daily 24/7
Test code SCOV SCOVS
Reporting Not Detected
Not Detected. Presumptive result
(Presumptive negative specimens will be reflex tested on the Abbott system; changes to this policy are anticipated and will be updated.)
EUA status EUA approved EUA approved

Specimen requirements:
Collect: Nasopharyngeal swab (only wire or plastic shaft; wooden swabs are not acceptable) in any viral transport media or universal transport media.
Preparation: Remove cap and place swab in transport media. Break shaft extending beyond tube and discard. Replace cap and tighten securely.
Transport: Send to the laboratory immediately.
Minimum volume: 1 ml of viral transport media.

Room temperature: Acceptable if received immediately.
Refrigerated: 3 days.
Frozen: 3 months.

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.

  1. Pan Y. et al.  2020.  Viral load of SARS CoV-2 in clinical samples.  Lancet Infect Dis 2020 DOI:10.1016/S1473-3099(20)30113-4.
  2. Kim J.Y. et al.  2020.  Viral load kinetics of SARS CoV-2 infection in first two patients in Korea.  J. Korean Med Sci. 35(7):e86.
  3. Kam K‐Q. et al. 2020. A well infant with coronavirus disease 2019 (COVID‐19) with high viral load. Clin Infect Dis.
  4. Wolfel R. et al. Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster. medRxiv preprint
  5. Centers for Disease Control and Prevention.
  6. Centers for Disease Control and Prevention and US Food and Drug Administration.

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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