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Coronavirus 2019 (COVID-19) Nucleic Acid Detection Tests
Effective immediately, the Department of Pathology and Laboratory Medicine will be testing nasopharyngeal, oropharyngeal and nasal specimens collected from individuals with suspected COVID-19 infection on two additional platforms. The Cepheid Xpert Xpress SARS-CoV-2 and DiaSorin Molecular Simplexa COVID-19 Direct are real-time reverse transcription polymerase chain reaction (rRT-PCR) assays intended for the qualitative detection of nucleic acid from SARS-CoV-2. The table below highlights the differences between the 4 platforms that are now available.

Effective date: April 10, 2020                                                                                              

Important Considerations: 
  • For simplicity and conservation, one nasopharyngeal swab is sufficient and recommended for both COVID-19 and influenza/RSV testing if both tests are requested using the Xpert Flu kits.
  • Oropharyngeal and nasal swabs should be combined in one vial.
  • The rapid ePlex, Cepheid, and DiaSorin platforms 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, viral cultures (code: CULVRS) from respiratory sources are temporally discontinued at UCI and our reference laboratories per government COVID-19 guidelines.
  • Turnaround time (TAT) estimates do not include order-to-collection or collection-to-receipt times.
Cepheid Xpert DiaSorin Abbott m2000 GenMark ePlex
Methodology rRT-PCR against two SARS-CoV-2 target genes (N2 and E genes) rRT-PCR against two SARS-CoV-2 target genes (ORF1ab and S genes) rRT-PCR against two SARS-CoV-2 target genes (RdRp and N genes) RT-PCR against one SARS-CoV-2 target gene, coupled with exonuclease digestion and electrochemical detection
Lower limit of detection (LoD) 250 copies/mL
(0.25 copies/uL)
500 copies/mL
(0.5 copies/uL)
100 copies/mL
(0.1 copies/uL)
105 copies/mL
(100 copies/uL; may change upon resubmission to the FDA)
(receipt in Microbiology-to-report)
1-2 hours 2-4 hours 24 – 48 hours (batch runs required for reagent conservation) 3 hours
Assay run times 45 minutes 90 minutes 6-9 hours 90 minutes
STAT By approval By approval Not available Not available routinely (backup option only)
Runs 24/7 7AM-9PM Daily 24/7
Reporting - Detected.
- Presumptive Positive result to be confirmed. (When E gene, but not N2 gene is detected; will be repeated on Abbott.)
- Not Detected.
- Invalid due to inhibition. (Will be repeated on DiaSorin; recollection may be necessary if unresolved after repeat testing.)
- Detected.
- Not Detected.
- Invalid due to inhibition. (Will be repeated on Cepheid; recollection may be necessary if unresolved after repeat testing.)
- Detected.
- Not Detected.
- Invalid due to inhibition. (Will be repeated on Cepheid; recollection may be necessary if unresolved after repeat testing.)
- Detected.
- Not Detected. Presumptive result to be confirmed.
(Will be repeated on Abbott.)
- Invalid.
EUA status EUA authorized EUA authorized EUA authorized EUA authorized
Daily capacity (based on reagent availability and machine capacity) ~ 80 tests ~ 80 tests ~ 300 tests ~ 80 tests

Specimen requirements:
Collect: 1) Nasopharyngeal swab (only wire or plastic shaft; wooden swabs are not acceptable) in any viral transport media or universal transport media, or 2) Oropharyngeal and Nasal swab combined in 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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