Background:
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
Detected
|
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.
Stability:
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.
References:
- 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.
- 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. DOI.org/10.3346/jkms.2020.35.e86
- Kam K‐Q. et al. 2020. A well infant with coronavirus disease 2019 (COVID‐19) with high viral load. Clin Infect Dis.
- Wolfel R. et al. Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster. medRxiv preprint DOI.org/10.1101/2020.03.05.20030502.
- Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/lab/index.html
- Centers for Disease Control and Prevention and US Food and Drug Administration. https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations
A summary of all tests offered by our laboratory services can be found here:
http://www.pathology.uci.edu/services/index.asp
Sincerely,
Cassiana Bittencourt, MD
Director
Division of Clinical Microbiology
Edwin S. Monuki, MD, PhD
Chair
Department of Pathology & Laboratory Medicine |
