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Test Code COVOO Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA Detection, Varies

Reporting Name

SARS Coronavirus 2 RNA, PCR, V

Useful For

Diagnosis of coronavirus disease 2019 (COVID-19) illness due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

 

Recommended only for patients who meet current clinical and/or epidemiologic criteria defined by federal, state, or local public health directives.

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Specimen Type

Varies


Advisory Information


Due to the non-specific clinical presentation of coronavirus disease (COVID-19) during the early stages of illness, testing for other respiratory tract infections (eg, influenza) may be warranted.

 

For the most up-to-date COVID-19 epidemiology and testing recommendations, visit www.cdc.gov/coronavirus/2019-ncov/index.html



Shipping Instructions


Ship specimens refrigerated (if less than 72 hours from collection to arrive at MCL) or frozen (if 72 hours or more from collection to arrive at MCL).



Specimen Required


Specimen Type: Nasopharyngeal (NP), oropharyngeal (OP; ie, throat), nasal mid-turbinate, or nares/nasal swab

Supplies: Swab, Sterile Polyester (T507)

Container/Tube: Universal transport media, viral transport media, or equivalent (eg, Copan UTM-RT, BD VTM, MicroTest M4, M4-RT, M5)

Media should not contain guanidine thiocyanate (GTC).

For more information on acceptable transport media, see www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testing-sars-cov-2

Specimen Volume: Entire specimen with a minimum of 1.5 mL (maximum 3 mL) of transport media.

 

Collection Instructions:

1. Collect specimen by swabbing back and forth over nasal or pharyngeal mucosa surface to maximize recovery of cells. For more information on OP swab specimen collection, see COVID-19 Oropharyngeal Collection Instructions in Special Instructions.

2. NP and OP swab specimens may be combined at collection into a single vial of transport media but only one swab is required for analysis.

3. Swab must be placed into transport medium. Swab shaft should be broken or cut so that there is no obstruction to the sample or pressure on the media container cap.

4. Do not send in glass tubes, vacutainer tubes, or tubes with push caps.

5. Do not overfill with more than 3 mL total volume of media.

 

Specimen Type: Nasopharyngeal aspirate or nasal washings

Container/Tube: Sterile container

Specimen Volume: Minimum of 1.5 mL

Additional Information: Do not aliquot into viral transport media, glass tubes, vacutainer tubes, or tubes with push caps.


Specimen Minimum Volume

See Specimen Required

Testing Algorithm

See Coronavirus Disease 2019 (COVID-19), Influenza, and Respiratory Syncytial Virus Testing Algorithm in Special Instructions.

 

In response to the new Centers for Medicare and Medicaid Services (CMS) payment strategy for coronavirus disease 2019 (COVID-19) diagnostic testing, a bill-only code will be added for orders that meet the new CMS turn-around-time requirement. For additional information refer to www.cms.gov/newsroom/press-releases/cms-changes-medicare-payment-support-faster-covid-19-diagnostic-testing.

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Frozen (preferred) 14 days
  Refrigerated  72 hours

Reference Values

Undetected

Day(s) and Time(s) Performed

Monday through Sunday; Varies

Test Classification

This test has received Emergency Use Authorization (EUA) by the U.S. Food and Drug Administration and is used per manufacturer's instructions. Performance characteristics were verified by Mayo Clinic in a manner consistent with CLIA requirements.

CPT Code Information

U0003

U0005-(If applicable)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
COVOO SARS Coronavirus 2 RNA, PCR, V 94500-6

 

Result ID Test Result Name Result LOINC Value
CVOOS SARS-CoV-2 Specimen Source 31208-2
CRACE Patient Race 72826-1
CETHN Patient Ethnicity 69490-1
610013 SARS-CoV-2 RNA 94500-6
610016 Method Summary 62364-5

Clinical Reference

1. Zhu N, Zhang D, Wang W, et al: A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727-733. doi: 10.1056/NEJMoa2001017

2. Loeffelholz MJ, Tang YW: Laboratory diagnosis of emerging human coronavirus infections-the state of the art. Emerg Microbes Infect. 2020;9(1):747-756. doi: 10.1080/22221751.2020.1745095

3. Mohammadi A, Esmaeilzadeh E, Li Y, Bosch RJ, Li JZ: SARS-CoV-2 detection in different respiratory sites: a systematic review and meta-analysis. EBioMedicine. 2020 Jul 18;102903. doi: 10.1016/j.ebiom.2020.102903

4. Centers for Disease Control and Prevention (CDC). Overview of testing for SARS-CoV-2. CDC; Updated March 17, 2021. Accessed March 18, 2021. Available at  www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html

5. Food and Drug Administration (FDA). FAQs on diagnostic testing for SARS-CoV-2. FDA; Updated November 16, 2020. Accessed November 17, 2020. Available at www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testing-sars-cov-2

Method Description

cobas Severe Acute Respiratory Syndrome Coronavirus-2 Assay:

The assay is a TaqMan probe-based, real-time reverse transcription polymerase chain reaction (RT-PCR) assay designed for qualitative detection of sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from human upper respiratory tract specimens processed on the fully automated cobas 6800 or 8800 system. Viral target-specific primers and probes are used to amplify and detect both the ORF1ab (nonstructural protein) sequence of SARS-CoV-2 and the E gene (structural envelope protein) sequence of Sarbecovirus group. Samples containing SARS-CoV-2 should generate positive results for both targets by this assay. Clinical samples undergo automated sample preparation (nucleic acid extraction and purification), during which viral nucleic acid in patient samples and added internal control RNA (RNA IC) molecules are simultaneously extracted. Nucleic acid is released by the addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors, are removed with subsequent wash steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature. External controls (positive and negative) are processed in the same way in each assay run.(Package insert: cobas SARS-CoV-2: Qualitative assay for use on the cobas 6800/8800 Systems. Roche Molecular Systems, Inc; Doc Rev. 3.0, 05/2020)

 

Fact sheets for this EUA assay can be found at the following URL:

For health care providers: www.fda.gov/media/136047/download

For patients: www.fda.gov/media/136048/download

 

PerkinElmer New Coronavirus Nucleic Acid Detection Kit:

This assay is a TaqMan probe-based, RT-PCR assay designed for detection of SARS-CoV-2 in human upper respiratory tract specimens, and it amplifies and detects the ORF1ab (ROX) and N gene (FAM) sequences of SARS-CoV-2, with the bacteriophage MS2 as the internal control (VIC) for extraction and amplification / detection. An automated liquid handing workstation is used to prepare the 96-well sample extraction plates, and the samples undergo nucleic acid extraction and purification. Post-elution 96-well RT-PCR plates are prepared on another workstation prior to loading onto the RT-PCR thermocyclers.(Package insert: Instructions for PerkinElmer New Coronavirus Nucleic Acid Detection Kit. PerkinElmer, Inc; Doc Rev. 4.0, 07/28/2020)

 

Fact sheets for this assay can be found at the following URL:

For healthcare providers: www.fda.gov/media/136408/download

For patients: www.fda.gov/media/136409/download

 

TaqPath COVID-19 Combo Kit:

This assay is a TaqMan probe-based, RT-PCR assay designed for detection of SARS-CoV-2 in human upper respiratory tract specimens, and it amplifies and detects the ORF1ab, N, and S gene sequences of SARS-CoV-2, with the bacteriophage MS2 as the internal control for extraction and amplification/detection. An automated liquid handing workstation is used to prepare the 96-well sample extraction plates, and the samples undergo nucleic acid extraction and purification. Post-elution 96-well RT-PCR plates are prepared on another workstation prior to loading onto the RT-PCR thermocyclers.(Package insert: TaqPath COVID-19 Combo Kit. Life Technologies Corp; Doc Rev. D.0, 05/2020)

 

Fact sheets for this assay can be found at the following URL:

For healthcare providers: www.fda.gov/media/136111/download

For patients: www.fda.gov/media/136114/download

Analytic Time

1 day

Reject Due To

Calcium alginate-tipped swab, wooden shaft swab, or swab collection tubes containing gel or charcoal additive.
Transport media tubes containing the entire swab (shaft and knob attached)
Glass transport media tubes
Bloody specimen
Reject
Thawed Cold OK; Warm reject

Method Name

Real-Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

Forms

If not ordering electronically, complete, print, and send a General Request (T239) with the specimen.

Secondary ID

610012

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
TATCH TAT <=2 days additional charge No, (Bill Only) No