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


Ordering Guidance


Due to the non-specific clinical presentation of 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 Mayo Clinic Laboratories [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.

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.


Useful For

Diagnosing COVID-19 illness due to SARS-CoV-2

 

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

Highlights

This test provides qualitative detection of SARS-CoV-2 RNA from select upper respiratory tract specimens from patients under investigation for COVID-19. Based on sequence analysis, it is predicted that this test will detect the United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) variants.

 

The assay used for testing has received emergency use authorization (EUA) from the US Food and Drug Administration. Testing will be performed using the cobas SARS-CoV-2 (Roche Molecular Systems) kit.

 

URL links to the fact sheets this EUA assay is provided in the Method Description.

Method Name

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

Reporting Name

SARS Coronavirus 2 RNA, PCR, V

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

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

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

Clinical Information

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA virus that causes COVID-19. Like other coronaviruses that infect humans, SARS-CoV-2 can cause both upper and lower respiratory tract infection. Symptoms can range from mild (ie, common cold) to severe (ie, pneumonia) in both healthy and immunocompromised patients. SARS-CoV-2 transmission occurs primarily via respiratory droplets. During the early stages of COVID-19, symptoms maybe nonspecific and resemble other common respiratory tract infections, such as influenza. If testing for other respiratory tract pathogens is negative, specific testing for SARS-CoV-2 may be warranted.

 

SARS-CoV-2 is likely to be at the highest concentrations in the nasopharynx during the first 3 to 5 days of symptomatic illness. As the disease progresses, the viral load tends to decrease in the upper respiratory tract, at which point lower respiratory tract specimens (eg, sputum, tracheal aspirate, bronchoalveolar fluid) would be more likely to have detectable SARS-CoV-2.

Reference Values

Undetected

Interpretation

Based on sequence analysis, this assay is predicted to detect the circulating variants reported by the US Centers for Disease Control and Prevention (www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html), such as the United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) variants.

 

A "Detected" result indicates that SARS-CoV-2 RNA is present and suggests the diagnosis of COVID-19. Test result should always be considered in the context of patient's clinical history, physical examination, and epidemiologic exposures when making the final diagnosis. A summary of available treatment options for COVID-19 can be found at the US Department of Health and Human Services website: https://combatcovid.hhs.gov/i-have-covid-19-now/available-covid-19-treatment-options.

 

An "Undetected" result indicates that SARS-CoV-2 is not present in the patient's specimen. However, this result may be influenced by the stage of the infection, as well as the quality and type of the specimen collected for testing. Result should be correlated with patient's history and clinical presentation.

 

An "Indeterminate" result suggests that the patient may be infected with a variant SARS-CoV-2 or SARS-related coronavirus. Additional testing with an alternative molecular method may be considered if the patient does not have signs and/or symptoms of COVID-19.

 

An "Inconclusive" result indicates that the presence or absence of SARS-CoV-2 RNA in the specimen could not be determined with certainty after repeat testing in the laboratory, possibly due to reverse transcription polymerase chain reaction inhibition. Submission of a new specimen for testing is recommended.

Cautions

The US Food and Drug Administration has provided emergency use authorization of these assays for testing human nasopharyngeal and oropharyngeal swab specimens.

 

The sensitivity of the assays is dependent on the timing of the specimen collection (in relation to symptom onset), as well as the quality and type of the specimen submitted for testing.

 

The test is specific for SARS-CoV-2, and positive test results do not exclude the possibility of concurrent infection with other respiratory viruses.

 

Undetected (ie, negative) results do not rule out COVID-19 in patients and should not be used as the sole basis for treatment or other patient management decisions. Result should be correlated with patient's history and clinical presentation.

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;59:102903. doi:10.1016/j.ebiom.2020.102903

4. Centers for Disease Control and Prevention (CDC). Overview of testing for SARS-CoV-2. CDC; Updated May 11, 2023. Accessed May 10, 2023. Available at www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html

5. US Food and Drug Administration (FDA). FAQs on testing for SARS-CoV-2. FDA; Updated January 12, 2023. Accessed May 10, 2023. Available at www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/faqs-testing-sars-cov-2

Method Description

The assay is a TaqMan probe-based, real-time reverse transcription polymerase chain reaction (RT-PCR) assay designed for qualitative detection of 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. 8.0, 02/2022)

 

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

Day(s) Performed

Monday through Sunday

Report Available

1 to 3 days

Test Classification

This test has received Emergency Use Authorization (EUA) by the US 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

87635

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