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Test Id : SCOVT

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), RNA Detection, ddPCR, Tissue

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Overview

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Useful For
Suggests clinical disorders or settings where the test may be helpful

Detection of severe respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in formalin-fixed, paraffin-embedded tissue

Highlights

This test detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in formalin-fixed, paraffin-embedded tissue.

 

This test method is a laboratory-developed modification of the Bio-Rad SARS-CoV-2 droplet digital polymerase chain reaction (ddPCR) test, which received FDA emergency use authorization (EUA) during the coronavirus disease 2019 (COVID-19) pandemic.

Method Name
A short description of the method used to perform the test

Droplet Digital Polymerase Chain Reaction (ddPCR)

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

No

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

SARS CoV-2 RNA ddPCR, Qual, FFPE

Aliases
Lists additional common names for a test, as an aid in searching

Coronavirus

COVID

COVID-19

SARS

SARS-CoV-2 Qual

SARS-CoV-2 FFPE

SCOVT

Specimen Type
Describes the specimen type validated for testing

Varies

Necessary Information

Specimen source is required.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
MG141 SARS CoV-2 Specimen Source Lung tissue
Sputum (cell block)
Tracheal aspirate (cell block)
Bronchoalveolar fluid (cellblock)
Cardiac tissue,
Brain tissue
Kidney tissue
Other

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Specimen Type: Formalin-fixed, paraffin-embedded tissue.

Sources: Lung tissue, sputum (cell block), tracheal aspirate (cell block), bronchoalveolar fluid (cell block), cardiac tissue, brain tissue, kidney tissue, other

 

Preferred:

Specimen Type: Tissue

Container/Tube: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded (FFPE) tissue block.

 

Acceptable:

Specimen Type: Tissue

Container/Tube: Slides

Specimen Volume: 5 unstained

Collection Instructions: Submit 5 unstained, non-baked slides with 10-micron thick sections of tissue, preferably along with an Hematoxylin and Eosin slide (not required).

 

Acceptable:

Specimen Type: Tissue

Container/Tube: Scrolls

Specimen Volume: 5 scrolls

Collection Instructions: Submit 5 scrolls of FFPE tissue cut at 10 microns thick, preferably along with an H&E slide (not required).

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded 		Reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
Refrigerated

Useful For
Suggests clinical disorders or settings where the test may be helpful

Detection of severe respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in formalin-fixed, paraffin-embedded tissue

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is a positive-sense, single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Like other coronaviruses that infect humans, SARS-CoV-2 can cause both upper and lower respiratory tract illness. Symptoms can range from mild (ie, the common cold) to severe (ie, pneumonia) in both healthy and immunocompromised patients. SARS-CoV-2 transmission occurs primarily via respiratory droplets. 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, transbronchial biopsy, wedge biopsy of lung, autopsy lung specimen) would be more likely to have detectable SARS-CoV-2. Infection of other tissue has been reported.

 

The SARS-CoV-2 RNA detection in formalin-fixed and paraffin-embedded (FFPE) tissue by droplet digital polymerase chain reaction (ddPCR) assay will be used to detect the nucleocapsid N1 and N2 target sequences of SARS-CoV-2 virus in FFPE surgical and autopsy tissue. The identification of SARS-CoV-2 in surgical tissue may aid in the diagnosis of COVID-19 and may lead to a better understanding of unusual disease presentations. Detection of SARS-CoV-2 in deceased patients (autopsy tissue) may similarly confirm a suspected diagnosis among individuals with clinical or pathologic manifestations of COVID-19 (ie, pulmonary, cardiac) and may increase understanding of SARS-CoV-2 pathobiology.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Not applicable

Interpretation
Provides information to assist in interpretation of the test results

This test will be reported as positive, negative, or indeterminate. An "indeterminate" result indicates that the presence or absence of severe respiratory syndrome coronavirus 2 (SARS-CoV-2 RNA) in the specimen could not be determined with certainty after repeated testing in the laboratory. This could be due to reverse transcriptase polymerase chain reaction (RT-PCR) inhibition or very low viral load. Submission of a new specimen for testing is recommended.

 

Test results should always be considered in the context of patient's clinical history, physical examination, and epidemiologic exposures when making the final diagnosis.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

The assay is adapted from an qualitative severe respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detection assay that has received FDA emergency use authorization (EUA), and it is modified by the performing laboratory for qualitative detection of SARS-CoV-2 RNA present in formalin-fixed and paraffin-embedded (FFPE) tissue.

 

The sensitivity of the assay is dependent on the timing of the specimen collection (in relation to symptom onset) and the quality, quantity, and type of specimen submitted. This test is not normalized to the size of the submitted tissue per section.

 

The test is specific for detection of SARS-CoV-2. Therefore, negative results do not exclude the possibility of infection with other respiratory viruses.

 

Negative results do not rule out coronavirus disease 2019 (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
Recommendations for in-depth reading of a clinical nature

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

2. Holshue ML, DeBolt C, Lindquist S, et al: First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020 Mar 5;382(10):929-936. doi: 10.1056/NEJMoa2001191

3. 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.org/10.1080/22221751.2020.1745095

4. Liu X, Feng J, Zhang Q, et al: Analytical comparisons of SARS-COV-2 detection by qRT-PCR and ddPCR with multiple primer/probe sets. Emerg Microbes Infect. 2020 Dec;9(1):1175-1179

5. Suo T, Liu X, Feng J, et al: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerg Microbes Infect. 2020 Dec;9(1):1259-1268

Method Description
Describes how the test is performed and provides a method-specific reference

The assay is a laboratory-developed modification of the Bio-Rad severe respiratory syndrome coronavirus 2 (SARS-CoV-2) droplet digital polymerase chain reaction (ddPCR) assay to generate results in formalin-fixed paraffin-embedded (FFPE) tissue specimens. RNA is extracted from either scraped unstained slides or tissue scrolls. The eluate is incorporated into the reaction mixture, followed by generation of individual reaction droplets by the QX200 Automated Droplet Generator. After completion of PCR, the droplets are analyzed for presence or absence of amplified viral target sequences using the QX200 Droplet Reader.

 

The PCR reaction mixture contains primers and probes for 2 target sequences within the SARS-CoV-2 nucleocapsid gene (N1 and N2) and a reference human ribonuclease P protein subunit 30-encoding gene (RPP30) sequence. Results are generated and reported as positive, negative, or indeterminate. The sensitivity of the assay is dependent on the timing of the specimen collection (in relation to symptom onset) and the quality, quantity, and type of specimen submitted. This test is not normalized to the size of the submitted tissue per section. The limit of detection varies based on the number of droplets generated but is approximately 5 copies of the viral genome.(Package insert: Bio-Rad SARS-CoV-2 ddPCR Test for use on the QX200 and QXDx Droplet Digital PCR Systems. Bio-Rad Laboratories, Inc; 04/2020)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Weekly

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

7 to 10 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Unused portions of blocks will be returned. Unused slides and/or scrolls are stored indefinitely.

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

87635

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
SCOVT SARS CoV-2 RNA ddPCR, Qual, FFPE 94316-7
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
610691 Result 94316-7
610692 Additional Information 94736-6
MG141 SARS CoV-2 Specimen Source 31208-2
610693 Method 85069-3
610694 Disclaimer 62364-5

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports