Test Id : SCOVT
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), RNA Detection, ddPCR, Tissue
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.
Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test
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. The minimum volume is sufficient for one attempt at testing.
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
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.
Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location
Indicates the location of the laboratory that performs the test
Fees :
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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. It 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.
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 |