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


Ordering Guidance


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



Specimen Required


Preferred:

Specimen Type: Nasopharyngeal swab

Container/Tube: Sterile container with viral transport media

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 mucosa surface to maximize recovery of cells.

2. Swab must be placed into viral transport media (eg, M4-RT, M4 or M5), saline, or phosphate buffered saline (PBS). Media should not contain guanidine thiocyanate (GTC).

 

Specimen Type: Bronchoalveolar lavage fluid

Container/Tube: Sterile container

Specimen Volume: 0.6 mL

Additional Information: Do not aliquot into viral transport media.

 

Acceptable:

Specimen Type: Oropharyngeal (throat) swab, nasal mid-turbinate, or nares/nasal swab

Supplies:

-Culturette (BBL Culture Swab) (T092)

-Mid Turbinate (MT) Swab (FLOQSwab/COPAN) (T864)

-Swab, Sterile Polyester (T507)

Container/Tube: Sterile container with transport media

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

Preferred: BBL Culture Swab, COPAN Mid-turbinate Swab

Acceptable: Dacron-tipped swab with plastic handle

Collection Instructions: Swab must be placed into viral transport media (eg, M4-RT, M4, or M5), saline, or PBS. Media should not contain guanidine thiocyanate (GTC).

 

Specimen Type: Bronchial washings, endotracheal aspirate, sputum

Container/Tube: Sterile container

Specimen Volume: 0.6 mL

Additional Information: Do not aliquot into viral transport media.


Secondary ID

614020

Useful For

Diagnosis of COVID-19 illness due to SARS-CoV-2

Highlights

This test qualitatively detects SARS-CoV-2 RNA present in select upper and lower respiratory specimens from patients under investigation for COVID-19.

 

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

For health care providers: https://www.fda.gov/media/136154/download

For patients: https://www.fda.gov/media/136155/download

Method Name

Reverse Transcription, Real-Time Polymerase Chain Reaction (RT-qPCR)

Reporting Name

SARS CoV-2 RNA, PCR, Varies

Specimen Type

Varies

Specimen Minimum Volume

Upper respiratory tract swab: See Specimen Required; lower respiratory specimens: 0.3 mL

Specimen Stability Information

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

Reject Due To

Bloody specimen Calcium alginate-tipped swab
Wooden shaft swab
Dry swab Glass transport media tubes
Transport swab containing gel or charcoal additive Sample tubes containing guanidine isothiocyanate, guanidine thiocyanate, or guanidine hydrochloride		 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 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. During the early stages of COVID-19 disease, the symptoms maybe nonspecific and resemble other common respiratory infections, such as influenza. If testing for other respiratory infections is negative, specific testing for SARS-CoV-2 (COVID-19) may be warranted.

 

Severe acute respiratory syndrome coronavirus 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) may be more likely to have detectable SARS-CoV-2.

Reference Values

Undetected

Interpretation

A "Detected" (positive) result indicates that SARS-CoV-2 RNA is present and suggests the diagnosis of COVID-19. The test result should always be considered in the context of patient's clinical history, physical examination, and epidemiologic exposures when making the final diagnosis.

 

An "Undetected" (negative) 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 "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 inhibition. Submission of a new specimen for testing is recommended.

Method Description

Specimens are transferred first to a specimen lysis tube, which lyses the cells, releases target nucleic acid, and protects them from degradation during storage. The internal control-S (IC-S) is added to each test specimen and control via the working Panther Fusion capture reagent-S. The IC-S in the reagent monitors all aspects of the testing process, including nucleic acid capture, elution, amplification, and detection. Capture oligonucleotides hybridize to nucleic acid in the test specimen. Hybridized nucleic acid is then separated from the specimen in a magnetic field. Wash steps purify the hybridized nucleic acid by removing extraneous components from the reaction tube. The resulting purified nucleic acid is then isolated during the elution step.

 

During the elution transfer step, purified nucleic acid is transferred to a Panther Fusion reaction tube already containing reconstituted master mix overlaid with oil reagent. Amplification of the target sequences occurs via real-time reverse transcription polymerase chain reaction. A reverse transcriptase generates a DNA copy of the target sequences. Target-specific forward and reverse primers and probes amplify and detect 2 regions of the orf1ab gene of SARS-CoV-2 in conjunction with the internal control. The amplified orf1ab target products are detected on the ROX channel, while the internal control is detected on RED677. The assay software compares the viral target and internal control fluorescence signals to predetermined cut-off values to produce a qualitative result for the presence or absence of the virus.(Instruction manual: SARS-CoV-2 Assay [Panther Fusion System]. AW-21159-001. Hologic, Inc; Rev. 006, 05/2022)

Day(s) Performed

Monday through Sunday

Performing Laboratory

Mayo Clinic Laboratories in Rochester

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
HPCOV SARS CoV-2 RNA, PCR, Varies 94559-2

 

Result ID Test Result Name Result LOINC Value
614021 SARS CoV-2 RNA, PCR 94559-2
HPCVS SARS CoV-2 RNA, PCR, Source 31208-2