Test Id : CVOOA

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

Due to the non-specific clinical presentation of coronavirus disease 2019 (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 https://www.cdc.gov/coronavirus/2019-ncov/index.html

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 Type: Nasopharyngeal (NP), oropharyngeal (OP; ie, throat).

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 https://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: Lower respiratory tract

Sources: Bronchoalveolar lavage (BAL) fluid, bronchial washings, endotracheal aspirate, sputum

Container/Tube: Sterile container

Specimen Volume: Minimum of 2.2 mL

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

• COVID-19 Oropharyngeal Collection Instructions
• Coronavirus Disease 2019 (COVID-19), Influenza, and Respiratory Syncytial Virus Testing Algorithm

See Specimen Required

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

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

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 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 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.

Undetected

A "Detected" result indicates that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is present and suggests the diagnosis of coronavirus disease 2019 (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.

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 "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 real-time reverse transcription polymerase chain reaction (RT-PCR) inhibition. Submission of a new specimen for testing is recommended.

The FDA has provided emergency use authorization (EUA) of these assays for testing human nasopharyngeal and oropharyngeal swab specimens. Bronchoalveolar lavage fluid specimens were validated in a manner consistent with CLIA requirements.

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 severe acute respiratory syndrome coronavirus 2 (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 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.

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

4. Centers for Disease Control and Prevention. Overview of testing for SARS-CoV-2. Available at www.cdc.gov/coronavirus/2019-nCoV/hcp/clinical-criteria.html

5. Food and Drug Administration. FAQs on diagnostic testing for SARS-CoV-2. Available at www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testing-sars-cov-2

Abbott m2000rt assay:

The Abbott m2000 Sample Preparation System kit is used with the automated Abbott m2000sp sample preparation system to extract and purify viral RNA from human nasopharyngeal specimens, based on magnetic particle technology. Amplification and detection of target sequence is performed on the Abbott m2000rt instrument. This kit contains primers and probes targeting the N and RdRp genes specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). An internal RNA control is also added to the extraction reagents and carried through the entire process in each specimen to ensure adequate extraction has occurred free of inhibitory substances.(Package insert: Abbott RealTime SARS-CoV-2. Abbott Molecular Inc; 03/2020)

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

For health care providers: https://www.fda.gov/media/136256/download

For patients: https://www.fda.gov/media/136257/download

Abbott Alinity m assay:

The Alinity m SARS-CoV-2 assay is a dual target assay for the RdRp and N genes.

An RNA sequence that is unrelated to the SARS-CoV-2 sequence is introduced into each specimen at the beginning of sample preparation. This unrelated RNA sequence is simultaneously amplified by real-time reverse transcription polymerase chain reaction (RT-PCR) and serves as an internal control (IC) to demonstrate that the process has proceeded correctly for each sample.

The Alinity m SARS-CoV-2 assay detects the SARS-CoV-2 virus and IC target sequences through the use of target-specific fluorescent-labeled oligonucleotide probes. The probes do not generate a signal unless they are specifically bound to the amplified product. The 2 SARS-CoV-2-specific probes are labeled with the same fluorophore and the IC-specific probe is labeled with a different fluorophore, thus allowing for simultaneous detection of both SARS-CoV-2 and IC amplified products in the same reaction vessel.(Package insert: Abbot SARS-CoV-2 AMP Procedure. Abbott Molecular Inc; 05/2020) 

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

For healthcare providers: https://www.fda.gov/media/137978/download

For patients: https://www.fda.gov/media/137981/download

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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.

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