Test Id : SCOFR

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

Due to the non-specific clinical presentation of coronavirus disease 2019 (COVID-19), influenza and respiratory syncytial virus during the early stages of flu-like illness, concurrent testing for these 4 respiratory tract viral pathogens may be warranted.

For the most up-to-date information and testing recommendations, visit:

www.cdc.gov/coronavirus/2019-ncov/index.html

www.cdc.gov/flu/professionals/diagnosis/index.htm

www.cdc.gov/rsv/clinical/index.html#lab

Ship specimens refrigerated (if less than 72 hours from collection to arrive at MCL) or frozen (if greater or equal to 72 hours from collection to arrive at MCL).

Specimen Type: Nasopharyngeal (NP), oropharyngeal (OP; ie, throat), nasal mid-turbinate, or nares/nasal swab

Supplies:

-Swab, Sterile Polyester, 10 per package (T507)

-Dacron-tipped swab with plastic shaft is acceptable

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. For more information on OP swab specimen collection, see COVID-19 Oropharyngeal Collection 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: 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.

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

See Specimen Required

Simultaneous detection and differentiation of coronavirus disease 2019 (COVID-19) (due to severe acute respiratory syndrome coronavirus 2: SARS-CoV-2), influenza A, influenza B, and respiratory syncytial viral infection in a single upper respiratory tract specimen from an individual with flu-like illness

See following websites on indications and recommendations for testing:

www.cdc.gov/coronavirus/2019-ncov/index.html

www.cdc.gov/flu/professionals/diagnosis/index.htm

www.cdc.gov/rsv/clinical/index.html#lab

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

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, 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, 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.

Influenza, also known as the "flu," is an acute, contagious respiratory illness caused by influenza A, B, and C viruses. Of these, only influenza A and B are thought to cause significant disease, with infections due to influenza B usually being milder than infections with influenza A. Influenza A viruses are further categorized into subtypes based on the 2 major surface protein antigens: hemagglutinin (H) and neuraminidase (N).

Common symptoms of influenza infection include fever, chills, sore throat, muscle pains, severe headache, weakness, fatigue, and a nonproductive cough. Certain patients, including infants, the elderly, the immunocompromised, and those with impaired lung function, are at risk for serious complications.  In the northern hemisphere, annual epidemics of influenza typically occur during the fall or winter months. However, the peak of influenza activity can occur as late as April or May, and the timing and duration of flu seasons vary.

Influenza infection may be treated with supportive therapy, as well as antiviral drugs such as the neuraminidase inhibitors, oseltamivir (Tamiflu) and zanamivir (Relenza). These drugs are most effective when given within the first 48 hours of infection, so prompt diagnosis and treatment are essential for proper management.

Respiratory syncytial virus (RSV) is an infectious pathogen that infects the human respiratory tract causing an influenza-like illness. Most healthy people spontaneously recover from RSV infection in 1 to 2 weeks, but infection can be severe in infants, young children, and older adults. The virus is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia in children under 1 year of age in the United States, and it is recognized increasingly as a frequent cause of respiratory illnesses in older adults.

RSV can be detected by polymerase chain reaction in the human upper and lower respiratory tract specimens. Nasopharyngeal swabs or aspirates are the preferred specimen types for detection of RSV RNA. Nasal swabs may not yield as high detection rate as those of nasopharyngeal specimens for molecular detection of RSV RNA.

Undetected

A "Detected" result indicates that the specific virus is present and suggests infection with the virus. Test results 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 the specific virus is not present in the patient's specimen. However, this result may be influenced by the stage of the infection, quality, and type of the specimen collected for testing. Result should be correlated with patient's history and clinical presentation.

An "Indeterminate" result of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2 RNA) polymerase chain reaction (PCR) suggests that the patient may be infected with a variant SARS-CoV-2 or SARS-related coronavirus. Additional testing with an alternative molecular method is recommended on a newly collection specimen may be considered if the patient does not have signs and/or symptoms of coronavirus disease 2019 (COVID-19).

An "Inconclusive" result indicates that the presence or absence of the specific virus in the specimen could not be determined with certainty after repeat testing in the laboratory, possibly due to reverse transcription-PCR inhibition. Submission of a new specimen for testing is recommended.

The sensitivity of the assay is dependent on the timing of the specimen collection (in relation to symptom onset), quality, and type of the specimen submitted for testing. This test should not be performed unless the patient meets clinical and epidemiologic criteria for testing.

The test is specific for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses, and RSV, positive test results do not exclude the possibility of concurrent infection with other respiratory viruses. This assay does not distinguish among the different subtypes of influenza A virus.

Undetected (ie, negative) results do not rule out SARS-CoV-2, influenza A, influenza B, or RSV infection in patients and should not be used as the sole basis for treatment or other patient management decisions. Results should be correlated with patient's history and clinical presentation. This assay detects both viable and nonviable virus.

1. Centers for Disease Control and Prevention (CDC). Overview of testing for SARS-CoV-2. CDC; Updated March 17, 2021. Accessed March 18, 2021. Available at www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html

2. Centers for Disease Control and Prevention (CDC), National Center for Immunization and Respiratory Diseases (NCIRD). Information for clinicians on influenza virus testing. Updated November 2020. Accessed December 17, 2021. Available at www.cdc.gov/flu/professionals/diagnosis/index.htm

3. US Food and Drug Administration. FAQs on testing for SARS-CoV-2. Accessed December 17, 2021. Available at www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/faqs-testing-sars-cov-2

4. National Center for Immunization and Respiratory Diseases (NCIRD), Division of Viral Diseases, Centers for Disease Control and Prevention (CDC). Respiratory syncytial virus infection (RSV). Updated December 2020. Accessed December 17, 2021. Available at www.cdc.gov/rsv/clinical/index.html

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

Severe Acute Respiratory Syndrome Coronavirus 2, Influenza A, and Influenza B: The assay is a TaqMan probe-based, real-time reverse transcription polymerase chain reaction (RT-PCR) assay with emergency-use authorization from the U.S. Food and Drug Administration.  It is designed for qualitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, influenza A RNA, and influenza B RNA in human upper respiratory tract specimens. Viral target-specific primers and probes are used to amplify and detect the ORF1ab (nonstructural protein) sequence of SARS-CoV-2, E gene (structural envelope protein) sequence of Sarbecovirus group, encoding gene sequence for the matrix proteins 1 and 2 (M1/M2) of influenza A virus, and encoding sequence of the nuclear export protein (NEP)/nonstructural protein 1(NS1) genes of influenza B virus. Clinical samples undergo automated sample preparation (nucleic acid extraction and purification), during which viral nucleic acid in patient samples and added internal control RNA 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 and Influenza A/B: Qualitative assay for use on the cobas 6800/8800 Systems. Roche Molecular Systems, Inc; Doc Rev. 1.0, 09/2020)

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

For health care providers: www.fda.gov/media/141885/download

For patients: www.fda.gov/media/141886/download

Respiratory Syncytial Virus:

This assay is a laboratory-developed, TaqMan probe-based, RT-PCR assay using a commercially available test designed for qualitative detection of respiratory syncytial virus (RSV) in human upper respiratory tract specimens. Viral target-specific primers and probe are used to amplify and detect the matrix protein (M)-encoding sequence of RSV. Clinical samples undergo automated sample preparation (nucleic acid extraction and purification), during which viral nucleic acid in patient samples and added internal control RNA 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. Known positive and negative controls are processed in the same way in each assay run.(Package insert: cobas Influenza A/B & RSV UC: Qualitative nucleic acid test for use on the cobas 6800/8800 Systems. Roche Molecular Systems, Inc; Doc Rev. 1.0, 09/2021)

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See Individual Test IDs

87636-COFLU

87634-RSVQL

Sample Reports

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

Normal Reports | Abnormal Reports

SI Sample Reports

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SI Normal Reports | SI Abnormal Reports