Expanded Respiratory Pathogen Panel by PCR, Routine
Test Mnemonic
RPPCR
CPT Codes
- 0202U - QTY (1)
LOINC ®
82159-5
Aliases
- Respiratory Viral panel
- RVP
- resp pathogen
- resp viral panel
- resp virus
- respiratory virus
- RPPCR
- SQRPPCR
Includes
- SARS-CoV-2
- Human Rhinovirus/Enterovirus
- Influenza A virus
- Influenza A virus A/H1
- Influenza A virus A/H3
- Influenza A virus A/H1-2009
- Influenza B virus
- Respiratory syncytial virus
- Bordetella parapertussis
- Bordetella pertussis
- Chlamydia pneumoniae
- Human Metapneumovirus
- Adenovirus
- Parainfluenza virus 1
- Parainfluenza virus 2
- Parainfluenza virus 3
- Parainfluenza virus 4
- Coronavirus 229E
- Coronavirus OC43
- Coronavirus NL63
- Coronavirus HKU1
- Mycoplasma pneumoniae
Performing Laboratory
Cleveland Clinic Laboratories
Specimen Requirements
| Volume | Type | Container | Collect Temperature | Transport Temperature | Special Instructions |
|---|---|---|---|---|---|
| 3 mL | Nasopharyngeal swab | Universal Transport Media (UTM) | Refrigerated | 1. Tilt patient's head back 70 degrees. 2. Gently and slowly insert a mini-tipped flocked swab with a flexible shaft (ie. Oracle 1172111) through the nostril parallel to the palate (not upwards) until resistance is encountered or the distance is equivalent to that from the ear to the nostril of the patient, indicating contact with the nasopharynx. 3. Gently rub and roll the swab. 4. Leave swab in place for several seconds to absorb secretions. 5. Slowly remove swab while rotating it. Specimens can be collected from both sides using the same swab, but it is not necessary to collect specimens from both sides if the swab is saturated with fluid from the first collection. If a deviated septum or blockage create difficulty in obtaining the specimen from one nostril, use the same swab to obtain the specimen from the other nostril. 6. Place swab, tip first, into the transport tube provided. Break the swab shaft at the score line, discard the top portion of the stem, and close the cap. |
Alternate Specimen Requirements
| Volume | Type | Container | Collect Temperature | Transport Temperature | Special Instructions |
|---|---|---|---|---|---|
| 1 mL | Bronch (BAL) | Sterile container | Refrigerated | Collect 2-3 mL into a sterile, leak-proof, screw-cap collection cup or sterile dry container (i.e. Oracle 1619591). If aliquotting is necessary, sterile aliquot tubes must be used. Do not dilute with transport media. | |
| 1 mL | Sputum, induced | Sterile container | Refrigerated | Before collecting a sputum, have the patient rinse their mouth with water and discard the rinse fluid. Ask the patient to breathe deeply for three or four breaths, then hold their breath and expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap collection cup or sterile dry container (i.e. Oracle 1619591). Induced sputum is also acceptable. If aliquotting is necessary, sterile aliquot tubes must be used. Do not dilute with transport media. | |
| 1 mL | Aspirate, tracheal | Sterile container | Refrigerated | Collect 2-3 mL into a sterile, leak-proof, screw-cap collection cup or sterile dry container (i.e. Oracle 1619591). If aliquotting is necessary, sterile aliquot tubes must be used. Do not dilute with transport media. | |
| 3 mL | Swab(s) | Viral Transport Media | Refrigerated | Viral transport media (including VTM, M4RT, M5, or M6) may be used to collect swabs if UTM cannot be sourced. | |
| 3 mL | Swab(s) | Saline | Refrigerated | Sterile saline may be used to collect swabs if UTM cannot be sourced. | |
| 1 mL | Swab(s) | E Swab | Refrigerated | E-swabs in liquid amies may be used to collect swabs if UTM cannot be sourced. |
Stability
| Environmental Condition | Description |
|---|---|
| Refrigerated | 3 days for nasopharyngeal swabs; 7 days for lower respiratory specimens (BAL, sputum, tracheal aspirate) |
| Frozen | 30 days |
| Ambient | 4 hours for nasopharyngeal swabs; 24 hours for lower respiratory specimens (BAL, sputum, tracheal aspirate) |
Days Performed
Sun - Sat
Turnaround Time
2 - 3 days
Methodology
| Name | Description |
|---|---|
| Reverse Transcription/Polymerase Chain Reaction (RT/PCR) |
Reference Range
Special Info
For Cleveland Clinic providers, note that this test can only be ordered from an ambulatory setting, unless it is for a lower respiratory specimen. Inpatient/ED providers should order the expedited version of this test (SQRPRACV) on upper respiratory specimens. Patients who may benefit include immunocompromised patients, those with severe underlying respiratory comorbidities, and those in whom testing may help avoid hospital admission. The test is very expensive, and if not covered by insurance, the patient will incur a substantial charge. Recommend discussing risks and benefits with the patient, and considering seeking insurance preauthorization.
Clinical Info
Respiratory pathogens cause acute local and systemic disease, with the most severe cases occurring in children, the elderly, and immunocompromised individuals. Due to the similarity of diseases caused by many viruses and bacteria, diagnosis based on clinical symptoms alone is difficult. Identification of potential causative agents provides data to aid providers in determining appropriate patient treatment or triage, and public health response for disease containment. The BioFire Respiratory Panel 2.1 (RP2.1) is a multiplexed nucleic acid test that qualitatively detects and identifies nucleic acids from the following viral and bacterial targets from respiratory specimens: SARS-CoV-2 (Agent of COVID-19); Influenza A and subtypes H1, H1N1 2009, H3; Influenza B; Respiratory syncytial virus (RSV); Human metapneumovirus (hMPV); Human rhinovirus/enterovirus; Adenovirus; Parainfluenza 1-4; Coronaviruses 229E, OC43, NL63, HKU1; Chlamydia pneumoniae; Mycoplasma pneumoniae; and Bordetella pertussis and parapertussis. These respiratory pathogens are assayed in a single pouch through array-based localization and endpoint melting curve data analysis. The assay is FDA-cleared for nasopharyngeal swab testing, and has been modified and validated as a lab-developed test for lower respiratory specimens including bronchoalveolar lavage, sputum, and tracheal aspirate. B. pertussis and parapertussis targets are not reported for lower respiratory specimens.
Clinical Limitation
For full limitations, refer to the assay instructions for use available on the manufacturer's website. The most important limitations are summarized as follows. This assay has lower sensitivity than others for detecting Bordetella pertussis. If pertussis infection is suspected, a dedicated B.pertussis molecular test should be ordered. Cross reactivity has been reported between B. bronchiseptica/parapertussis with B. pertussis, and between B. pertussis and Human rhinovirus/enterovirus. Recent administration of intranasal vaccines (ie. FluMist) may lead to false positive results. As with any nucleic acid amplification test, positive results do not rule out coinfection with other organisms, detected organisms may not be the definite cause of disease, and negative results do not rule out infection. Some patients may experience financial toxicity with this expanded multiplex panel, as it is variably reimbursed by insurance.
Clinical Reference
1. Berry GJ, Zhen W, Smith E, Manji R, Silbert S, Lima A, Harington A, McKinley K, Kensinger B, Neff C, Lu D. Multicenter Evaluation of the BioFire Respiratory Panel 2.1 (RP2.1) for Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. J Clin Microbiol. 2022 May 18;60(5):e0006622. doi: 10.1128/jcm.00066-22. Epub 2022 Apr 7. PMID: 35387475. 2. Leber AL, Everhart K, Daly JA, Hopper A, Harrington A, Schreckenberger P, McKinley K, Jones M, Holmberg K, Kensinger B. Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples. J Clin Microbiol. 2018 May 25;56(6):e01945-17. doi: 10.1128/JCM.01945-17. PMID: 29593057. 3. U.S. Food and Drug Administration (FDA). Evaluation of Automatic Class III Designation for Biofire Respiratory Panel 2.1 Decision Summary DEN200031. Accessed May 28, 2024. https://www.accessdata.fda.gov/cdrh_docs/reviews/DEN200031.pdf.