Guidance for Clinicians on the Use of RT-PCR and Other Molecular Assays for Diagnosis of Influenza Virus Infection
On this Page
- Use in Clinical Decision Making
- Testing of Hospitalized Patients
- Detecting Institutional Outbreaks
- Detecting Novel Influenza A Cases
- Factors Influencing Results
- Interpreting Results
- Advantages/Disadvantages
- Rapid Molecular Assays
- References
- Table 1. FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses (PDF Available)
Background
Tests for influenza include molecular assays, rapid influenza diagnostic tests, immunofluorescence, viral culture or serology. This guidance focuses upon molecular assays for influenza as they are increasingly being used in clinical settings (1). Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and other molecular assays can identify the presence of influenza viral RNA in respiratory specimens. (See Table 1below.) Some molecular assays are able to detect and discriminate between infections with influenza A and B viruses; other tests can identify specific seasonal influenza A virus subtypes [A(H1N1)pdm09, or A(H3N2)]. These assays can yield results in 1-6 hours. Notably, the detection of influenza viral RNA by these assays does not always indicate detection of viable virus or on-going influenza viral replication. It is important to note that not all assays have been cleared by the FDA for diagnostic use. FDA-cleared assays are listed in Table 1.
1 One FDA-cleared rapid molecular assay is available in the United States. This assay has high sensitivity and yields results in 15 minutes.
Use in Clinical Decision Making
- Influenza testing is not needed for all patients with signs and symptoms of influenza to make antiviral treatment decisions (See Figure 1, Figure 2). Once influenza activity has been identified in the community or geographic area, a clinical diagnosis of influenza can be made for outpatients with signs and symptoms consistent with suspected influenza, especially during periods of peak influenza activity in the community. Rapid molecular assays (for example, the Alere i Influenza A&B that produces results in 15 minutes) or other molecular assays that detect influenza viruses (such as the Cepheid or Biofire assays that produce results in one hour) are now becoming available in hospitals.
- Molecular testing is not needed on all patients with suspected influenza, but is most appropriate for hospitalized patients if a positive test would result in a change in clinical management.
- Clinicians should be aware of the approved clinical specimens for the molecular assay being used (see Table 1, FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses[305 KB, 6 pages] ).
- If treatment is clinically indicated, antiviral treatment should NOT be withheld from patients with suspected influenza while awaiting testing results during periods of peak influenza activity in the community when the likelihood of influenza is high. More information about antiviral treatment of influenza is available at Antiviral Drugs, Information for Health Care Professionals.
- Since results from molecular assays may not always be available when initial therapy decisions must be made, antiviral treatment should be started as soon as possible because the greatest clinical benefit is when treatment is initiated as close to illness onset as possible, especially for patients at high risk of serious outcomes.
Influenza Testing of Hospitalized Patients
- Hospitalized patients with suspected influenza without lower respiratory tract disease should have upper respiratory tract specimens collected for influenza testing. More information about antiviral treatment of influenza is available at Antiviral Drugs, Information for Health Care Professionals.
- Collection of lower respiratory tract specimens from hospitalized patients with suspected influenza and pneumonia can be considered for influenza testing by RT-PCR and other molecular assays if influenza testing of upper respiratory tract specimens is negative and if positive testing would result in a change in clinical management. Hospitalized patients with suspected influenza and respiratory failure on mechanical ventilation can have an endotracheal aspirate specimen collected for influenza testing by RT-PCR if a laboratory diagnosis of influenza has not been determined. Bronchoalveolar lavage fluid, if collected for other diagnostic purposes, can also be tested by RT-PCR for influenza viruses. Currently, only the CDC RT-PCR assay is FDA-cleared for lower respiratory tract specimens; this test is available only at qualified public health laboratories (see Table 1, FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses[305 KB, 6 pages] ). Clinicians may elect to order other FDA-cleared assays for off-label use in evaluating lower respiratory tract specimens. Performance of these assays for these specimens has not been evaluated by FDA; however, these assays may be more readily accessible at some institutions.
Use in Detecting Institutional Influenza Outbreaks
- Molecular assays such as RT-PCR are particularly useful to identify influenza virus infection as a cause of respiratory outbreaks in institutions (e.g., nursing homes, chronic care facilities, and hospitals).
- Positive results from one or more ill persons with suspected influenza can support decisions to promptly implement prevention and control measures for influenza outbreaks. Clinicians should be aware of requirements from their public health authorities regarding prompt notification of any suspected or confirmed institutional influenza outbreaks, and when respiratory specimens should be collected from ill persons and sent to a public health laboratory for laboratory confirmation of influenza.
Use in Detecting Novel Influenza A Cases
- Molecular assays, such as RT-PCR, are designed to accurately identify influenza A and B viral RNA by using conserved gene targets. Some assays will detect influenza A or B viruses but will not determine the influenza A virus subtype, and thus will not be able to indicate if the infection is due to a novel influenza A virus. Novel influenza A viruses are antigenically and genetically distinct from currently circulating influenza A viruses among humans and usually represent zoonotic transmission from avian or swine species to humans.
- Some FDA-cleared devices can not only detect influenza A or B viruses, but also can identify influenza A hemagglutinin genes, allowing for determination of some or all of the seasonal influenza A virus subtypes [i.e., A(H1N1)pdm09 or A(H3N2)]. These assays will not only identify the currently circulating influenza A virus strains, but also may identify viruses that are detected as influenza A for which no subtype could be identified. These “unsubtypables” may represent novel influenza A virus infections.
- Clinicians and laboratorians using molecular assays that are capable of detecting all currently circulating seasonal influenza A virus subtypes [i.e., A(H1N1)pdm09 or A(H3N2)], and who identify an “unsubtypable” result (i.e., influenza A with no subtype detected), should contact their state or local public health laboratory immediately for additional testing to determine if the infection is due to a novel influenza A virus.
Factors Influencing Results of Molecular Assays
Many factors can influence influenza testing results. Influenza viral shedding in the upper respiratory tract generally declines substantially after 4 days in immunocompetent patients with uncomplicated influenza. Patients with lower respiratory tract disease may have prolonged influenza viral replication in the lower respiratory tract. Immunosuppressed patients and persons receiving systemic corticosteroids can also have prolonged influenza viral replication in the lower respiratory tract. Molecular tests can detect influenza viral RNA (positive results) for a longer duration than other influenza testing (e.g., antigen testing - immunofluorescence or rapid influenza diagnostic tests). Although RT-PCR is the most sensitive influenza test and is highly specific, negative results can occur in persons with influenza for multiple reasons, so negative RT-PCR results may not always exclude a diagnosis of influenza. If clinical suspicion of influenza is high, antiviral treatment should continue in patients with severe illness or at high risk for complications while additional respiratory specimens are collected and influenza testing is performed.
Factors that can influence influenza testing results are:
Factors that can influence influenza testing results are:
- Time from illness onset to collection of respiratory specimens for testing
- Respiratory specimens should ideally be collected as early as possible (ideally less than 4 days after illness onset when influenza viral shedding is highest) in persons without lower respiratory tract disease and tested as soon as possible. Molecular assays may be able to detect influenza viral RNA in respiratory tract specimens longer than other influenza tests (e.g., after 72 hours from illness onset).
- Source of respiratory specimens tested and specimen handling
- The best upper respiratory tract specimens to detect influenza viral RNA by RT-PCR and other molecular assays are nasopharyngeal swabs, washes or aspirates; other acceptable specimens are a nasal and/or throat swab. A swab with a wood shaft should not be used for respiratory specimen collection because it may interfere with RT-PCR and other molecular assays. Clinicians should be aware of the approved clinical specimens for the molecular assay being used and what type of swabs are recommended for use with the assay as included in the manufacturer’s instructions included in the assay.
- Hospitalized patients with lower respiratory tract disease may have prolonged lower respiratory tract influenza viral replication compared to the upper respiratory tract. In patients with lower respiratory tract disease, lower respiratory tract specimens should be collected and tested if influenza is clinically suspected and testing of upper respiratory tract specimens is negative. For critically ill patients with suspected influenza, even when testing by RT-PCR or other molecular assays is negative, consideration should be given to collecting additional respiratory specimens from multiple sites, especially lower respiratory tract (endotracheal aspirate, or bronchoalveolar lavage – if clinically indicated for other diagnostic purposes) and re-tested for influenza viruses by RT-PCR or other molecular assays. Antiviral treatment should be continued in such patients pending additional influenza testing.
- If testing is delayed or is done at a facility other than where the patient is hospitalized, specimens should be placed in sterile viral transport media, consistent with test specifications, and refrigerated until transported to the laboratory for testing as soon as possible. Freezing and thawing should be avoided or minimized to avoid degradation of influenza viruses if viral culture will be performed.
- Manufacturer's instructions, including acceptable specimens, handling, and storage and processing, should be followed to achieve optimum test performance. Deviations from recommended procedures may result in false negative results.
Interpretation of Testing Results
Sensitivities and specificities of RT-PCR and other molecular assays that have been cleared by the FDA for diagnostic use are high compared to other FDA-cleared assays which use different methods. However, even with RT-PCR, false negative results can occur due to improper or poor clinical specimen collection or from poor handling of a specimen after collection and before testing. A negative result can also occur by testing a specimen that was collected when the patient is no longer shedding detectable influenza virus. False positive results, although rare, can occur (e.g., due to lab contamination or other factors).
- Negative result
- A negative result means that there is no evidence of influenza viral RNA in the specimen tested. For hospitalized patients, especially for patients with lower respiratory tract disease, if no other etiology is identified and influenza is still clinically suspected, additional specimens should be collected and tested, and antiviral treatment should be initiated or continued.
- Positive result
- A positive result indicates detection of influenza viral RNA, confirming influenza virus infection, but does not necessarily mean viable virus is present or that the patient is contagious.
- A positive result on testing an upper respiratory tract specimen in a person who recently received intranasal administration of live attenuated influenza virus vaccine (LAIV) may indicate detection of vaccine virus. LAIV contains influenza virus strains that undergo viral replication in respiratory tissues of lower temperature (e.g., nasal passages) than internal body temperature. Since the nasal passages are infected with live influenza virus vaccine strains during LAIV administration, sampling the nasal passages within a few days after LAIV vaccination can yield positive influenza testing results. It may be possible to detect LAIV vaccine strains up to 7 days after vaccination, and in rare situations, for longer periods.
- Influenza molecular assay interpretation will depend on the individual test that is performed. For example, a negative result from an influenza molecular assay that only detects influenza A virus and the A(H1N1)pdm09 subtype does not preclude infection with influenza B virus. Clinicians can consult for detailed descriptions of each FDA-cleared test and what the result may or may not signify.
Advantages/Disadvantages of Molecular Assays
Advantages:
- Molecular assays are more sensitive and specific for detecting influenza viruses than other influenza tests (e.g., rapid influenza diagnostic tests, immunofluorescence, and viral culture)
- The likelihood of a false positive or false negative result is low and therefore, the interpretation of the result is less impacted by the level of influenza activity in the community
- Some, but not all molecular assays can distinguish between specific influenza A virus subtypes
Disadvantages:
- Results of RT-PCR and other molecular assays may not be available in a clinically relevant time frame to inform clinical management decisions.
- RT-PCR and other molecular assays may not always be available in all outpatient or emergency room settings. For hospitalized patients, these assays are not always available on-site.
- Respiratory specimens may need to be sent to a state public health laboratory or commercial laboratory for RT-PCR. Therefore, although the test can yield results in 1-8 hours, the actual time to receive results may be substantially longer.
- Most FDA-cleared molecular assays are not approved to test lower respiratory tract specimens
- RT-PCR and other molecular assays are generally more expensive than other influenza tests
- Some molecular assays may not specifically identify all currently circulating influenza A virus subtypes. Depending on the test, a negative result for one influenza A virus subtype may not preclude infection with another influenza A virus subtype.
- Some influenza molecular assays being used are not FDA-cleared and an evaluation has not been performed to assess the accuracy of all available RT-PCR and molecular assays. A list of FDA-cleared tests is available in Table 1, FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses[305 KB, 6 pages] .
Rapid Molecular Assays
Rapid molecular assays are a new type of molecular influenza diagnostic test for upper respiratory tract specimens. These platforms use isothermal nucleic acid amplification and have high sensitivity and yield results in 15 minutes or less. Sensitivities of available rapid molecular assays range from 70-100%. As with other molecular diagnostic tests, if treatment is clinically indicated, antiviral treatment should NOT be withheld from patients with suspected influenza while awaiting testing results during periods of peak influenza activity in the community when the likelihood of influenza is high. More information about antiviral treatment of influenza is available at Antiviral Drugs, Information for Health Care Professionals.
References
Ali T, Scott N, Kallas W, Halliwell ME, Savino C, Rosenberg E, Ferraro M, Hohmann E. Detection of influenza antigen with rapid antibody-based tests after intranasal influenza vaccination (FluMist). Clin Infect Dis. 2004 Mar 1;38(5):760-2.
Bell J, Bonner A, Cohen DM, Birkhahn R, Yogev R, Triner W, Cohen J, Palavecino E, Selva-rangan R. Multicenter clinical evaluation of the novel Alere™ i Influenza A&B isothermal nucleic acid amplification test. J Clin Virol. 2014 Sep;61(1):81-6.
Block SL, Yogev R, Hayden FG, Ambrose CS, Zeng W, Walker RE. Shedding and immunogenicity of live attenuated influenza vaccine virus in subjects 5-49 years of age. Vaccine. 2008 Sep 8;26(38):4940-6.
Hazelton B, Gray T, Ho J, Ratnamohan VM, Dwyer DE, Kok J. Detection of influenza A and B with the Alere i Influenza A & B: a novel isothermal nucleic acid amplification assay. Influenza and Other Respiratory Viruses 2015;9(3):151-4.
Mahony JB. Nucleic acid amplification-based diagnosis of respiratory virus infections. Expert Rev Anti Infect Ther. 2010 Nov;8(11):1273-92.
Shu B, Wu KH, Emery S, Villanueva J, Johnson R, Guthrie E, Berman L, Warnes C, Barnes N, Klimov A, Lindstrom S. Design and performance of the CDC real-time reverse transcriptase PCR swine flu panel for detection of 2009 A (H1N1) pandemic influenza virus. J Clin Microbiol. 2011 Jul;49(7):2614-9.
Talbot TR, Crocker DD, Peters J, Doersam JK, Ikizler MR, Sannella E, Wright PE, Edwards KM. Duration of virus shedding after trivalent intranasal live attenuated influenza vaccination in adults. Infect Control Hosp Epidemiol. 2005 May;26(5):494-500.
Wang R, Taubenberger JK. Methods for molecular surveillance of influenza. Expert Rev Anti Infect Ther. 2010 May;8(5):517-27.
Additional Information
- Antiviral Agents for the Treatment and Chemoprophylaxis of Influenza[1 MB, 28 pages]. Recommendations of the Advisory Committee on Immunization Practices (ACIP).
- Harper SA, Bradley JS, Englund JA, File TM, Gravenstein S, Hayden FG, McGeer AJ, Neuzil KM, Pavia AT, Tapper ML, Uyeki TM, Zimmerman RK; Expert Panel of the Infectious Diseases Society of America. Seasonal influenza in adults and children--diagnosis, treatment, chemoprophylaxis, and institutional outbreak management: clinical practice guidelines of the Infectious Diseases Society of America. Clin Infect Dis. 2009 Apr 15;48(8):1003-32.
- World Health Organization. Clinical management of human infection with pandemic (H1N1) 2009: revised guidance[304 KB, 15 pages].
- WHO Global Influenza Surveillance Network. Manual for the laboratory diagnosis and virological surveillance of influenza[2 MB, 153 pages].
Table 1. FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses
| Products | Manufacturer(s) | Influenza Virus Type Detected | Influenza Virus Subtype(s) Differentiated | Other Respiratory Viruses Differentiated | Acceptable Specimens1 | Test Time2/ Complexity3 |
|---|---|---|---|---|---|---|
| Alere i NAT Flu A/B (CLIA Waived) | Alere | Influenza A and B | None | None | Nasal swabs (Direct) | 0.25h/ CLIA Waived |
| Alere i NAT Flu A/B (Moderate) | Alere | Influenza A and B | None | None | Nasal swabs (in VTM5) | 0.25 h/ Moderate |
| CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel (Influenza A/B Typing Kit4) | CDC Influenza Division | Influenza A and B | A/H1, A/H3, A/2009 H1, A/H5N1 (Asian Lineage | None | Nasopharyngeal swabs, nasal swabs, throat swabs, nasal aspirates, nasal washes, dual nasopharyngeal/ throat swabs broncheoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, and viral culture | ~4 h/ High |
| CDC Human Influenza Virus Real-Time RT-PCR Detection and Characterization Panel | CDC Influenza Division | Influenza A | A/HI, A/H3, | None | Nasopharyngeal swabs, nasal swabs (in VTM5), or viral culture | ~4 h/ High |
| CDC Influenza A/H5 (Asian Lineage) Virus Real-Time RT-PCR Primer and Probe Set | CDC Influenza Division | Influenza A | A/H5N1 (Asian lineage) | None | respiratory specimens and viral culture | ~4 h/ High |
| CDC Influenza 2009 A(H1N1)pdm Real-Time RT-PCR Panel | CDC Influenza Division | Influenza A | 2009 H1 | None | Nasopharyngeal swabs, nasal swabs, nasal aspirates, nasal washes, dual nasopharyngeal/ throat swabs, broncheoalveolar lavages, tracheal aspirates, bronchial washes, and viral culture | ~4 h/ High |
| Cepheid Xpert Flu Assay | Cepheid | Influenza A and B | A/2009 H1 | None | Nasopharyngeal swabs (in VTM5), nasal aspirates, and nasal washes, | 1.0 h/ Moderate |
| Cepheid Xpert Flu/RSV XC Assay | Cepheid | Influenza A and B | None | Respiratory Syncytial Virus | Nasopharyngeal swabs and nasal wash and nasal aspirate (in VTM) | <1.0 h/ Moderate |
| eSensor® Respiratory Viral Panel (RVP) | GenMark Diagnostics, Inc. | Influenza A and B | A/HI, A/H3, A/2009 H1 | Respiratory Syncytial Virus subtype A, Respiratory Syncytial Virus subtype B, Parainfluenza 1, 2, and 3 virus, Human Metapneumovirus, Adenovirus Species B/E, Adenovirus Species C, and Human Rhinovirus | Nasopharyngeal swabs (in VTM5) | ~8 h/ High |
| FilmArray Respiratory Panel | BioFire Diagnostics, LLC | Influenza A and B | A/HI, A/H3, A/2009 H1 | Respiratory Syncytial Virus, Parainfluenza 1, 2, 3 and 4 virus, Human Metapneumovirus, Rhinovirus/Enterovirus, Adenovirus, Coronavirus HKU1, Coronavirus NL63 | Nasopharyngeal swabs (in VTM5) | 1.0 h/ Moderate |
| Ibis PLEX-ID Flu | Ibis/Abbott | Influenza A and B | A/HI, A/H3, A/2009 H1 | None | Nasopharyngeal swabs (in VTM5) | ~8 h/ High |
| IMDx Flu A/B and RSV for Abbottm2000 | IMDx | Influenza A and B | A/HI, A/H3, A/2009 H1 | Respiratory Syncytial Virus | Nasopharyngeal swabs (in VTM5) | ~4 h/ High |
| IQuum Liat Influenza A/B Assay | IQuum/Roche Molecular Diagnostics | Influenza A and B | None | None | Nasopharyngeal swabs (in VTM5) | ~0.5 h/ Moderate |
| Prodesse PROFLU™+ | GenProbe/Hologic | Influenza A and B | None | Respiratory Syncytial Virus | Nasopharyngeal swabs (in VTM5) | <4h/ High |
| Prodesse ProFAST™+ | GenProbe/Hologic | Influenza A | A/HI, A/H3, A/2009 H1 | None | Nasopharyngeal swabs (in VTM5) | <4h/ High |
| Qiagen Artus Influenza A/B Rotor-gene RT-PCR kit | Qiagen | Influenza A and B | None | None | Nasopharyngeal swabs (in VTM5) | ~4 h/ High |
| Quidel Molecular Influenza A+B Assay | Quidel | Influenza A and B | None | None | Nasopharyngeal swabs and nasal swabs (in VTM5) | ~4 h/ High |
| Simplexa™ Flu A/B & RSV | Focus Diagnostics, 3M | Influenza A and B | None | RSV | Nasopharyngeal swabs (in VTM5) | <4h/ High |
| Simplexa™ Flu A/B & RSV Direct | Focus Diagnostics, 3M | Influenza A and B | None | RSV | Nasopharyngeal swabs (in VTM5) | <2h/ Moderate |
| Simplexa™ Influenza A H1N1 (2009) | Focus Diagnostics, 3M | Influenza A | A/2009 H1 | None | Nasopharyngeal swabs, nasal swabs (in VTM5), and nasopharyngeal aspirates | <4h/ High |
| U.S. Army JBAIDS Influenza A&B Detection Kit4 | Biofire Defense | Influenza A and B | None | None | Nasopharyngeal swabs (in VTM5) and Nasopharyngeal washes | ~4 h/ High |
| U.S. Army JBAIDS Influenza A Subtyping Kit4 | Biofire Defense | Influenza A | A/HI, A/H3, A/2009 H1 | None | Nasopharyngeal swabs (in VTM5) and Nasopharyngeal washes | ~4 h/ High |
| U.S. Army JBAIDS Influenza A/H5 Kit4 | Biofire Defense | Influenza A | A/H5N1 (Asian Lineage) | None | Nasopharyngeal and throat swabs (in VTM5) | ~4 h/ High |
| Verigene® Respiratory Virus Nucleic Acid Test | Nanosphere, Inc | Influenza A and B | None | Respiratory Syncytial Virus subtype A, Respiratory Syncytial Virus subtype B | Nasopharyngeal swabs (in VTM5) | 3.5 h/ Moderate |
| Verigene® Respiratory Virus Plus Nucleic Acid Test (RV+) | Nanosphere, Inc | Influenza A and B | A/HI, A/H3, A/2009 H1 | Respiratory Syncytial Virus subtype A, Respiratory Syncytial Virus subtype B | Nasopharyngeal swabs (in VTM5) | 3.5 h/ Moderate |
| Verigene® Respiratory Pathogen Nucleic Acid Test (RP Flex) | Nanosphere, Inc | Influenza A and B | A/H1 (including H1 and 2009 H1), and A/H3 | Respiratory Syncytial Virus subtype A, Respiratory Syncytial Virus subtype B, Parainfluenza 1, 2 3, and 4 virus, Human Metapneumovirus, Adenovirus, and Rhinovirus | Nasopharyngeal swabs (in VTM5) | 3.5 h/ Moderate |
| x-TAG® Respiratory Viral Panel (RVP) | Luminex Molecular Diagnostics Inc. | Influenza A and B | A/H1, A/H3 | Respiratory Syncytial Virus subtype A, Respiratory Syncytial Virus subtype B, Parainfluenza 1, 2, and 3 virus, Human Metapneumovirus, Rhinovirus, and Adenovirus | Nasopharyngeal swabs (in VTM5) | ~8 h/ High |
| x-TAG® Respiratory Viral Panel Fast (RVP FAST) | Luminex Molecular Diagnostics Inc. | Influenza A and B | A/H1, A/H3 | Respiratory Syncytial Virus Human Metapneumovirus, Rhinovirus, and Adenovirus | Nasopharyngeal swabs (in VTM5) | ~6 h/ High |
- These specimen types are specified in product package inserts cleared by the U.S. Food and Drug Administration (FDA)
- Test Time is inclusive of actual test time and is exclusive of transport, handling, laboratory run schedules, and generating results. Timing may vary depending on extraction process used. Contact laboratory for expected turn-around time.
- Clinical Laboratory Improvement Amendments require categorization of tests as waived, moderate or high complexity. Ref: http://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index.html
- Available only to qualified DoD laboratories, U.S. public health laboratories, and NREVSS collaborating laboratories.
- VTM = Viral transport media
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