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Bradley
Viral respiratory tract infections are the most common diseases in humans worldwide. Adenoviruses, human metapneumovirus (HMPV), influenza viruses, coronaviruses, human parainfluenza viruses (HPIVs), and respiratory syncytial virus (RSV) commonly cause respiratory infections. Respiratory viruses can be associated with both self-limiting upper respiratory tract infections (e.g., the common cold) and more severe lower respiratory tract infections (LRTIs), such as bronchitis, bronchiolitis, pneumonitis, and pneumonia. LRTIs are a major cause of hospitalization, morbidity, and mortality in infants and the elderly and are associated with significant disease burden. ,
Laboratory testing to identify the specific pathogen causing the respiratory illness is only necessary if clinical management would be altered; for example, testing for the influenza virus during flu seasons can help to determine whether antiviral treatment should be administered. Respiratory virus testing may also be indicated in certain populations (e.g., infants, immunocompromised persons, the elderly) to help with patient management, epidemiologic surveillance, and infection control measures. Laboratory testing options include rapid antigen, direct fluorescent antibody (DFA), and polymerase chain reaction (PCR) tests.
Refer to the ARUP Consult Influenza Virus, COVID-19 - SARS-CoV-2, and Respiratory Syncytial Virus - RSV topics for detailed information about the recommended laboratory testing strategies for these specific respiratory viruses.
Quick Answers for Clinicians
Unless testing is performed for epidemiologic purposes, testing is generally indicated only for the following populations:
- At-risk patients with influenza-like symptoms (during flu season); refer to the ARUP Consult Influenza Virus topic for more information
- Infants and children who present with severe respiratory infections (respiratory syncytial virus [RSV] testing is indicated); refer to the ARUP Consult Respiratory Syncytial Virus- RSV topic for more information
- Immunocompromised patients
Indications for Testing
Although testing to identify a specific pathogen is not often indicated, it can be useful if the specific diagnosis will alter clinical management. Testing for respiratory viruses in general is indicated for immunocompromised patients presenting with severe LRTIs. Influenza testing is indicated in at-risk patients with influenza-like symptoms, and RSV testing is indicated in infants and children presenting with severe respiratory infections. For more detailed indications, refer to the ARUP Consult Influenza Virus, COVID-19 - SARS-CoV-2, and Respiratory Syncytial Virus - RSV topics.
Laboratory Testing
Diagnosis
The following table details the recommended diagnostic testing for various etiologic agents of respiratory infections.
| Virus | Recommended Diagnostic Testing | Additional Notes |
|---|---|---|
| Adenovirus | PCR | Testing is recommended for immunocompromised patients |
| HMPV | DFA PCRa | Coinfection is common, consider concurrent viral testing |
| Influenza A and B viruses | Near-point-of-care PCR | Testing is only recommended if the results will influence management decisions (e.g., antiviral therapy) |
| RSV | DFA and rapid antigen testing (in immunocompetent children) PCR (in adults, hospitalized patients, and immunocompromised patients) | Laboratory testing is only indicated when diagnosis would change the course of patient management |
| SARS-CoV-2b | NAA Rapid antigen testing | If a definitive diagnosis is required, rapid antigen test results should generally be confirmed by NAA |
| HPIV | Concurrent DFA for other common respiratory viruses PCRc | Clinical diagnosis is usually sufficient |
aPCR testing may be considered when DFA results are negative, but the clinician’s suspicion of infection is high. bFor more information concerning COVID-19 testing, refer to the ARUP Consult COVID-19 - SARS-CoV-2 topic. cPCR testing has a slower turnaround time but can detect the less common HPIV type 4. NAA, nucleic acid amplification | ||
ARUP Laboratory Tests
Qualitative Reverse Transcription Polymerase Chain Reaction
Qualitative Polymerase Chain Reaction
Direct Fluorescent Antibody Stain
Qualitative Real-Time Polymerase Chain Reaction
Qualitative Polymerase Chain Reaction (PCR)
Qualitative Polymerase Chain Reaction
Qualitative Nucleic Acid Amplification (NAA)
Direct Fluorescent Antibody Stain
Direct Fluorescent Antibody (DFA) Stain/Cell Culture
Cell Culture/Immunofluorescence
References
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Tregoning JS, Schwarze J. Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology. Clin Microbiol Rev. 2010;23(1):74-98.
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Seo YB, Song JY, Choi MJ, et al. Etiology and clinical outcomes of acute respiratory virus infection in hospitalized adults. Infect Chemother. 2014;46(2):67-76.
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ASM - Current Best Practices for Respiratory Virus Testing
Ginocchio CC, McAdam AJ. Current best practices for respiratory virus testing. J Clin Microbiol. 2011;49(9 Suppl):S44-S48.
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Miller JM, Binnicker MJ, Campbell S, et al. A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. 2018;67(6):e1-e94.