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FeedbackViral respiratory tract infections are the most common diseases affecting humans worldwide. Respiratory viruses can be associated with both self-limiting upper respiratory tract infections (eg, the common cold) and more severe lower respiratory tract infections (LRTIs) (eg, bronchitis, bronchiolitis, pneumonitis, 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 the flu season can help to determine whether antiviral treatment should be administered. Respiratory virus testing may also be indicated in certain populations (eg, infants, immunocompromised persons, the elderly) to help with patient management, epidemiologic surveillance, and infection control measures. Laboratory testing options include rapid antigen detection tests (RADTs), direct fluorescent antibody (DFA) and polymerase chain reaction (PCR) tests, and viral culture.
Quick Answers for Clinicians
Nucleic acid amplification testing (NAAT) is recommended for diagnosis, screening, and surveillance of COVID-19.
Serology testing is used to evaluate exposure to the virus. Two types of serology tests are available: laboratory-based immunoassays and rapid lateral flow immunoassays that can be used near the point of care. Some tests detect total antibodies, whereas others detect specific isotypes (immunoglobulin G [IgG], IgM, IgA).
Refer to the ARUP Consult COVID-19 topic for more information.
Laboratory testing is the only way to distinguish between SARS-CoV-2 and the flu. Importantly, laboratory testing is also the only way to determine cases of viral coinfection. Infection with one respiratory virus does not exclude the possibility of infection with another because patients may be infected with more than one virus at the same time. When SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) are cocirculating (eg, during flu season), the National Institute of Health (NIH) recommends cotesting to determine proper medical management.
Unless testing is performed for epidemiologic purposes, testing is generally indicated only for the following populations:
- At-risk patients with influenzalike symptoms (during flu season); refer to the ARUP Consult Influenza topic for more information
- Infants and children presenting with severe respiratory infection (respiratory syncytial virus [RSV] testing is indicated); refer to the ARUP Consult Respiratory Syncytial Virus topic for more information
- Immunocompromised patients
Point-of-care and near-point-of-care tests are available for respiratory syncytial virus (RSV) (certain rapid antigen detection tests [RADTs]) and influenza virus (polymerase chain reaction [PCR] tests and RADTs). Direct fluorescent antibody (DFA) testing is available for influenza, RSV, adenovirus, and human metapneumovirus (hMPV). PCR testing can detect the most common respiratory viruses and, if identifying the specific pathogen is important for treatment, is typically the recommended methodology. However, if a strong suspicion for a particular agent is present, testing for that pathogen alone may be indicated (refer to specific virus information in the Laboratory Testing section below).
Next generation sequencing (NGS) is a rapidly evolving methodology that may be available at some laboratories. NGS tests might be considered when more traditional panel test results are negative and serious suspicion of infectious disease remains, and when identification of the underlying etiologic agent causing the illness may change or impact patient management. However, negative NGS test results do not definitively rule out viral, bacterial, or fungal infections. Targeted polymerase chain reaction (PCR)-based tests are generally more sensitive and are preferred when specific pathogens are suspected.
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 LRTI. Influenza testing is indicated in at-risk patients with influenzalike symptoms, and respiratory syncytial virus (RSV) testing is indicated in infants and children presenting with severe respiratory infection. For more detailed indications, refer to the Influenza and Respiratory Syncytial Virus Consult topics.
Laboratory Testing
Diagnosis
Adenovirus
Adenoviruses usually cause mild, self-limiting respiratory illnesses, primarily in children. In immunocompetent patients, the diagnosis is typically based on clinical presentation. In immunocompromised individuals, adenovirus may cause severe, fatal disease, and laboratory testing is indicated. PCR testing is the preferred method for detecting adenovirus in this group.
Human Metapneumovirus
Human metapneumovirus (hMPV) is an agent of acute respiratory tract disease in people of all ages. The virus has been associated with bronchiolitis in infants and pneumonia, exacerbations of asthma and croup, and upper respiratory infections in children. Clinical presentation ranges from the common cold to pneumonia. When testing is indicated, DFA testing is generally preferred; PCR testing may be considered when DFA test results are negative but suspicion of infection is high. Because coinfection with other respiratory viruses is common, concurrent viral testing should be considered.
Influenza Virus
Influenza (commonly referred to as the flu) is an acute viral infection that is highly transmissible, leading to outbreaks of varying severity during the winter in temperate regions. In most healthy individuals, the flu is self-limited and uncomplicated, but in high-risk patients, it can lead to serious complications. The Infectious Diseases Society of America (IDSA) recommends testing if the results will influence management decisions, such as whether to initiate antiviral therapy. If available, the near-point-of-care PCR test is preferred for diagnosis because of its rapid results and reasonably high sensitivity. For more information, refer to the Influenza Virus topic.
COVID-19
Coronaviruses are a large family of respiratory viruses. Common coronaviruses usually cause mild illness. Rarer coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently discovered coronavirus, SARS-CoV-2, which causes COVID-19, can lead to more severe illness.
SARS-CoV-2 is widespread in the United States and many other countries. Spread of infection has been person-to-person through the respiratory route of transmission, similar to other respiratory viruses.
Identification of patients with SARS-CoV-2 can help to isolate cases and prevent further person-to-person transmission, thus limiting the number of cases, slowing the spread of infection, and mitigating the impact on healthcare resources.
Molecular testing is recommended for COVID-19 diagnosis. Testing decisions should be based on local epidemiology, clinical signs and symptoms, and the course of illness. Serology (antibody) testing is recommended for evaluating exposure to SARS-CoV-2; it is not recommended for the diagnosis of acute illness.
The environment surrounding COVID-19 testing is evolving rapidly. For more information, refer to the COVID-19 topic.
Parainfluenza Virus
Parainfluenza virus is a common cause of croup (laryngotracheobronchitis), bronchiolitis, pneumonia, and upper respiratory tract infections. Clinical diagnosis is usually sufficient. If laboratory testing is necessary, consider concurrent DFA testing for other common respiratory viruses (eg, influenza, adenovirus, RSV). PCR testing is more expensive and less rapid than DFA testing, but unlike DFA, can detect the less common parainfluenza type 4.
Respiratory Syncytial Virus
RSV is one of the most common agents of lower respiratory illnesses (including bronchiolitis and pneumonia) in infants and children worldwide. Laboratory testing is only indicated when diagnosis would change the course of patient management. For immunocompetent children, DFA testing and RADTs have adequate sensitivity. However, for adults and for all hospitalized and immunocompromised patients, the more sensitive PCR test is preferred. For more information, refer to the Respiratory Syncytial Virus topic.
Laboratory Tests for Common Respiratory Viruses
| Test Methodology | Advantage(s) | Disadvantage(s) |
|---|---|---|
| RADTs |
Often available as point-of-care test for influenza and RSV Rapid turnaround time (<30 min) Acceptable sensitivity and specificity in young children |
Sensitivity may be low when compared to other methodologies, especially in adults False-negative results are possible |
| DFA testing |
Useful in infants and children due to high sensitivity and specificity in this patient population Shorter turnaround time than for viral culture or PCR Less expensive than PCR or culture |
May not be available for less common respiratory viruses, thus requiring NAAT Sensitivity may be low when compared with other methodologies, especially in adults Adequate specimen influences sensitivity of the assay False-negative results are possible Negative results may be confirmed with culture or NAAT if high suspicion remains |
| PCR testing/NAAT |
Very high sensitivity and specificity PCR panels can detect other respiratory viruses Low likelihood of false-positive or false-negative result Detects viruses in adults and older children, despite their lower viral shedding |
Longer turnaround time than for DFA More expensive than DFA May detect virus after the infection has been cleared |
| Viral culture |
Traditional gold standard for diagnosis May aid in detecting coinfections Virus can be stored for diagnostic studies High specificity |
Long turnaround time May require specific media for each virus Lower sensitivity |
| Serologic testing | n/a | Not useful for diagnosis |
|
n/a, not applicable |
||
ARUP Laboratory Tests
Preferred testing for RSV and influenza in general inpatients and adults
Qualitative Reverse Transcription Polymerase Chain Reaction
Preferred testing for broad respiratory viruses (including RSV and influenza) in high-risk patients
Qualitative Polymerase Chain Reaction
Rapid detection of RSV in children
Direct Fluorescent Antibody Stain
Qualitative Real-Time Polymerase Chain Reaction
Quantitative Real-Time Polymerase Chain Reaction
Qualitative Polymerase Chain Reaction
Qualitative Polymerase Chain Reaction
Qualitative Polymerase Chain Reaction
Qualitative Nucleic Acid Amplification
Direct Fluorescent Antibody Stain/Cell Culture
Direct Fluorescent Antibody Stain/Qualitative Polymerase Chain Reaction
Direct Fluorescent Antibody Stain
Direct Fluorescent Antibody Stain/Qualitative Polymerase Chain Reaction
Direct Fluorescent Antibody Stain/Cell Culture
Direct Fluorescent Antibody Stain
Cell Culture/Immunofluorescence
Cell Culture/Immunofluorescence
Cell Culture/Immunofluorescence
Medical Experts
Shakir
Hillyard
References
-
20065326
Tregoning JS, Schwarze J. Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology. Clin Microbiol Rev. 2010;23(1):74-98.
-
25024868
Bin Seo Y, Song JYoung, Choi MJu, et al. Etiology and clinical outcomes of acute respiratory virus infection in hospitalized adults. Infect Chemother. 2014;46(2):67-76.
-
28869984
Uyeki TM. Influenza. Ann Intern Med. 2017; 167 (5): ITC33-ITC48. -
ASM - Current Best Practices for Respiratory Virus Testing
Ginocchio CC, McAdam AJ. Current best practices for respiratory virus testing. American Society for Microbiology. 2011. [Accessed: Feb 2019]
-
CDC - Coronavirus Disease 2019 (COVID-19) Overview of Testing for SARS-CoV-2
U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19). Testing overview. [Updated: Aug 2, 2021; Accessed: Aug 20, 2021]
-
NIH - Influenza and COVID-19
National Institutes of Health. Influenza and COVID-19. [Updated: Oct 22, 2020; Accessed: Aug 20, 2021]
-
CDC - COVID-19 FAQs
U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19). FAQs. [Updated: Mar 4, 2021; Accessed: Aug 20, 2021]
-
CDC - Coronavirus Disease 2019 (COVID-19) Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19)
U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19). Clinical care guidance. [Updated: Feb 16, 2021; Accessed: Aug 20, 2021]
-
29955859
Miller M, 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.
-
30566567
Uyeki TM, Bernstein HH, Bradley JS, et al. Clinical practice guidelines by the Infectious Diseases Society of America: 2018 update on diagnosis, treatment, chemoprophylaxis, and institutional outbreak management of seasonal influenza. Clin Infect Dis. 2019;68(6):e1-e47.
-
25349312
Ralston SL, Lieberthal AS, Meissner C, et al. Clinical practice guideline: the diagnosis, management, and prevention of bronchiolitis. Pediatrics. 2014;134(5):e1474-1502.
-
26354816
Chartrand C, Tremblay N, Renaud C, et al. Diagnostic accuracy of rapid antigen detection tests for respiratory syncytial virus infection: systematic review and meta-analysis. J Clin Microbiol. 2015;53(12):3738-3749.
-
18090198
Henrickson KJ, Hall CB. Diagnostic assays for respiratory syncytial virus disease. Pediatr Infect Dis J. 2007;26(11 Suppl):S36-40.
-
20981303
Loeffelholz M, Chonmaitree T. Advances in diagnosis of respiratory virus infections. Int J Microbiol. 2010; 2010 126049. -
USFDA - FAQs on Diagnostic Testing for SARS-CoV-2
U.S. Department of Health and Human Services, Food and Drug Administration. FAQs on testing for SARS-CoV-2. [Last updated: Mar 25, 2021; Accessed: Aug 20, 2021]