Laboratory Diagnosis of Respiratory Viruses

Publication Date: May 2, 2024
Last Updated: May 6, 2024

Summary of Recommendations

  • Testing should be performed following FDA-approved manufacturers’ recommendations.
  • The preferred specimen type for URTI is an NPS. Alternatives when an NPS is not practical includes nasal washes (pediatrics), mid-turbinate swabs, nasal swabs, throat, or saliva as validated.
  • For infections in the lower respiratory tract, BAL can be used.
  • The preferred method for diagnosis is an NAAT. When an NAAT is not readily available, antigen tests could provide an alternative; however, they have lower sensitivity compared to NAATs.
  • DFA, serology, and viral culture are not recommended for routine diagnosis.
  • Viral load test results should be interpreted in light of clinical symptoms.
  • Positive molecular or antigen test results in patients without symptoms may reflect asymptomatic carriage, pre-symptomatic infection, or shedding following resolved infections. While shedding will be detected for longer by molecular tests, it is expected that antigen tests may also remain positive once the acute infection has resolved. A disclaimer to that effect may be added to a test report to highlight that point.
  • Negative test results in symptomatic patients may be false-negative results and repeat testing is recommended. A disclaimer to that effect may be added to a test report to highlight that point.
  • Unusual positivity rates that are discordant from local prevalence should be investigated.
  • Co-infections with multiple viruses can occur but results with greater than 4 viruses are unusual and should be investigated.
  • Correlates of viral loads (e.g., threshold cycle) provided by some NAATs should be interpreted with caution given the lack of standardization.
  • Testing should be performed if there is high pretest probability of respiratory viral infection based on clinical presentation and local prevalence.
  • Testing should be performed in the following scenarios (a) if the results will change management (for example, initiation of appropriate antivirals, discontinuation of unnecessary antibiotics), (b) infection control guidance (for example, implementation of appropriate isolation measures, cohorting of patients, and surveillance during outbreak situations), or (c) evaluation of local seroprevalence.
  • Testing of pediatric patients should be limited to hospitalized children or children with underlying conditions. Depending on the season, small, targeted panels (e.g., influenza/RSV) might be sufficient.
  • Aging, ill patients, and immunocompromised patients should be tested using multiplexed respiratory pathogens panels.
  • Immunocompetent adult patients should be tested if results will impact management, primarily for influenza and SARS-CoV-2.
  • Educational material should be available to clinicians to guide respiratory tests selection.
  • Built-in electronic medical record algorithms to drive appropriate test selection and ordering should be considered.
  • In general, small, multiplexed panels or targeted NAATs should be used first when available instead of broad multiplexed panels unless patients are immunocompromised.

Recommendation Grading


The information in this patient summary should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.



Laboratory Diagnosis of Respiratory Viruses

Authoring Organization

Publication Month/Year

May 2, 2024

Last Updated Month/Year

May 6, 2024

Document Type


Country of Publication


Document Objectives

Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.

Health Care Settings

Laboratory services

Intended Users

Nurse, nurse practitioner, physician, physician assistant


Assessment and screening, Management


viral pathogens, laboratory diagnosis

Source Citation

Berry GJ, Jhaveri TA, Larkin PMK, Mostafa H, Babady NE. ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses. J Appl Lab Med. 2024 May 2:jfae010. doi: 10.1093/jalm/jfae010. Epub ahead of print. PMID: 38695489.