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.



Laboratory Diagnosis of Respiratory Viruses

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