Upper respiratory tract specimens can be collected for influenza virus testing in hospitalized patients, but molecular assays are recommended for hospitalized patients with suspected influenza. For hospitalized patients with severe lower respiratory tract disease with negative results from influenza testing of upper respiratory tract specimens, lower respiratory tract specimens should be collected and tested by molecular assays because influenza viral replication in the lower respiratory tract may be detectable for longer periods than in the upper respiratory tract. Patients who are critically ill with respiratory failure, immunosuppressed persons, and patients receiving systemic corticosteroids may have prolonged influenza virus shedding in the lower respiratory tract. If the patient is critically ill on invasive mechanical ventilation, and has tested negative on an upper respiratory tract specimen, a lower respiratory tract specimen (endotracheal aspirate or bronchioalveolar lavage fluid) should be collected for influenza testing by RT-PCR or other molecular assays.
Infection prevention and control guidance for seasonal influenza, including performing aerosol-generating procedures, is available at: Prevention Strategies for Seasonal Influenza in Healthcare Settings.