Information on Collection of Respiratory Specimens for Influenza Virus Testing

Outpatients

Influenza virus shedding in the upper respiratory tract of most patients with uncomplicated influenza declines substantially about 3-4 days after illness onset. Therefore, to maximize detection of influenza viruses, respiratory specimens should be collected as close to illness onset as possible (ideally <3-4 days after onset), although molecular assays may be able to detect influenza viruses in respiratory specimens for longer periods. Infants and immunosuppressed persons of any age may have influenza virus replication for longer periods. Nasopharyngeal specimens typically have higher yield than nasal or throat swab specimens. Preferred respiratory specimens for influenza virus testing include a nasopharyngeal or nasal swab, or a nasal wash or aspirate. Nasal and throat swabs combined in the same specimen increases detection of influenza viruses than either specimen type alone. Because the approved respiratory tract specimens differ among the FDA-cleared influenza tests, clinicians should check the package insert for the approved respiratory specimens for the specific influenza test used. Rapid molecular assays and rapid diagnostic tests are available for outpatients.

Hospitalized patients

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 Measures

Infection prevention and control guidance for seasonal influenza, including performing aerosol-generating procedures, is available at: Prevention Strategies for Seasonal Influenza in Healthcare Settings.