Indications for Testing
According to the Infectious Diseases Society of America (IDSA), the populations to test for influenza vary depending on the time of year. Individuals who should be tested during flu season include :
- Immunocompetent outpatients at high risk for influenza complications who have acute febrile respiratory illness and present within 5 days of illness onset
- Immunocompromised outpatients with acute febrile respiratory illness
- Inpatients with acute febrile respiratory illness
- Individuals with fever and respiratory symptoms after hospital admission
At any time of year, test the following patients if they present within 5 days of illness onset :
- Healthcare workers, residents, or visitors in an institution experiencing influenza outbreak who present with acute febrile respiratory illness
- Individuals epidemiologically linked to an influenza outbreak
Polymerase Chain Reaction (PCR) Testing
PCR (molecular assays) can detect influenza virus, as well as other respiratory viruses, in respiratory specimens with high sensitivity and specificity. Molecular testing is recommended for all hospitalized patients with suspected influenza. Rapid, Clinical Laboratory Improvement Amendments (CLIA)-waived near-point-of-care PCR testing is preferred, if available. With their rapid results and reasonably high sensitivity, these assays can aid in determining whether to administer antivirals.
Other Testing (Useful Only in Certain Situations)
Rapid Antigen Testing
These traditional immunoassays offer rapid results but a much lower sensitivity than traditional PCR, rapid molecular assays, and viral cultures.
Direct Fluorescent Antibody (DFA) Stain
Molecular testing (PCR) is preferred to DFA, particularly for immunocompromised and hospitalized patients. DFA assays have low to moderate sensitivity for detecting influenza, and false-negative results are not uncommon. If DFA is used, the combination of DFA with reflex to culture or PCR increases sensitivity.
Serology should only be used for retrospective epidemiological investigations and is not recommended for primary diagnosis because of the need for acute and convalescent samples. Testing of a single specimen is not interpretable and has no role in diagnosis of influenza.
Cultures are not recommended for initial clinical management due to slow turnaround time. Cultures can be useful for research or surveillance purposes.
Comparison of Testing Methodologies
||Can be performed on site
Rapid turnaround time (15-30 mins)
High sensitivity and specificity
|Lower sensitivity and specificity than more complex PCR assays
Cannot detect other respiratory viruses
|Singleplex and multiplex PCR
||Very high sensitivity and specificity
Can detect influenza viral RNA for longer duration than other influenza tests
Likelihood of false-positive or false-negative result is low
Some panels provide detection of other respiratory viruses
|Longer turnaround time (1-8 hrs)
||Rapid turnaround time (<15 mins)
||Low to moderate specificity and sensitivity
False negatives common
||Fast turnaround time (1-4 hrs)
|Moderate sensitivity compared to PCR and culture
||Useful for community surveillance and antigenic characterization of new virus strains
||Long turnaround time (3-10 days)
||n/a (should not be used for routine diagnosis)
||Cannot inform clinical management
|n/a, not applicable