Influenza Virus

Content Review: June 2020 Last Update:

Influenza, commonly referred to as the flu, is an acute viral infection that is highly transmissible and leads to outbreaks of varying severity during the winter in temperate regions. The 2018-2019 influenza season, for example, was of moderate severity and resulted in an estimated 35.5 million illnesses and 34,200 deaths.  Although the flu is generally self-limited and uncomplicated in healthy persons, populations at risk for more serious outcomes include infants, the elderly, immunocompromised persons, and pregnant women.  

Influenza virus testing is not required to make a clinical diagnosis in the outpatient setting, particularly during flu season. However, testing should be considered if the result will inform clinical decisions (eg, whether to begin antiviral treatment).   Near-point-of-care testing using a U.S. Food and Drug Administration (FDA)-cleared molecular methodology is preferable to other methodologies in outpatient settings due to its rapid results and reasonably high sensitivity.  

Quick Answers for Clinicians

Who should be tested for influenza?

In most healthy individuals, the flu is self-limited and uncomplicated. In high-risk individuals (eg, the immunocompromised, infants, the elderly, pregnant women, residents of long-term care facilities), the flu can result in serious complications, including hospitalization and increased mortality risk.  The Infectious Diseases Society of America (IDSA) and the CDC recommend testing if the results will influence management decisions, such as whether to initiate antiviral therapy. If influenza has been documented in the area, testing is not necessary for otherwise healthy outpatients with signs and symptoms consistent with influenza.   See the Indications for Testing section for specific testing recommendations.

When is it appropriate to perform combined testing (cotesting) for SARS-CoV-2, respiratory syncytial virus, and influenza?

Laboratory testing is the only way to distinguish between SARS-CoV-2 and the flu. Importantly, laboratory testing is also the only way to determine cases of viral coinfection.  Infection with one respiratory virus does not exclude the possibility of infection with another because patients may be infected with more than one virus at the same time.  When SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) are cocirculating (eg, during flu season), the National Institute of Health (NIH) recommends cotesting to determine proper medical management.  

When should a person with signs of influenza be tested?

Ideally, influenza testing should occur as soon as possible after illness onset, using respiratory specimens collected within 4 days of symptom onset. 

Which tests are available to detect influenza?

Influenza can be detected by polymerase chain reaction (PCR) tests, direct fluorescent antibody (DFA) stains, rapid influenza diagnostic tests (RIDTs), culture, and serology (which should only be used for retrospective epidemiologic investigations, not for primary diagnosis). PCR is preferred because of its increased sensitivity and specificity.  If influenza virus is the main concern, rapid molecular detection near the point of care is recommended. If other respiratory viruses are of concern, PCR panels are available that include testing for a spectrum of respiratory viruses, including influenza. 

What are the advantages/disadvantages of the different influenza virus testing methodologies?

Near-point-of-care polymerase chain reaction (PCR) testing offers a more rapid turnaround time than other molecular test types, as well as high sensitivity and specificity, although more complex assays provide greater sensitivity and specificity. Singleplex and multiplex PCR testing may also enable the detection of other respiratory viruses. Rapid influenza diagnostic tests (RIDTs) offer rapid results but low to moderate sensitivity and specificity. Direct fluorescent antibody (DFA) testing provides fairly quick turnaround time, but only moderate sensitivity and specificity compared with PCR testing.  Refer to the Comparison of Influenza Virus Testing Methodologies table for further information.

Indications for Testing

According to the 2018 Infectious Diseases Society of America (IDSA) guidelines, the populations to test for influenza vary depending on the individual (outpatient vs inpatient) and the time of year.

Individuals who should be tested during flu season include immunocompromised and high-risk outpatients with influenzalike illness, pneumonia, or nonspecific respiratory illness and hospitalized individuals (including immunocompromised and high-risk persons) with any of the following :

  • Acute respiratory illness with or without fever on presentation
  • Acute worsening of chronic cardiopulmonary disease on presentation
  • Acute onset of respiratory symptoms during hospital stay with or without fever

During periods of low influenza activity, the IDSA recommends testing all hospitalized patients with acute respiratory illness with or without fever who are epidemiologically linked to an influenza outbreak. The following individuals might also warrant testing:

  • Outpatients (especially those who are immunocompromised) who present with acute febrile respiratory tract illness but no link to an influenza outbreak
  • Hospitalized patients with acute febrile respiratory illness if the results might influence the decision to give antiviral therapy or chemoprophylaxis to the household contacts of high-risk individuals

Laboratory Testing

Recommended Testing

Polymerase Chain Reaction Testing

Polymerase chain reaction (PCR) tests (molecular assays) can detect influenza virus and other respiratory viruses in respiratory specimens with high sensitivity and specificity.   Molecular testing is recommended for all hospitalized patients with suspected influenza.  Multiplex PCR tests that target a panel of respiratory pathogens, including influenza, are recommended in hospitalized immunocompromised patients.  Rapid, Clinical Laboratory Improvement Amendments (CLIA)-waived, near-point-of-care PCR testing is preferred over rapid influenza diagnostic tests (RIDTs) in outpatients.  With their rapid results and reasonably high sensitivity, these molecular assays can aid in determining whether to administer antivirals.

Other Testing (Useful Only in Certain Situations)

Rapid Influenza Diagnostic Tests

These traditional immunoassays offer rapid results but a much lower sensitivity than traditional PCR tests, rapid molecular assays, and viral cultures.  RIDTs are not recommended unless more sensitive molecular assays are unavailable. 

Direct Fluorescent Antibody Stains

Molecular testing (PCR) is preferred to direct fluorescent antibody (DFA) stains, 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. 

Serologic Tests

Serology should only be used for retrospective epidemiologic 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 the diagnosis of influenza.  

Viral Cultures

Cultures are not recommended for initial clinical management due to slow turnaround time. Cultures can be useful for research or surveillance purposes.  

Comparison of Influenza Virus Testing Methodologies

Test MethodologyAdvantage(s)Disadvantage(s)
Rapid molecular assay (near-point-of-care PCR)

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 compared with rapid molecular assays (1-8 hrs)
RIDTRapid turnaround time (<15 mins)

Low to moderate specificity and sensitivity

False-negative results common


Fast turnaround time (1-4 hrs)

High specificity

Moderate sensitivity compared with PCR and culture
Viral cultureUseful for community surveillance and antigenic characterization of new virus strainsLong turnaround time (3-10 days)
SerologyUseful for epidemiologic purposes

Should not be used for routine diagnosis

Cannot inform clinical management

Sources: Uyeki, 2019 ; CDC, 2018 

ARUP Laboratory Tests

Recommended Testing

Influenza A and B, Rapid

Panel includes testing for influenza A and B and RSV

Panel includes testing for influenza A and B, RSV, human metapneumovirus, human rhinovirus, adenovirus, and parainfluenza 1-4

Other Testing (Useful Only in Certain Situations)

Immunofluorescence (DFA)
Rapid Culture


Medical Experts



Marc Roger Couturier, PhD, D(ABMM)
Professor of Pathology (Clinical), University of Utah
Medical Director, Emerging Public Health Crises, Parasitology/Fecal Testing, and Infectious Disease Antigen Testing, ARUP Laboratories


David R. Hillyard, MD
Adjunct Associate Professor of Pathology, University of Utah
Medical Director, Molecular Infectious Diseases, ARUP Laboratories