Influenza Virus

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 2017-2018 influenza season, for example, resulted in more than 48 million illnesses and 79,000 deaths and was more severe than any other flu season since the 2009 influenza pandemic.  Although the flu is generally self-limited and uncomplicated in healthy persons, populations at risk 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 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), direct fluorescent antibody (DFA), 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 below 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
  • Hospitalized individuals (including immunocompromised and high-risk persons) with:
    • Acute respiratory illness with or without fever upon presentation
    • Acute worsening of chronic cardiopulmonary disease upon 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) (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.  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 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 Methodology Advantage(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 (1-8 hrs)
RIDT Rapid turnaround time (<15 mins) Low to moderate specificity and sensitivity

False-negative results common

DFA Fast turnaround time (1-4 hrs)

High specificity

Moderate sensitivity compared with PCR and culture
Viral culture Useful for community surveillance and antigenic characterization of new virus strains Long turnaround time (3-10 days)
Serology n/a (should not be used for routine diagnosis) Cannot inform clinical management
n/a, not applicable

Sources: Uyeki, 2019 ; CDC, 2018 

ARUP Lab Tests

Recommended Testing

Rapid point-of-care testing for influenza

Influenza A and B, Rapid

Orderable only at University Hospital and Clinics important information

Preferred testing for respiratory syncytial virus (RSV) and influenza in general inpatients and RSV in adults

Panel includes testing for influenza A and B and RSV

Preferred testing for broad respiratory viruses (including influenza) in high-risk (eg, severely immunocompromised or critically ill) patients

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)

PCR with Subtyping
Next Generation Sequencing
Immunofluorescence (DFA)

AlertThis test has been temporarily inactivated. In compliance with guidance issued by government agencies, respiratory viral cultures are being temporarily discontinued for the safety of laboratory staff during the COVID-19 pandemic. PCR testing is available for a variety of specific viruses; refer to the Laboratory Test Directory.

AlertThis test has been temporarily inactivated. In compliance with guidance issued by government agencies, respiratory viral cultures are being temporarily discontinued for the safety of laboratory staff during the COVID-19 pandemic. PCR testing is available for a variety of specific viruses; refer to the Laboratory Test Directory.

Rapid Culture

AlertThis test has been temporarily inactivated. In compliance with guidance issued by government agencies, respiratory viral cultures are being temporarily discontinued for the safety of laboratory staff during the COVID-19 pandemic. PCR testing is available for a variety of specific viruses; refer to the Laboratory Test Directory.

AlertThis test has been temporarily inactivated. In compliance with guidance issued by government agencies, respiratory viral cultures are being temporarily discontinued for the safety of laboratory staff during the COVID-19 pandemic. PCR testing is available for a variety of specific viruses; refer to the Laboratory Test Directory.

AlertThis test has been temporarily inactivated. In compliance with guidance issued by government agencies, respiratory viral cultures are being temporarily discontinued for the safety of laboratory staff during the COVID-19 pandemic. PCR testing is available for a variety of specific viruses; refer to the Laboratory Test Directory.

Serology

Medical Experts

Contributor

Couturier

Marc Roger Couturier, PhD, D(ABMM)
Associate Professor of Clinical Pathology, University of Utah
Medical Director, Parasitology/Fecal Testing, Infectious Disease Antigen Testing, Bacteriology, and Molecular Amplified Detection, ARUP Laboratories
Contributor

References

Additional Resources
Resources from the ARUP Institute for Clinical and Experimental Pathology®