Influenza Virus

Medical Experts

Contributor

Couturier

Professor of Pathology (Clinical), University of Utah

Head of Clinical Operations for Clinical Microbiology and Immunology; Medical Director, Emerging Public Health Crises, Parasitology/Fecal Testing, and Infectious Disease Antigen Testing, ARUP Laboratories

Contributor

Hillyard

David R. Hillyard, MD

Professor of Pathology, University of Utah

Medical Director, Molecular Infectious Diseases, ARUP Laboratories

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. Although the flu is generally self-limited and uncomplicated in healthy persons, populations at risk for more serious outcomes include infants, elderly individuals, immunocompromised persons, and pregnant individuals.

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 an 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, immunocompromised persons, infants, elderly individuals, pregnant individuals, and residents of long-term care facilities), the flu can result in serious complications, including hospitalization and death. 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. Refer to 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?

The CDC recommends cotesting for SARS-CoV-2 and influenza in individuals with acute respiratory illness who require hospitalization. In an outpatient setting, testing is generally not indicated; however, cotesting can be considered when results would impact clinical management and disease control measures.

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 testing should be performed to detect H5N1 bird flu, and who should be tested?

Highly pathogenic avian influenza A (HPAI A, which includes H5N1 bird flu) is a zoonotic disease that largely affects birds and livestock, although infection is possible in humans and other animal populations. Testing for HPAI A should be performed in individuals with acute respiratory symptoms and a history of exposure to the disease within the last 10 days. Relevant sources of exposure include close proximity (ie, 6 feet or less) to animals with the disease or their byproducts, consumption of uncooked or undercooked products sourced from infected animals, and close unprotected contact with another person who has a suspected or confirmed infection. Testing is not recommended in asymptomatic individuals.

When testing is indicated, an H5N1-specific reverse-transcription polymerase chain reaction (RT-PCR) assay should be ordered through local or state health authorities. Specimens for testing should include a nasopharyngeal swab and a combined throat-nasal swab (ie, mingled in a single transport media vial), all collected as soon as possible after the onset of symptoms. Lower respiratory tract specimens should be collected in patients with severe respiratory illness.

What are the advantages and 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 persons and high-risk outpatients with influenza-like 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 a 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 have 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 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 durations than other influenza tests Likelihood of false-positive or false-negative results is low Some panels provide detection of other respiratory viruses	Longer turnaround time compared with rapid molecular assays (1-8 hrs)
RIDT	Rapid turnaround time (<15 mins)	Low to moderate specificity and sensitivity False-negative results are 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	Useful for epidemiologic and research purposes	Should not be used for routine diagnosis Cannot inform clinical management
Sources: Uyeki, 2019