Influenza Signs and Symptoms and the Role of Laboratory Diagnostics

Signs and Symptoms

The signs and symptoms of influenza can vary by age, immune status, and presence of underlying medication conditions. Uncomplicated influenza can include any or all of these signs and symptoms: fever, muscle aches, headache, lack of energy, dry cough, sore throat, nasal congestion, and possibly runny nose. Fever is not always present in influenza patients, especially in elderly persons. The fever and body aches can last 3-5 days and the cough and lack of energy may last for 2 or more weeks, especially in the elderly. Influenza can be difficult to diagnose based on clinical signs and symptoms alone because the signs and symptoms of influenza can be similar to those caused by other infectious agents including, but not limited to, Mycoplasma pneumoniae, adenoviruses, respiratory syncytial viruses, rhinoviruses, parainfluenza viruses, and Legionella spp. 

Complications associated with influenza can vary by age, immune status, and underlying medical conditions. Some examples include worsening of underlying chronic medical conditions (e.g. worsening of congestive cardiac failure; asthma exacerbation; exacerbation of chronic obstructive pulmonary disease); lower respiratory tract disease (pneumonia, bronchiolitis, croup, respiratory failure); invasive bacterial co-infection; cardiac (e.g. myocarditis); musculoskeletal (e.g. myositis, rhabdomyolysis); neurologic (e.g. encephalopathy, encephalitis); multi-organ failure (septic shock, renal failure, respiratory failure).

Appropriate treatment of patients with respiratory illness depends on accurate and timely diagnosis. Early diagnosis of influenza can reduce the inappropriate use of antibiotics and provide the option of using antiviral therapy. However, because certain bacterial infections can produce signs and symptoms similar to influenza, bacterial infections should be considered and appropriately treated, if suspected. In addition, bacterial co-infection can occur as a complication of influenza.

Influenza surveillance information about the prevalence of circulating influenza viruses and diagnostic testing can aid clinical judgment and help guide treatment decisions. The accuracy of clinical diagnosis of influenza on the basis of signs and symptoms alone is limited because symptoms from illness caused by other pathogens can overlap considerably with influenza. Influenza surveillance by state and local health departments and CDC can provide information regarding the prevalence of influenza A and B viruses in the community. Surveillance can also identify the predominant circulating types, influenza A virus subtypes, and strains of influenza viruses.

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Laboratory Diagnostic Procedures

A number of tests can help in the diagnosis of influenza (see table). But, tests do not need to be done on all patients with suspected influenza. For individual patients, tests are most useful when they are likely to yield clinically useful results that will help with diagnosis and treatment decisions. During a respiratory illness outbreak in a closed setting (e.g., hospitals, long-term care facility,  cruise ship, boarding school, summer camp) testing for influenza can be very helpful in determining if influenza is the cause of the outbreak.

Diagnostic tests available for influenza include viral culture, serology, rapid antigen testing, reverse transcription polymerase chain reaction (RT-PCR), immunofluorescence assays, and rapid molecular assays. Sensitivity and specificity of any test for influenza might vary by the laboratory that performs the test, the type of test used, the time from illness onset to specimen collection, and the type of specimen tested. Among respiratory specimens for viral isolation or rapid detection of human influenza viruses, nasopharyngeal specimens typically have higher yield than nasal or throat swab specimens. As with any diagnostic test, results should be evaluated in the context of other clinical and epidemiologic information available to health care providers.

Preferred respiratory samples for influenza testing include nasopharyngeal or nasal swab, and nasal wash or aspirate, depending on which kind of test is used (see table). Samples should be collected within the first 3-4 days of illness. Rapid influenza diagnostic tests (RIDTs) provide results within approximately 15 minutes; viral culture provides results in 3-10 days. Most of the rapid influenza diagnostic tests that can be done in a physician’s office are approximately 50-70% sensitive for detecting influenza and approximately greater than 90% specific. Therefore, false negative results are more common than false positive results, especially during peak influenza activity in the community. Rapid molecular assays can produce results in approximately 20 minutes with high sensitivity and specificity. Other molecular assays are increasingly becoming available and can produce results in approximately 60-80 minutes with very high sensitivity and specificity.

To maximize detection of influenza viruses, respiratory specimens should be collected as close to illness onset as possible (ideally <3-4 days after onset; molecular assays may detect influenza viral RNA in respiratory tract specimens for longer periods after illness onset than antigen detection assays). For hospitalized patients with lower respiratory tract disease and suspected influenza, lower respiratory tract specimens should be collected and tested for influenza viruses by RT-PCR because influenza viral shedding in the lower respiratory tract may be detectable for longer periods than in the upper respiratory tract. If the patient is critically ill on invasive mechanical ventilation, and has tested negative on an upper respiratory tract specimen, including by a molecular assay, a lower respiratory tract specimen (endotracheal aspirate or bronchioalveolar lavage fluid) should be collected for influenza testing by RT-PCR or other molecular assays.

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Viral Culture

During outbreaks of respiratory illness when influenza is suspected, some respiratory samples should be tested by molecular assays and both rapid influenza diagnostic tests and by viral culture. The collection of some respiratory samples for viral culture is essential for determining the influenza A virus subtypes and influenza A and B virus strains causing illness, and for surveillance of new virus strains that may need to be included in the next year’s influenza vaccine. During outbreaks of influenza-like illness, viral culture also can help identify other causes of illness.

During outbreaks of respiratory illness when influenza is suspected, some respiratory samples should be tested by molecular assays and viral culture. The collection of some respiratory samples for viral culture is essential for determining the influenza A virus subtypes and influenza A and B virus strains causing illness, and for surveillance of new virus strains that may need to be included in the next year’s influenza vaccine. During outbreaks of influenza-like illness, viral culture also can help identify other causes of illness.

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RIDTS

Commercial rapid influenza diagnostic tests (RIDTs) are antigen detection assays that can detect influenza viruses within 15 minutes with low to moderate sensitivity and high specificity. Some tests are CLIA-waived and approved for use in any outpatient setting, whereas others must be used in a moderately complex clinical laboratory. These rapid influenza diagnostic tests differ in the types of influenza viruses they can detect and whether they can distinguish between influenza virus types. Different tests can detect 1) only influenza A viruses; 2) both influenza A and B viruses, but not distinguish between the two types; or 3) both influenza A and B viruses and distinguish between the two. Some RIDTs utilize an analyzer reader device to standardize results to and improve sensitivity.  

None of the rapid influenza diagnostic tests provide any information about influenza A virus subtypes. The types of specimens acceptable for use (i.e., throat, nasopharyngeal, or nasal aspirates, swabs, or washes) also vary by test. The specificity and, in particular, the sensitivity of rapid influenza diagnostic tests are lower than for viral culture and RT-PCR and vary by test. Because of the lower sensitivity of the rapid influenza diagnostic tests, physicians should consider confirming negative test results with RT-PCR, viral culture or other means, especially in hospitalized patients or during suspected institutional influenza outbreaks because of the possibility of false-negative RIDT results, especially during periods of peak community influenza activity. In contrast, false-positive RIDT results are less likely, but can occur during periods of low influenza activity. Therefore, when interpreting results of a rapid influenza diagnostic test, physicians should consider the positive and negative predictive values of the test in the context of the level of influenza activity in their community. Package inserts and the laboratory performing the test should be consulted for more details regarding use of rapid influenza diagnostic tests.

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Immunofluorescence

Immunofluorescence assays are antigen detection assays that generally require use of a fluorescent microscope to produce results in approximately 2-4 hours with moderate sensitivity and high specificity. Both direct (DFA) and indirect fluorescent antibody (IFA) staining assays are available to detect influenza A and B viral antigens in respiratory tract specimens. Subtyping or further identification of influenza A viruses is not possible by immunofluorescent assays. One rapid immunofluorescence assay is an RIDT and utilizes an analyzer device to produce results in approximately 15 minutes.

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Rapid Molecular Assays

Rapid molecular assays are a new kind of molecular influenza diagnostic test for upper respiratory tract specimens with high sensitivity and specificity.1 One platform uses isothermal nucleic acid amplification and has high sensitivity and yields results in 15 minutes or less. Another platform uses RT-PCR and has high sensitivity and produces results in approximately 20 minutes. See Rapid Diagnostic Testing for Influenza: Information for Health Care Professionals for more information.

¹ Two FDA-cleared rapid molecular assays are available in the United States. Rapid molecular assays can provide results in approximately 20 minutes. Alere i Influenza A&B was FDA cleared for use with both nasal swabs (direct) and NP or nasal swabs in VTM. It was CLIA-waived for use with nasal swabs (direct) only. Roche Cobas Influenza A/B was cleared and CLIA-waived by FDA for use with nasopharyngeal swabs only.

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Other Molecular Assays

Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and other molecular assays can identify the presence of influenza viral RNA in respiratory specimens with very high sensitivity and specificity. Some molecular assays are able to detect and discriminate between infections with influenza A and B viruses; other tests can identify specific seasonal influenza A virus subtypes [A(H1N1)pdm09, or A(H3N2)]. These assays can yield results in approximately 1-8 hours depending upon the assay. Notably, the detection of influenza viral RNA by these assays does not necessarily indicate detection of viable infectious virus or on-going influenza viral replication. It is important to note that not all assays have been cleared by the FDA for diagnostic use. See Influenza Virus Testing Methods for more information.

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Serologic Testing

Routine serological testing for influenza requires paired acute and convalescent sera, does not provide results to help with clinical decision-making, is only available at a limited number of public health or research laboratories and is not generally recommended, except for research and public health investigations. Serological testing results for antibodies to human influenza viruses on a single serum specimen is not interpretable and is not recommended.

Influenza Diagnostic Table

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