Influenza Diagnosis

• The clinical spectrum of influenza ranges from asymptomatic infection to primary viral pneumonia that may progress to death
• Patients presenting with influenza-like illness (ILI) might be infected with different types of influenza virus [eg avian influenza A(H5N1)], as well as other respiratory pathogens
• A high index of suspicion is needed to recognize influenza in hospitalized patients

Seasonal Influenza

• May present as a mild respiratory illness similar to the common cold or it may present without characteristic signs and symptoms
• Diagnosis based on typical symptoms may be difficult because other pathogens cause similar symptoms
  • Identification is made easier when it is known that the influenza virus is present in the community

Course of Illness

• Uncomplicated influenza illness typically resolves after 3-7 days for most patients
• Cough and malaise can persist for >2 weeks

Avian Influenza

• During the initial stages of illness that is caused by avian influenza infection, clinical exam does not accurately distinguish it from other causes of community-acquired pneumonia (CAP), ILIs, acute gastroenteritis or acute encephalitis

Course of Illness

• Avian influenza illness often presents as a rapidly progressive pneumonia with respiratory failure ensuing over several days
• Hospital care is warranted during the initial stages
• Incubation period for human H5N1 and H7N9 infection following exposure to infected poultry is ≤7 days and is often 2-5 days

Risk Stratification for Avian Influenza

• High-risk exposure groups are currently defined as:
  • Household or close family contacts of a strongly suspected or confirmed H5N1 patient because of potential exposure to a common environmental or poultry source as well as exposure to the index case

• Moderate-risk exposure groups are currently defined as:
  • Personnel involved in handling sick animals or decontaminating affected environments (including animal disposal) if personal protective equipment may not have been used properly
  • Individuals with unprotected and very close direct exposure to sick or dead animals infected with the H5N1 virus or to particular birds that have been directly implicated in human cases
  • Healthcare personnel in close contact with strongly suspected or confirmed H5N1 patients, eg during intubation or performing tracheal suctioning, or delivering nebulized drugs, or handling inadequately screened/sealed body fluids without any or with insufficient personal protective equipment. This group also includes lab personnel who might have an unprotected exposure to virus-containing samples

• Low-risk exposure groups are currently defined as:
  • Healthcare workers not in close contact (distance >1 meter) with a strongly suspected or confirmed avian influenza patient and having no direct contact with infectious material from that patient
  • Healthcare workers who used appropriate personal protective equipment during exposure to infected patients
  • Personnel involved in culling non-infected or likely non-infected animal populations as a control measure
  • Personnel involved in handling sick animals or decontaminating affected environments (including animal disposal), who used proper personal protective equipment

• Patient may appear flushed and have pain on eye movement
• Nonexudative pharyngitis, scattered rales or rhonchi may be present
• Elderly patients may have hot, dry or diaphoretic skin

• May be appropriate to confirm diagnosis

• Persons to be considered for testing during the influenza season include the following:
  • Outpatient immunocompetent persons of any age at high risk for complications of influenza (eg hospitalization, death) presenting with acute febrile respiratory symptoms within 5 days of illness onset
  • Outpatient immunocompromised persons of any age presenting with febrile respiratory symptoms irrespective of time from illness onset
  • Hospitalized persons of any age (immunocompetent or immunocompromised) with fever and respiratory symptoms, including those with a diagnosis of community-acquired pneumonia (CAP) irrespective of time from illness onset
  • Elderly persons and infants presenting with suspected sepsis or fever of unknown origin irrespective of time from illness onset
  • Children with fever and respiratory symptoms presenting for medical evaluation irrespective of time from illness onset
  • Persons that develop fever and respiratory symptoms after hospital admission irrespective of time from illness onset
  • Immunocompetent persons with acute febrile respiratory symptoms but not at high risk for complications secondary to influenza infection may be tested for purposes of obtaining local surveillance data

• Persons who should be tested during any time of the year include the following:
  • Healthcare personnel and residents or visitors in an institution experiencing an influenza outbreak who present with febrile respiratory symptoms within 5 days of illness onset
  • Persons who are epidemiologically linked to an influenza outbreak (eg household and close contacts of persons with suspected influenza, returned travelers from countries where influenza viruses may be circulating, participants in international mass gatherings, cruise ship passengers) within 5 days of illness onset

• Sensitivity of any test will depend on the lab that performs the test, the type of specimen used and the type of test used

• Immunofluorescence
  • Direct fluorescent antibody staining (DFA) or indirect fluorescent antibody staining (IFA) for influenza antigen detection are used as screening tests
  • Results are available within a few hours of specimen submission
  • Has slightly lower sensitivity and specificity than viral culture
  • Highly dependent on lab expertise and the quality of specimen collected (ie must include respiratory epithelium cells)

• Rapid viral tests
  • Office-based tests which detect influenza A and B viruses can diagnose influenza A and B in 10-20 minutes
  • May help in clinical management and infection control decisions
  • Lack of sensitivity of these tests limit their use during the influenza season within a community
  • If results are negative, viral culture or reverse transcriptase-polymerase chain reaction (RT-PCR) may be indicated

• Reverse transcriptase-polymerase chain reaction (RT-PCR)
  • Preferred test for specimens from persons with a history of exposure to animals with possible influenza illness
  • Useful for quickly differentiating between influenza types and subtypes
  • More sensitive than standard viral culture in detecting influenza
  • May be used as a confirmatory test
  • Not widely available for clinical use and expensive
  • A positive result does not exclude SARS-CoV-2 infection and vice versa; SARS-CoV-2 nucleic acid detection assay is recommended, especially if suspicion for coronavirus disease 2019 (COVID-19) is high (eg high SARS-CoV-2 community prevalence or recent close exposure to a person with COVID-19) 

• Viral culture
  • Most accurate but impractical since antiviral therapy needs to be instated within 48 hours of symptoms
  • Takes 2-10 days for results of viral culture and it can be costly
  • Valuable for monitoring antiviral resistance, identifying strains that may possibly cause pandemics and formulating vaccine for the following year

• During the initial stages of illness that is caused by avian influenza infection, clinical exam does not accurately distinguish it from other causes of CAP, ILIs, acute gastroenteritis or acute encephalitis

• Specimens
  • For non-ventilated patients, throat and nasal swab specimens should be collected preferably before antiviral treatment
  • For mechanically ventilated patients, throat, nasal cavity, bronchoalveolar lavage and endotracheal aspirates should be collected
• Conventional and real-time RT-PCR
  • Primary method for diagnosing H5N1 and H7N9 virus infection using respiratory specimens
  • Results in <5 hours
• Immunofluorescence
  • Rapid and sensitive method for directly detecting the presence of avian influenza antigens in clinical samples
  • Specific positive immunofluorescence staining is characterized by intense intracellular apple-green fluorescence
  • Sensitivity of 70-100% and specificity of 80-100%
  • Test of choice when fairly rapid results are required
  • Results in <24 hours
• Hemagglutination inhibition tests (HAI)
  • Used to type the patient antibodies to avian influenza virus when standard avian influenza antigen is available as reference material
  • Positive if there is a fourfold increase in H5 antibody titer
  • Results in approximately 2-3 days
• Microneutralization test
  • Sensitive and specific assay for detecting virus-specific antibody to avian influenza A(H5N1) virus in human serum, and potentially for detecting antibody to other avian subtypes
  • Positive if there is a fourfold increase in H5 antibody titer
  • Results in approximately 3 days
• Rapid detection of viral antigens
  • Designed to be performed under field conditions, point-of-care of patients or at the bedside by non-lab-trained persons
  • Directly detected from infected cells shed in patients’ specimens
  • The rapid tests take from 1-2 hours to perform
  • Has limited sensitivity for detection of human cases of avian influenza
  • Not recommended for routine detection of avian influenza viruses
• Viral culture
  • Standard reference method for avian influenza virus diagnosis-
  • Sensitivity and specificity of 100%
  • Should only be performed in approved biosafety level 3 enhanced laboratory conditions by experienced personnel wearing appropriate personal protective equipment
  • Positive results in a few days and negative results in approximately 10-14 days

WHO recommends that laboratories with no capacity for diagnosis of influenza A viruses send representative specimens from suspect cases of influenza A to one of the WHO Collaborating Centers for influenza 

• Pneumonia is the most common complication of influenza virus
  • Influenza may be followed by viral pneumonia and secondary bacterial pneumonia
• Other complications: Otitis media, parotitis, tracheobronchitis, acute sinusitis, rhabdomyolysis with renal failure, myocarditis, hemophagocytic syndrome, multi-organ failure, encephalitis and worsening of underlying conditions