Influenza Virus

Diagnosis

Indications for Testing

  • Respiratory illness consistent with influenza and usually presenting during influenza season (usually diagnosed clinically)

Laboratory Testing

  • CDC - testing recommendations
  • Rapid antigen detection
    • Rapid detection necessary to use antivirals early
    • Best specimens – nasopharyngeal swabs
    • More sensitive in young children
    • Clinical Laboratory Improvement Amendments (CLIA) waived point-of-care tests – NOW Influenza A,B; QuickVue Influenza; SAS Influenza A,B; Zstat Flu
      • Sensitivity – ~70-80% during peak season depending on circulating strains
      • Specificity – 95-100%
      • Performance decreases when disease incidence is low (eg, tail-end of respiratory season)
      • Cannot differentiate H1 from H3
  • Direct fluorescent antibody stain (DFA)
    • Rapid turnaround time
    • ~75% sensitivity for influenza compared to culture
  • Real-time polymerase chain reaction (RT-PCR) – most sensitive
  • Culture
    • Considered the gold standard
    • Conventional culture may require as many as 7-10 days

Differential Diagnosis

Clinical Background

Influenza is an acute viral infection that occurs in outbreaks of varying severity mainly during the winter in temperate regions and year-round in the tropics.

Epidemiology

  • Incidence – >1/1,000
  • Age
    • Highest occurrence in young children – as many as 30% of children annually
    • Highest mortality in the elderly
  • Transmission – respiratory droplet, airborne route
    • 10-15% transmission rate among household contacts

Organism

  • Single-stranded RNA virus in the Orthomyxoviridae family
  • Three types based on antigenic differences – A, B, C
    • Only A undergoes antigenic shift responsible for epidemics and pandemics
  • Classified by hemagglutinin (HA)/neuraminidase (NA) activity
    • Named by H and N components (H1-15 and N1-9)
    • H1N1 was pandemic strain of 2009-2010

Risk Factors for Severe Disease

  • Age – infants and elderly
  • Chronic pulmonary disease (especially asthma)
  • Chronic renal, cardiovascular, hematologic (eg, hemoglobinopathies), or metabolic diseases (eg, diabetes)
  • Immunocompromised state
  • Nursing home residents
  • Pregnancy

 Clinical Presentation

  • Abrupt onset of cough, fever, chills, myalgias, malaise
  • Severe retro-orbital headache, sore throat
  • Upper respiratory infection signs and symptoms – 3-4 days after initial onset
  • Shedding of influenza virus peaks 24-48 hours after onset of symptoms and then rapidly declines
    • In immunocompetent hosts, influenza virus usually not shed for more than 5-10 days
      • May be detected later in immunocompromised hosts
  • Complications

  Prevention

  • Yearly vaccination for all persons >6 months of age (CDC recommendation)
    • Inactivated – intramuscular
    • Live attenuated – intranasal
      • Contraindicated in immunocompromised persons or households with persons who are immunocompromised
        • Antiretroviral prophylaxis with neuraminidase inhibitors when vaccination is contraindicated
  • For more information on prevention, see CDC Seasonal Influenza Vaccination Resources for Health Professionals

Indications for Laboratory Testing

  • Tests generally appear in the order most useful for common clinical situations
  • Click on number for test-specific information in the ARUP Laboratory Test Directory
Test Name and Number Recommended Use Limitations Follow Up
Influenza A and B Antigen Test Rapid detection of influenza

Time-sensitive test

Negative rapid influenza virus test does not rule out an infection with influenza A or B; 70% sensitive, 95% specific

Rapid tests administered within 4 weeks after vaccination with live, attenuated influenza virus vaccines may produce false-positive results

 
Respiratory Viruses DFA with Reflex to Respiratory Virus Mini Panel by PCR 2002565
Method: Direct Fluorescent Antibody Stain/Qualitative Polymerase Chain Reaction

Rapid detection of respiratory viruses

If DFA is negative or inadequate for influenza, respiratory virus mini panel by RT-PCR will be added

DFA is specific and sensitive in children; may not be as sensitive in adults

Sensitivity of DFA is dependent upon adequacy of specimen; if <20 cells, DFA will be reported as inadequate

 
Respiratory Viruses DFA with Reflex to Viral Culture, Respiratory 0060281
Method: Direct Fluorescent Antibody Stain/Cell Culture

Rapid detection of common respiratory viruses

DFA is specific and sensitive in children; may not be as sensitive in adults

 
Respiratory Virus Mini Panel by PCR 0060764
Method: Qualitative Reverse Transcription Polymerase Chain Reaction

Detect influenza A and B, and RSV

May be less sensitive in children

 
Influenza Virus A and B DFA with Reflex to Influenza Virus A and B Rapid Culture 0060284
Method: Direct Fluorescent Antibody Stain/Cell Culture

Rapid detection of influenza

If DFA negative, culture will be added

Culture less sensitive than PCR

 
Influenza Virus A and B DFA with Reflex to Respiratory Virus Mini Panel by PCR 2002643
Method: Direct Fluorescent Antibody Stain/Qualitative Polymerase Chain Reaction

Rapid detection of influenza and RSV

DFA is specific and sensitive in children; may not be as sensitive in adults

 
Influenza A Virus H1/H3 Subtyping by Real-Time RT-PCR  2007469
Method: Qualitative Reverse Transcription Polymerase Chain Reaction

Identify H3 and 2009-H1 hemagglutinin genes

Current circulating influenza A strains are detected and typed (H1N1 and H3N2); however, other H1 and H3 subtypes may also be detected

   
Additional Tests Available
 
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Influenza Virus A and B Rapid Culture 0060286
Method: Cell Culture/Immunofluorescence

Diagnose influenza

Culture less sensitive than PCR

Respiratory Viruses Rapid Culture 2001504
Method: Cell Culture/Immunofluorescence

Isolates other respiratory viruses, including influenza A and B; parainfluenza types 1,2,3; adenovirus; and RSV

Respiratory Viruses DFA 0060289
Method: Direct Fluorescent Antibody Stain

Tests other common respiratory viruses; can help diagnose other causes of influenza-like illness

Lower sensitivity for H1N1 type

Influenza A Virus Antibody, IgG 0051074
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Requires paired serum samples to be clinically informative

Influenza A Virus Antibody, IgM 0051081
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Antibodies appear ~2 weeks after initial inoculation

Influenza B Virus Antibody, IgG 0051080
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Requires paired serum samples to be clinically informative

Influenza B Virus Antibody, IgM 0051079
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Antibodies appear ~2 weeks after initial inoculation

Influenza A & B Virus Antibodies, IgG & IgM 0051069
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Antibodies appear ~2 weeks after initial inoculation

Influenza A Virus Antibodies, IgG & IgM 2004421
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Antibodies appear ~2 weeks after initial inoculation

Influenza B Virus Antibodies, IgG & IgM 2004422
Method: Semi-Quantitative Enzyme-Linked Immunosorbent Assay

Antibodies appear ~2 weeks after initial inoculation

Viral Culture, Respiratory and Cytomegalovirus Rapid Culture 2006497
Method: Cell Culture/Immunofluorescence