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 (12-36 hours after illness onset) necessary to use antivirals early
    • Recommended specimens – nasal washes/aspirates may be necessary in young children; 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
    • Less rapid turnaround time
  • 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
    • 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
    • Aquatic birds considered reservoir for influenza A
  • Three types based on antigenic differences – A, B, C
    • Only A undergoes antigenic shift responsible for epidemics and pandemics
    • C causes only mild illness
  • Classified by hemagglutinin (HA)/neuraminidase (NA) activity
    • Named by H and N subtypes (H1-16 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 residency
  • Pregnancy

 Clinical Presentation

  • Upper respiratory infection signs and symptoms – 3-4 days after initial onset
    • Abrupt onset of cough, fever, chills, myalgias, malaise
    • Severe retro-orbital headache, sore throat
  • 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
      • Immunocompromised hosts may have delayed and prolonged viral shedding
  • 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 Virus Mini Panel by PCR 0060764
Method: Qualitative Reverse Transcription Polymerase Chain Reaction

Preferred test to confirm influenza or RSV in general inpatients and RSV in adults

Panel detects influenza A and B, and RSV

May be less sensitive in children

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

Order this test when the detection of respiratory viruses in addition to influenza is important

Test detects influenza (A, B), parainfluenza (1, 2, 3), adenovirus, respiratory syncytial virus (RSV), and human metapneumovirus (hMPV)

Molecular methods are preferred for immunocompromised and hospitalized patients

For general inpatient workup of influenza-like illness, order the respiratory virus mini panel by PCR

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

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

Not recommended for inpatients or immunocompromised individuals

Acceptable test for the detection of influenza in outpatients

Reflex pattern – if DFA is negative or inadequate, influenza culture will be added

Sensitivity of DFA methodology is dependent upon adequacy of the specimen; if specimen contains fewer than 20 cells, then the DFA result will be reported as "inadequate”

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

Acceptable test to detect influenza during influenza season

Reflex pattern – if DFA is negative or inadequate, then Respiratory Virus Mini Panel by PCR will be added

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

Sensitivity of DFA methodology is dependent upon adequacy of the specimen; if the specimen contains fewer than 20 cells, then DFA results will be reported as inadequate

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

Follow-up test for patients with documented influenza A

Not a first-line test for the detection of suspected influenza in most clinical situations

Detects and subtypes the 2 predominant strains of circulating influenza A (H1N1 and H3N2)

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

Not a recommended initial test

Rapid detection of respiratory viruses

Reflex pattern – 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

 
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

Not a preferred standalone test

Culture less sensitive than PCR

Respiratory Viruses Rapid Culture 2001504
Method: Cell Culture/Immunofluorescence

Detects common respiratory viruses (influenza A and B; parainfluenza types 1,2,3; adenovirus; and RSV)

Offers improved turnaround time over respiratory viral culture; molecular methods may offer improved sensitivity

Respiratory Viruses DFA 0060289
Method: Direct Fluorescent Antibody Stain

Not a preferred standalone test

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

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Do not use to diagnose acute influenza infections

Serological testing for influenza should be used for research and public health investigations only

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

Virus-specific tests are recommended

Viruses that can be isolated with this test – adenovirus; CMV; enterovirus; HSV; influenza A and B; parainfluenza types 1,2, and 3; RSV; and VZV