Respiratory Viruses

Diagnosis

Indications for Testing

  • Symptoms of severe lower respiratory tract infection

Laboratory Testing

  • Testing to identify specific pathogens may not be necessary if clinical management is unchanged
  • Nonspecific testing – CBC with differential
    • Normal to low white blood cell count most common
    • Differential – usually monocyte and lymphocyte predominant
  • Rapid antigen testing – often available as point-of-care test for influenza and RSV
    • Sensitivity may be low when compared with other methods
  • Direct fluorescent antibody (DFA) stain
    • Fairly rapid results (24 hours)
    • Requires nasopharyngeal swab or aspirate
  • Polymerase chain reaction (PCR) available for many respiratory viruses
    • More sensitive than DFA
    • Longer turnaround time than DFA
    • More expensive than DFA
  • Viral culture – gold standard
    • Difficult to grow some viruses
    • Not all viruses grow on same medium
    • Time consuming, expensive

Imaging Studies

  • Chest x-ray usually demonstrates bilateral interstitial infiltrates
    • Focal infiltrates are more suggestive of bacterial etiology

Differential Diagnosis

Clinical Background

Viral respiratory tract infections are the most common diseases affecting humans throughout the world.

Epidemiology

  • Incidence
    • Annually, >5 million children in the U.S. <6 years experience lower respiratory tract infections (LRTIs)
  • Age – bimodal peaks
    • Adults >55 years
    • For children, refer to Pediatrics tab

Organisms

  • Viruses are the fourth leading cause of hospital-treated pneumonia in otherwise healthy adults
  • Although a wide variety of viral agents are capable of causing LRTI, respiratory syncytial virus (RSV), adenovirus, influenza virus (A and B), and parainfluenza virus (1, 2, and 3) cause 80-90% of all LRTIs
    • RSV and influenza are associated with significant annual morbidity and mortality, despite available therapies

Risk Factors

  • Age – <2 years or >55 years
  • Compromised immune system
  • Chronic medical condition (cardiac, pulmonary, hepatic)

Clinical Presentation

  • Clinical presentation often does not distinguish viruses
    • Nonspecific symptoms – cough, fever, sore throat, rhinorrhea, hoarseness, bronchitis
    • Individuals with compromised cardiac, pulmonary or immune systems and the elderly are at greatest risk for serious complications from LRTI

Pediatrics

Clinical Background

Viral respiratory infection in children is responsible for more burden of disease than any other cause.

Epidemiology

  • Incidence
    • Annually, >5 million children in the U.S. <6 years experience lower respiratory tract infections (LRTIs)
  • Age – peaks in children <10 years

Organisms

Clinical Presentation

  • Most respiratory viruses confined to upper respiratory tract
    • Coryza, cough, hoarseness, rhinitis, pharyngitis, otitis
  • Lower respiratory tract involvement
    • Tachypnea, wheeze, severe cough, croup, bronchiolitis, respiratory distress (nasal flaring, intercostal retraction)
  • Complications
    • Severe viral pneumonia
    • Acute respiratory failure
    • Secondary bacterial pneumonia

Diagnosis

Indications for Testing

  • Severe LRTI

Laboratory Testing

  • In healthy infants, virological diagnosis generally not sought
  • Viral identification most important to rule out RSV since it is treatable, and influenza in order to administer therapeutics and reduce morbidity and mortality
    • Rapid antigen tests – often have low sensitivity
    • DFA testing – rapid testing; frequently performed as panel
      • Requires nasopharyngeal swab or aspirate
    • PCR testing
      • Requires nasopharyngeal swab or aspirate
      • Less rapid than DFA
      • More expensive
    • Viral culture – gold standard but difficult to grow viruses
  • Nonspecific testing – CBC with differential
    • Normal to low white blood cell count common
    • Differential – usually monocytes and lymphocytes predominant

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
CBC with Platelet Count and Automated Differential 0040003
Method: Automated Cell Count/Differential

Predominance of monocytes and lymphocytes may be diagnostic; white blood cell count is usually not elevated

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

DFA identifies the infectious agent of a pneumonia

Panel includes influenza A and B, parainfluenza (1,2,3), RSV, adenovirus, human metapneumovirus (hMPV)

If DFA is negative or inadequate for influenza, Respiratory Virus Mini Panel by RT-PCR will be added

Adequacy of the direct specimen significantly influences the sensitivity of DFA

Inadequate specimen collection or too few cells on the slide may lead to failure of direct smears

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

DFA identifies the infectious agent of a pneumonia

Panel includes influenza A and B, parainfluenza (1,2,3), RSV, adenovirus, hMPV

If DFA is negative or inadequate, a viral culture will be added

Adequacy of the direct specimen significantly influences the sensitivity of DFA

Inadequate specimen collection or too few cells on the slide may lead to failure of direct smears

Other viruses (eg,  HSV, CMV) will not be routinely detected in this culture; decreased sensitivity for adenovirus using rapid culture

Sputum and nasal swabs are best specimens

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

Identify the agent of a pneumonia

RT-PCR is a rapid and highly sensitive test for viruses; RT-PCR is also the most expensive test

Components include testing for influenza A and B and RSV

   
Additional Tests Available
 
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Respiratory Viruses Rapid Culture 2001504
Method: Cell Culture/Immunofluorescence

Isolate influenza A & B, RSV, adenovirus, and parainfluenza (1, 2, 3)

Respiratory Viruses DFA 0060289
Method: Direct Fluorescent Antibody Stain

Rapid test; detects adenovirus, influenza A & B, RSV, parainfluenza (1, 2, 3), hMPV

Significantly more rapid and less expensive than PCR

Human Metapneumovirus DFA  0060779
Method: Direct Fluorescent Antibody Stain

Use to detect all types of hMPV (A1, A2, B1, B2)

No cross reactivity with other common respiratory viruses

Sample requires adequate amount of intact cells

Viral Culture, Respiratory 2006499
Method: Cell Culture
Respiratory Culture and Gram Stain 0060122
Method: Stain/Culture/Identification
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