Respiratory Virus Detection

Reporting Name

Useful For

Detection of respiratory viruses causing upper- or lower respiratory tract infections.


Testing algorithm

Component Available separately Always performed
Respiratory PCR NO YES

* includes influenza A and B, RSV, hMPV, human parainfluenza -1,-2,-3, enterovirus and adenovirus.


Virus target PCR
Influenza A/B  X
Respiratory syncytial virus  X
Human parainfluenza virus 1, -2, -3  X
Adenovirus  X
Human metapneumovirus  X
Enterovirus  X


Method Name

Polymerase chain reaction (PCR)


Reporting Name

Respiratory Viruses









Tract Infection

Acute Respiratory Disease (ARD)


Acute Conjunctivitis

Acute hemorrhagic conjunctivitis


Specimen Required


NOTE: If the patient/client has excessive mucus please ask the patient/client to blow their nose to clear nasal passage of excessive mucus. Have the person dispose of the used tissue in a waste receptacle.



Upper respiratory tract infection (URTI)
Posterior nasopharynx Nasopharyngeal swab (NP swab) Preferred specimen for upper respiratory disease
Nasopharyngeal aspirate Not recommended for adults
Nasopharyngeal wash Only to be considered for thrombocytopenic patients for whom NP aspirate is contraindicated
Lower respiratory tract infections
Lung Bronchoalveolar lavage (BAL)
Bronchial brush
Lung tissue Ideal for lower respiratory disease
Nose and throat Swab/washings Not recommended

All swabs must be transported in Universal Transport
Medium (UTM) to retain viability.

Ensure collection of adequate cellular material.


Specimen Minimum Volume

Liquid: 2 ml


Transport Temperature

Specimen Room temperature Refrigerated Frozen
Fluids NO YES YES*
Tissue NO YES YES*

Maintain at 2-8°C and transport (cold packs) within 24 hours.

*For > 24h delay, freeze at -70°C and transport on dry ice.


Reject Due To

Specimens other than Respiratory swab, fluid, tissue
Excess mucus

Useful For

Detection of respiratory viruses causing upper- or lower respiratory tract infections.


Clinical Information

Most acute respiratory illnesses are caused by respiratory viruses and involve the upper airways, clinically manifesting as “colds”, pharyngitis, or tonsillitis. Upper respiratory tract illnesses (URTI) are usually self-limited and relatively mild but prompt many physician visits. The influenza like illness (ILI) and viral lower respiratory tract illness (LRTI) such as croup, bronchiolitis, and pneumonia are less frequent but associated with higher hospitalization rates and fatalities. Virus-triggered exacerbations of asthma or chronic obstructive pulmonary disease (COPD) can likewise be severe and sometimes fatal.


Relative importance of major respiratory viruses in upper and lower respiratory tract infections

Virus Importance in
Common cold Flu/ILI Croup Bronchiolitis Pneumonia
Influenza +++ ++++ + + ++++
RSV1 +++ + ++ ++++ ++++
hMPV2 ++ + + ++++ ++++
Parainfluenza +++ + ++++ +++ ++++
Rhinovirus ++++ ++ + ++
Adenovirus +++ ++ + ++++

1 Respiratory syncytial virus

2 Human metapneumovirus

Adapted from Robinson, C. Respiratory viruses


In countries with definite winters, annual epidemics of RSV, influenza virus, hMPV occur with reasonable regularity during the coolers months of the year. Influenza virus tends to produce short annual peak of respiratory illness lasting 6 – 8 weeks, whereas the peak of RSV tends to be broader with a median duration of 15 weeks. hMPV can be detected year-round but usually peak in late winter to spring, coincident with or slightly later than RSV.





Rhee, E. G., and Barouch, D. H. 2010. Adenoviruses, p. 2027-2033. In Mandell, D., Bennett, J. E., and Dolin, R. 2010. Principles and practice of infectious diseases, 7th ed., vol. 2. Churchill Livingstone, Elsevier, Philadelphia, PA.


Robinson, C., and Echavarria, M. 2007. Adenoviruses, p. 1589-1600. In Murray, P. R., Baron, E. J., Jorgensen, J. H., Landry, M. L., and Pfaller, M. A. Manual of Clinical Microbiology, 9th ed., vol. 2. ASM Press, American Society for Microbiology, Washington, DC.

Direct Fluorescent Antigen (DFA)
Microscopy for Emergency Room and In-patients


Status Days Analytic Time Maximum Laboratory Time Specimen Retention
Routine Monday – Friday Same day 24h 1 week



Culture (Rapid Shell Vial)


Status Days Analytic Time Maximum Laboratory Time Specimen Retention
Routine Monday – Friday 48h 72 h 1 week


Method Description

Direct Fluorescent Antigen Microscopy uses viral antigen-specific murine monoclonal antibodies that are directly labeled with fluorescein for the rapid detection and identification of 8 respiratory viruses targeting influenza A, influenza B, human parainfluenza 1 – 3, respiratory syncytial virus, human metapneumovirus and adenovirus.


Culture and isolation of adenoviruses from clinical specimens is accomplished employing the shell vial rapid culture technique with a mixed monolayer comprising A549 and MDCK cell lines. Shell vials are read at 24- and 48h.


Real-time polymerase chain reaction (PCR) targeting influenza A and influenza B virus matrix (M) gene employing Roche LightCycler® 480.


Performing Laboratory Location

Newfoundland & Labrador Public Health Laboratory

St. John’s


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