Virus detection

Keywords: Virus detection, NAA or culture, Culture virus


Lesion swab, vesicle fluid, conjunctival swab, nasopharyngeal aspirate, throat swab, CSF, tissue biopsy, faeces, urine, blood leucocytes (5 mL blood in EDTA or heparin).

Specimens should be collected as soon as possible after the onset of illness. NAA is now widely used, and is the method of choice for direct detection of most viral infections.

Fluid and aspirates are better than dry swabs whenever practicable.

Aspirates and swabs should be placed in viral transport medium if culture is required (rarely).

Culture specimens require rapid transport to the laboratory.

Consult laboratory for local requirements.


A clear clinical description of the illness on the request form allows selection of the most appropriate technique(s).

Nucleic acid probes - including use after PCR amplification (may be used directly on the specimen for rapid virus detection and identification, providing a much faster result than culture).

Less rarely used: Microscopy (DFA) for eg, HSV in vesicle aspirate or ulcer scrapings, respiratory pathogens in nasopharyngeal aspirates; EM.

Rarely used: Culture in cell culture systems (in which growth is detected by observing for indications of viral growth eg, cytopathic effects on microscopic examination, haemadsorption.

See Molecular genetics - microbial.


Investigation of:

genital ulcers;

oral ulcers;

vesicular skin lesions (especially if severe, atypical or in a neonate);


severe Bronchiolitis;

severe croup;

atypical or viral pneumonia;

aseptic Meningitis;



suspected congenital infection (eg, Rubella, CMV);

suspected Poliomyelitis; and

Rotavirus infection.

Investigation of a suspected new Influenza epidemic.


Interpretation requires an understanding of the natural history of viral infections; consult pathologist.


Forman MS and Valsamakis A. In: Murray PR et al eds. Manual of Clinical Microbiology. 8th ed. 2003. ASM Press.

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