Chapter 76 : Specimen Collection, Transport, and Processing: Virology

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In recent years, there have been many advances in diagnostic virology, including improvements in cell culture methods and the development of viral antigen (Ag) and nucleic acid (NA) assays. Regardless of the detection method chosen, accurate test results rely on preanalytical steps, including specimen selection, collection, transport, and processing, that are described in this chapter. General guidelines for these procedures are described. Collection and processing of specific specimen types are then discussed in detail. A final section on specimen transport containing general information and selected topics of importance is included. The use of viral transport medium (VTM) during specimen collection is highly dependent on specimen source. Important specimen information that should be provided includes patient data, ordering physician, specimen source, specific viruses suspected, time and date of specimen collection, and specific diagnostic tests requested. Manufacturers of commercials assays for NA or Ag detection either supply transport media or make recommendations for transport systems that are compatible with their assays. The manufacturer's package insert should therefore be consulted for information on appropriate collection and transport systems. Currently, the majority of diagnostic or clinical specimens can be shipped as biological substances, category B. Only specimens that have or may have a category A pathogen are classified as infectious substance. However, as the field of diagnostic virology evolves, new collection devices, transport systems, and processing methods that enhance detection will continue to be developed.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76

Key Concept Ranking

Human immunodeficiency virus 1
Severe Acute Respiratory Syndrome
Lower Respiratory Tract Infections
Hepatitis C virus
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Methods used for detection of viruses

Refer to specific chapters for individual viruses; only major viral pathogens, not including rare causes of disease. LCMV, lymphocytic choriomeningitis virus; JCV, JC virus; HHV-6, human herpesvirus 6; HBV, hepatitis B virus; HTLV-1, human T-cell lymphotropic virus 1.

Most common detection methods used. NA assays include hybrid capture, NA sequence-based assays, and PCR. IA, immunoassay (includes immunofluorescentantibody assay, enzyme-linked immunosorbent assay, and immunochromatographic tests. EM, electron microscopy; EA, enzyme (neuraminidase) assay.

Hemorrhagic fever viruses and smallpox virus processing in BSL 4 facilities.

PML, progressive multifocal leukoencephalopathy.

Includes posttransplant lymphomas, immunoblastic B-cell lymphomas, and adult T-cell leukemia/lymphoma.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76
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Specimens for viral diagnostic tests

Includes direct virus detection tests such as culture, Ag detection, and NA detection. Serology is considered separately (see Table 3 ).

Includes throat and nasal swabs and nasal wash, nasopharyngeal aspirate, and BAL specimens.

Includes conjunctiva, cornea, and aqueous and vitreous fluids.

Similar specimen types for distantly related GBV virus C (also referred to as hepatitis G virus).

Neonatal infections.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76
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Serology as a primary diagnostic tool: timing of serum collection and antibody testing for relevant viruses

HAV, hepatitis A virus; HTLV, human T-cell lymphotropic virus; LCMV, lymphocytic choriomeningitis virus.

Convalescent-phase antibody; includes IgG and total antibody (IgG and IgM).

CSF IgM also useful.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76
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Plasma processing and storage conditions for selected NA tests

RUO, research use only; CE IVD, Conformité Européenne mark for in vitro diagnostics.

Test also verified for serum. Storage conditions apply to HighPure and AmpliPrep extraction.

Long-term storage of serum has not been evaluated.

Not available in the United States.

Once thawed, specimen may be stored at 2–8°C for ≤6 h.

ACD, acid-citrate-dextrose.

If viral pellets are prepared within 30 min of plasma separation.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76
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Commercial sources and formulations of VTM

Product available as swab-VTM tube combination.

Basal constituents: Hanks balanced salt solution, bovine serum albumin, l-glutamic acid, sucrose, HEPES buffer (pH 7.3), phenol red, and amphotericin B.

Citation: Forman M, Valsamakis A. 2011. Specimen Collection, Transport, and Processing: Virology, p 1276-1288. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch76

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