Virology

Section Director: Ben Pinsky, M.D., Ph.D.
Operations Manager: Merrie Bass, CLS (ASCP)

General Information
The Stanford Clinical Virology Laboratory offers a range of culture, antigen and molecular test procedures for the diagnosis of viral and chlamydia infections. We provide clinical technical expertise in a setting where the test procedures are incorporated into the diagnosis, treatment and prognosis of the disease state of immuno-compromised patients such as patients receiving chemotherapy, transplant patients and HIV. The services we provide include virus isolation and identification, rapid detection of viral antigens and determination of viral antibody response. Molecular methods are a major improvement in diagnosis of viral infections. These methods have superior sensitivity and rapid turnaround times compared with conventional diagnostic methods and play a critical role in testing protocols for managing viral infections.

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Hours
Specimens are accepted 24 hours a day, seven days a week, except as noted in test specimen requirements.

Consultation Services
The Laboratory provides Medical Directors with expertise to give comprehensive consultation service to assist the clinician in choosing the appropriate tests and interpreting the results of all viral testing.  For consultation services please call Customer Services AT 1-877-717-3733 and request the Virology Laboratory.

Contact Information
Joel Sun, CLS
Virology, Supervisor
(650) 725-4146

Specimen Collection Instructions

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Specimen Submission

Request Forms
Use individual requisition forms available from the laboratory or from our test requisition page.  All test requests require a physician's written order to process a specimen. Follow the collection instructions for each type of specimen.

Patient Identification
All patients from whom clinical specimens are obtained must be positively identified, utilizing at least two unique identifiers prior to specimen collection.  Positive identification is the responsibility of the person collecting the sample.

Required Information
All specimens must be labeled.

• Patient's full name (not a nickname)
• Medical Record Number or other unique identifier (ID)
• Date and, if appropriate, time when specimen was obtained
• Specimen source
• Signature/ initials of collector
• The label should be affixed directly to the specimen container and not the bag

Bar-coded pre-printed labels with accession numbers generated by an information system may be used.

• Place the labeled specimen in the provided leak proof sealed plastic biohazard bag
• Place the matching requisition in the outside pouch of the bag

Use of a request form wrapped around the container is not acceptable as a specimen label.

Specimens will not be accepted if the information on the specimen label does not match the information on the accompanying requisition.

On all requests forms, the following information is required

• Patient's name & address
• Patient's gender
• Date of birth
• The last six digits of the patient's social security number or other unique identifier (ID#)
• Date and if appropriate, time of collection
• Test requested
• Type or source of the specimen
• Requesting physician/ or Client Number
• Clinical information if requested
• All applicable medical necessity codes (ICD-9)
• Complete billing and insurance information

Providing additional relevant information may be important in alerting the laboratory of the need for special handling or specimen work-up.

Tests sent to reference laboratories must have patient history information.  The need for such information is indicated on the test request form.

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Nasopharyngeal Specimen Collection

Specimen Collection for Detection of Respiratory Viruses (including Adenovirus, CMV, Enterovirus, Influenza, Parainfluenza, RSV, and Rhinovirus).  Other appropriate specimens include throat/pharyngeal swabs, tracheal aspirates, and bronchial samples.

Place fluids in sterile leakproof containers and transport to the laboratory.

Nasopharyngeal Swab Method

Materials:

• Nasopharyngeal swab with synthetic fiber tip
• 1-2 mL viral transport medium (VTM)
• Specimen container

Do not use calcium alginate swabs. Dacron swabs are provided with viral transport medium.

• Insert swab into one nostril.
• Press swab tip on the mucosal surface of the midinferior portion of the inferior turbinate (see sketch), and rub the swab tip several times across the mucosal surface to loosen and collect cellular material.
• Withdraw swab; insert into container with VTM.

For best sample quality, repeating procedure for the second nostril will deliver optimal combined sample.  Collect two to three swabs of NP and/or pharynx.  Place swabs into viral transport medium. Tighten caps(s) securely. Samples must be kept cold and received within 24 hours of collection. Submit specimens promptly to the laboratory.  Refrigerate
For collection kits. call Customer Services at 1- (877) 717-3733.

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Conjunctival Specimen Collection for Detection of Viruses and Chlamydia (Adenovirus, Chlamydia trachomatis, Enterovirus, and Herpesvirus)

• Gently remove pus or discharge. Use for Gram stain or microbial cultures only.
• Swab inside of lower, then upper lid as pictured. Collect infected epithelial cells (not pus) on swabs for viral and chlamydial detection.
• Use dacron swabs supplied with viral transport medium (VTM). Do not use calcium alginate or wood swabs as these are inhibitory to viruses and Chlamydia.
• Collect multiple swabs for both eyes (if affected) and place in viral transport medium (VTM). Collection of throat or nasopharyngeal swabs may increase detection of viruses.
• Note: For detection of HSV from corneal ulcers, collect cells from affected area of cornea also and submit in viral transport medium (VTM).
• Submit specimens promptly to the laboratory.
• Eye specimens can be tested for the following agents:
  • Adenoviruses
  • Chlamydia trachomatis
  • Enteroviruses (Coxsackie, echovirus, poliovirus)
  • Herpes simplex virus

Collect multiple swabs if both culture and direct viral exams are desired. Two or three swabs can be submitted in each vial of viral transport medium (VTM).

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Collection of Lesion Samples for HSV and VZV Viral Detection

To increase the chance of obtaining positive results, it is necessary to collect the types of cells that the HSV typically infect.

• In figure 1, normal epithelium can be seen to consist of four distinct zones.
• In figure 2, these same zones are seen in herpetic lesions.

The non-superficial cells, intermediate, para-basal, and particularly the base cells - are the ones that can become infected. To obtain these cells it is critical that the base of the lesion be thoroughly scraped. If the laboratory sees only superficial cells, erythrocytes, or polymorphonuclear leukocytes, the sample is inappropriate for this test.

Figure 1

Figure 2

Collection Procedure

• To expose the base of lesion:
  • Vesicles: Use a sterile needle to lift up the cap of the vesicle. Note that while vesicular fluid is not an adequate sample for the direct test, it is ideal for isolation. If vesicular fluid is present, aspirate with a sterile needle and syringe and inject into an appropriate transport medium (VTM).
  • Ulcers: Use a sterile swab to remove any unwanted pus without disturbing the base of the lesion; discard the swab after use.
  • Crusts: Use a sterile needle to expose the base of the lesion.
• Moisten a large or small dacron swab in sterile water and vigorously swab the entire base of the lesion.  Vigorous scraping of the lesion base is essential and this can be expected to cause the patient momentary pain.

• Collect two to three lesion swabs and place in viral transport medium. Tighten cap securely. Transport promptly to the laboratory.

Samples must be kept cold and received within 24 hours of collection.
Submit specimens promptly to the Laboratory (24 hours/7 days).

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