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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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TESTS: Select a test to view Test Description & Clinical IndicationsTEST CODES:
Select a Test Code to view Test Specimen Collection Instructions
ADENOVIRUS QUANTITATIVE PCR, PLASMA ORDERADVQT
BK VIRUS DNA PCR PLASMA, QUANTITATIVEBKVPC
BK VIRUS DNA PCR URINE, QUANTITATIVEBKVPCU
CHLAMYDIA TRACHOMATIS AND NEISSERIA GONORRHOEAE (GC), NUCLIEC ACID AMPLIFICATION TESTING (NAAT)CLGC3
CYTOMEGALOVIRUS QUANTITATIVE (CMV VIRAL LOAD) PCRCMVQT
CYTOMEGALOVIRUS(CMV) DNA, QUALITATIVE PCR, NON-PLASMACMVQL
EPSTEIN BARR VIRUS (EBV) QUANTITATIVE PCR, PLASMAEBVQP
HEPATITIS B PCR QUANTITATIVE, SERUMHBPCR
HEPATITIS C VIRUS (HCV) RNA, QUANTITATIVE PCR, SERUM, WITH REFLEX TO GENOTYPINGHCVPCX
HHV-6 QUANTITATIVE PCR, PLASMA ORDERHHV6QT
HIV-1 ANTIVIRAL RESISTANCE TESTING - INTEGRASEAVIN
HIV-1 ANTIVIRAL RESISTANCE TESTING, PROTEASE AND REVERSE-TRANSCRIPTASE, PLASMAAVRT
HIV-1 RNA, QUANTITATIVE PCR, PLASMAHIVPCR
HPV 16/18 TYPINGHPVPCR
HPV 6/11 TYPINGHPV6PC
HUMAN PAPILLOMAVIRUS VIRUS (HPV), NUCLIEC ACID AMPLIFICATION TESTING (NAAT)HPVHR3

Looking for a test that isn't listed? View all tests on our Test Directory

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.


Specimen Collection Instructions

Table 1: Virology Specimen Collection for Viral Cultures, Direct Exam (DFA) and Rapid Antigen Testing (Refer to Test Directory for Molecular Testing Requirements)

Specimen Source/Type

Collection Container

Representative Viruses

Comments

Blood

10 mL in Yellow-top  tube (ACD) Acid Citrate Dextrose, Solution A

CMV, HSV, VZY, Adenovirus, Enterovirus

Specify suspected virus on requisition. If no virus is specified, only CMV PCR testing will be performed. Consider Molecular testing for specific viruses.

Bone marrow

2 mL in Yellow-top tube (ACD)  Acid Citrate Dextrose) or Blue-top tube (Sodium Citrate)

CMV

 

Eye, conjunctiva/cornea

Swab inside of lower, then upper lid. Collect infected epithelial cells not pus. Place 1-2 swabs, fluid or tissue into VTM tube. 

Adenovirus, HSV, Chlamydia, Enterovirus, CMV, VZV

Request both viral culture and DFA for optimal detection of Adenovirus, HSV and VZV.  If both tests are requested, must collect 2 swabs. Both swabs can be placed into 1 VTM tube.
Chlamydia culture is a separate test request.

Fluids

2-5 mL in sterile screw-cap tube

 Varies with source

 

CSF

1-5 mL in sterile screw cap tube

Enterovirus, HSV, Mumps, CMV, VZV, Measles, Influenza

Mumps or Measles culture must be specified on requisition. Consider Molecular testing for specific viruses.

Pericardial fluid

1-5 mL in sterile screw cap tube

Enterovirus, CMV

Consider Molecular testing for specific viruses
Request PCR for enterovirus, HSV, CMV, VZV, etc.

Genital swabs (cervix, vulva, urethra, penis)

Place 1-2 swabs into VTM tube. Collect adequate cells from infected area. Collect both fluid and cells from base of lesion.

HSV, CMV (Chlamydia)

Consider Molecular testing for Chlamydia.

Lesions, derma/mucosal vesicles

Place 1-2 swabs into VTM tube.  Collect both fluid and cells from base of lesion.

HSV, VZV,  Enterovirus

Request both culture and DFA for optimal detection. If both tests are requested, must collect 2 swabs. Both swabs can be placed into 1 VTM tube.

Respiratory
- NP/throat swabs
- Lung tissue
- BAL, other fluids

Place 1-3 swabs aspirates or tissue into VTM tube.

Fluids including BAL should be placed into sterile screw-cap tube

Adenovirus, CMV, HSV, RSV, Enterovirus, Influenza, Mumps, Parainfluenza, Rhinovirus, Rubeola, Rubella, VZV,  human Metapneumonovirus, (Chlamydia in neonates)

Rapid Antigen Testing (STAT) requires 1 swab in dedicated VTM tube.
Culture and Direct Slide (DFA) requests require 2 swabs, which can be combined into 1 VTM tube.
Consider molecular testing for human Metapneumonovirus, CMV or Chlamydia. Measles, mumps, and rubella must be specified on Requisition.

Stool

Place walnut size amount into a Screw-cap container

Adenovirus, Enterovirus, HSV, VZV

Adenovirus types 40/41 and Rotavirus are not detected by culture and must be requested individually.

Rectal

Place swabs into VTM tube.

Enterovirus, HSV, VZV

 

Tissues/Biopsy

Place tissue (3 mm or more) into VTM tube.

HSV, CMV, VZV
Varies with source

Consider Molecular testing for specific viruses.

Urine

Place into Sterile screw- cap container

CMV, Adenovirus, Enterovirus, HSV, Mumps

Mumps by special request only.

VTM - viral transport medium. Once specimens have been collected, keep refrigerated and transport promptly.

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Table 2: Viruses Associated With Disease Categories

Disease Category

Common Virus

Less Common

CNS

 

 

    Aseptic meningitis

Coxsackie, Echovirus, Mumps, HHV-6

Other enteroviruses, HSV-2, HIV, LCM, VZV

    Paralysis

Polio

Coxsackie, Enterovirus 71, other Enteroviruses

    Encephalitis

Arboviruses, HSV, Enteroviruses, HIV, CMV, HHV-6, Mumps

Herpes B, CMV, PML viruses (JCV), Rabies, VZV

Genitourinary

 

 

    Lesions

Herpes, Molluscum, HPV

CMV, VZV

    GU tract

CMV

Mumps, HSV

    Cystitis, Glomerulonephritis

Adenovirus, BKV

 

Gastrointestinal

Adenovirus, CMV, norwalk, rotavirus

Enteroviruses

Hepatitis

Hepatitis A, B, C, D, EBV, CMV

Hepatitis E, G, TTV, HSV, Togavirus (Yellow Fever),  Arenavirus

Neonatal disease

 

 

    TORCH

Rubella, CMV, HSV, Echovirus, Parvovirus, Hepatitis B

Adenovirus, VZV

    NB respiratory

Influenza, HSV, RSV

Adenovirus, Measles, Parainfluenza, Enteroviruses

Ocular

 

 

    Conjunctivitis

Adenovirus, enteroviruses, HSV, VZV, (Chlamydia)

Dengue, Newcastles

    Corneal Lesion

HSV

Respiratory

 

 

    Upper respiratory

 

 

        Colds, Pharyngitis

Adenovirus, Coxsackie, EBV, Echovirus, Influenza A & B, Respiratory Syncytial (RSV), Herpes, Parainfluenza, Rhinovirus

Coronavirus, Influenza C, Parainfluenza

        Croup, Bronchiolitis

RSV, Parainfluenza

Adeno, Influenza, Measles

    Lower Respiratory

 

 

        pneumonia, adults

Influenza

Adenovirus, measles, newcastles; immunocompromised: CMV, HSV, VZV

        pneumonia, children

RSV, influenza, parainfluenza

Adeno, measles, VZV

Skin

 

 

    hemorrhagic

Arboviruses

Ebola

    lesions, local

HSV, VZV, HPV, molluscum

Poxviruses

    maculopapular

Coxsackie, echovirus, parvovirus, rubella, rubeola (measles)

Adenoviruses, CMV, EBV

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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.
nasopharyngeal specimen collection

  • 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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