Geisinger Medical Laboratories Microbiology Specimen Collection Instructions

VIROLOGY STUDIES

I.GENERAL COMMENTS

Obtain specimens as early in the patient's illness as possible. In immunocompetent hosts, viruses are usually recoverable only for a few days after onset of illness.

Specimen Recovery Time

Most specimens should be collected in a sterile container and/or appropriate transport media.   Store and transport most specimens for viral studies at 2-8°C (on ice or Viral Transport Boxes). Blood specimens should be sent at room temperature (18-25°C). See appropriate instructions for individual specimen types.

Universal Transport Medium (UTM) is viral transport medium that is available from the Microbiology Laboratory. Viral Transport Boxes are available from Client Services.

A.  Respiratory Specimens

Testing is performed onsite by molecular methods on nasopharyngeal, throat, nasal, nose, nares, and bronchial specimens.  Other specimen sources will be sent to a reference lab for viral culture.

All requests for respiratory viruses on specimen types that are not approved for testing by PCR methodology will be forwarded to reference lab for viral culture testing.

  1. Nasopharyngeal Swabs (FDA approved, preferred specimen type)
    Use the flocked-swab packaged with the UTM for collection. Swab the posterior
    nasopharynx and any visible lesions. Immediately place swab into UTM. Store
    and transport to the laboratory at 2-8° C.
    Collecting COVID-19 Specimens

  2. Throat Swabs
    Use the flocked-swab packaged with UTM for collection. Vigorously swab the
    posterior pharynx and any visible lesions. Immediately place swab into UTM.
    Store and transport to the laboratory at 2-8° C.

  3. BAL or Bronchial Wash
    Collect as for bacteriological culture and place in a tube of UTM (I part BAL
    or bronchial wash plus 3 parts UTM for a 1:4 dilution). Discard swab packaged
    with UTM. Store and transport to the laboratory at 2-8° C.

  4. Nasopharyngeal aspirates or washings
    Introduce 1-3mL non-bacteriostatic physiological saline into one or both nostrils.
    Re-aspirate the saline and nasal secretions using a suction catheter/trap. (Use a
    suction catheter size 6 or 8.) Add a tube of UTM (Universal Transport Media) to
    the specimen. Store and transport to the laboratory at 2-8°C.

  5. Tracheal Aspirate (Inferior specimen type for respiratory PCR testing, other respiratory
    source recommended.) May be substituted for BAL or bronchial specimen in patients with lower
    respiratory disease, but it is considered an inferior specimen. Collect as for
    bacteriological culture and place in a tube of UTM. Discard swab packaged
    with UTM. Store and transport to the laboratory at 2-8°C.

  6. Sputum (Not tested for respiratory viruses by Geisinger Medical Laboratory. Other
    respiratory sources recommended, inferior specimen for respiratory PCR testing. If
    alternate specimen can not be collected, sputum is sent to reference lab for respiratory
    virus testing.) Collect as for bacteriological culture and place in a tube of UTM. Discard
    swab packaged with UTM. Store and transport to the laboratory at 2-8°C.

B. Gastrointestinal Specimens

  1. Stool: 5-10 g in sterile container (preferred specimen because of small number of viral particles present). Store and transport to the laboratory at 2-8°C.
  2. Rectal swab (use swab packaged with UTM): Collect with a plastic-shafted swab moistened with sterile saline and inserted into the anus until the cotton tip is no longer visible. Rotate 3-4 times. Immediately place swab into UTM. Store and transport to the laboratory at 2-8°C.

C.  Skin Specimens (Dermal or Genital)

  1. Vesicles or pox: Rupture lesion with a plastic-shafted swab (use swab packaged with UTM) scraping the base of the underlying ulcer to obtain both cells and fluid. Immediately place swab into UTM. Store and transport to the laboratory at 2-8°C.

    Alternate method: Aspirate fluid from the vesicle with a tuberculin syringe and eject into an equal amount of UTM.  Discard swab packaged with UTM. Store and transport to the laboratory at 2-8°C.

D.  Eye Specimens

  1. Conjunctival secretions: Use swab packaged with UTM to collect secretions from palpebral conjunctiva. Immediately place swab into UTM.   Store and transport to the laboratory at 2-8°C.
  2. Scrapings: This procedure may be performed by the Eye Department.  Place scrapings in UTM. Discard swab packaged with UTM. Store and transport to the laboratory at 2-8°C.

E.  Body Fluid Specimens

CSF, pleural, peritoneal, synovial fluids or pericardial effusions: Collect specimen in sterile tubes according to established procedures; 1-2 mL should be obtained.  Add an equal volume of UTM.  Discard swab packaged with UTM. Store and transport to the laboratory at 2-8°C.

NOTE: CSF specimens for Herpes PCR (PCRHSV) - Collect a minimum of 1 mL of CSF in a sterile collection tube according to established procedures.  Store and transport to the laboratory at 2-8°C.  Do not add UTM for PCR testing (dilution of specimen). 

F.  Urine Specimens

Clean catch/catheterized/suprapubic:  Collect 10-50 mL fresh urine (preferably first catch morning specimen) in a sterile container as for bacteriological culture (5-10 mL is sufficient for pediatric patients). Store and transport to the laboratory at 2-8°C.

G.  Tissue Specimens

Autopsy, biopsy, or clotted bone marrow specimens: Collect approximately 1 cm3 piece of tissue when possible using sterile technique and place in a sterile container with UTM added.  Specimens: Respiratory (lung, trachea), CNS (brain, spinal cord), myocarditis (heart, pericardium), disseminated disease (liver, spleen, kidney, lung). Collect as soon as possible post mortem.  Smaller samples can be placed directly into UTM. Discard swab packaged with UTM. Store and transport to the laboratory at 2-8°C.

H.  Blood Specimens for Viral Culture (Herpes simplex, adenovirus, enterovirus, measles)

Collect blood in EDTA tubes.  Collect two 2 mL tubes for neonates and two 6 mL tubes for other patients. Store and transport to the laboratory at room temperature.
Revised:  11/1/2011

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