Virology Specimen Collection Guidelines

Please contact the virology lab at (206) 685-8037 for questions about collection and handling of virology specimens.

Throat swab

Rub regular sized flocked swab over posterior pharynx or both tonsillar fossae. In cases of mumps, swab the inflamed orifices of Stenson's ducts. Swabs should be vigorously rubbed over any open lesions in mouth or throat. Break or cut swab making sure that the swab shaft doesn’t extend beyond the top of the vial, secure cap and check to see that the swab end is immersed in the universal transport media (UTM). Maintain and transport at 4° C. DO NOT FREEZE.

Nasopharyngeal swab

Gently insert mini-tipped flocked nasopharyngeal swab (swab on flexible plastic shaft) through the nostril and into the nasopharynx, reaching the posterior nasopharynx. Gently rotate swab, then remove, and break swab off into universal transport media (UTM). Make sure the swab is fully immersed in the UTM, and that the shaft is short enough to completely tighten the cap. Send to the laboratory as soon as possible. This specimen is appropriate for PCR or culture and fluorescent antibody (FA) examination for respiratory viruses, including RSV and Influenza A/B. As with all FA tests, obtaining as many columnar epithelial cells as possible will enhance reliability of the test. An instructional video showing how to collect a nasophryngeal (NP) swab is available here. This collection method can be used for any virology test method that requires an NP swab.

NOTE: It is reasonable and cost effective to pool throat and nasopharyngeal swabs in the same VTM.

Nasal Wash

The nasal wash is the preferred specimen for all respiratory viruses. Sterile saline should be used.

  1. Pour 5 – 10 mLs saline into sterile medicine cup and aspirate it into a sterile bulb syringe.
  2. Place infant/young child on his/her side.
  3. Irrigate the nose on the patient's dependent side and aspirate solution back into the bulb syringe.
  4. Return media to a sterile specimen tube or cup and label.
  5. Place at 4° C and transport to Virology lab as soon as possible.

An alternate method for older children and adults:

  1. Aspirate 10 mL sterile normal saline into a sterile syringe or bulb.
  2. Tilt head back and apply pressure to one nostril.
  3. Have patient hold breath and quickly “squirt” 5 mL saline into open nostril.
  4. Tilt head forward to allow fluid to drain or expel into sterile collection cup. Some fluid may be swallowed; however, several mLs of fluid will drain or be expelled from nostrils.
  5. Repeat with other nostril, if possible.
  6. Transfer this fluid to the sterile conical centrifuge tube or seal the collection cup.
  7. Place at 4° C and transport to lab.

Sputum, BAL, bronchial washes, and tracheal aspirates

These specimens should be placed in sterile containers, kept at 4° C, and transported to the laboratory as quickly as possible.

Rectal Swab

Gently insert regular flocked swab into rectum enough to dirty it. Break swab off immediately into universal transport media. Maintain at 4° C and transport to the laboratory as quickly as possible.

Conjunctiva (eye) Swab

Evert the lower eye lid and gently rub the conjunctival surface with mini-tipped flocked swab.  Swabbing pus collection in corner of eyes is not adequate. Break swab off immediately into universal transport media. Maintain at 4° C and transport to the laboratory as quickly as possible.


Collect 5-10 grams of stool in clean container and hold at 4° C.


Should be collected in clean container and kept at 4° C. First morning voids usually contain the highest titers of virus.

Cerebral Spinal Fluid (CSF)

Should be collected in sterile container. PCR is a much more sensitive method for diagnosing viral infections from CSF. 0.2 mL per PCR test ordered is needed. To culture CSF, a minimum of 0.5 mL of fluid insures a complete viral work up. Do not dilute in universal transport media (UTM).

Miscellaneous Body Fluids pericardial, peritoneal, etc.)

The general rule is that all body fluids should be collected in sterile containers, without transport media. Samples should be maintained at 4° C and transported to the laboratory as soon as possible.


Viruses can often be isolated from vesicular-pustular lesions. Macular lesions do not yield high titers of viruses. Vesicular lesions should be opened with a scalpel blade and vigorously swabbed with a regular or mini-tipped flocked swab or dacron-tipped swab such as Dacroswab I. The swab should be placed in a vial of universal transport media (UTM), maintained at 4° C and transported to the laboratory as soon as possible. Lesion specimens collected in this manner provide material both for viral isolation and FA exam for HSV and Varicella-Zoster antigens. The laboratory prefers to make FA slides from the lesion scrapings in the viral transport media. Swabs for PCR testing do not need to be placed in transport media.

Tissue Specimens

Small pieces of tissue should be placed in viral transport media or sterile PBS. Do NOT add the flocked swab to the transport media. Large pieces may be transported in dry sterile container, as long as the specimen will be moist when it arrives in the laboratory. Hold specimen at 4° C and transport to the laboratory as soon as possible. Tissues for PCR testing do not need to be placed in transport media.

Bone marrow

Bone marrow should be collected in an EDTA tube so that if PCR is later requested, the same sample can be used. A heparinized syringe is an acceptable preservative if culture only is requested. Understand that heparin is inhibitory to PCR and will preclude “add-on” PCR requests. Transportation should be at room temperature.

virology/specimens (last modified 2015-04-09 14:55:38)