Virology Specimen Collection Guide

Please contact the virology lab at (206) 685-8037 for questions about collection and handling of virology specimens.  Most PCR or culture samples should be held at 4oC and arrive in the lab within 24 hours of collection.

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. This specimen is appropriate for PCR or culture examination for respiratory viruses, including RSV and Influenza A/B.

Nasal Wash

All respiratory viruses can be detected in a nasal wash, however it is not a validated specimen type for most kit-based real time PCR assays.

  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.

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.

Sputum, BAL, bronchial washes, and tracheal aspirates

These specimens should be placed in sterile containers without addition of UTM.

Throat swab

Rub regular sized flocked swab over posterior pharynx or both tonsillar fossae. 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).

Rectal Swab

Gently insert regular flocked swab into rectum enough to dirty it. Break swab off immediately into universal transport media.

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.


Collect 5-10 grams of stool in clean container.


Should be collected in clean container. 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)

The general rule is that all body fluids should be collected in sterile containers, without transport media.


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. Place the swab into a vial of universal transport media (UTM).

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. 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”.  Bone marrow samples SHOULD BE STORED AND TRANSPORTED AT ROOM TEMPERATURE.

Paraffin Fixed Tissues

DO NOT SEND ENTIRE BLOCK.  Slice 3-4 slices per test that are 5-50 micron thick and put in sterile tube.

Dried Blood Spots

Use Newborn Screening Card.  Fill 1 circle completely with blood (be sure blood soaks through to other side).

QuantiFERON®-TB Gold PLUS (4 tube assay) Collect 1 mL blood in each tube:  one NIL (Grey top), one TB1 Ag (Green top), one TB2 Ag (Yellow top), one MIT (Lavender top). The black mark on the side of tubes indicates the 1 mL fill volume.  Do not under or over-fill. Immediately after filling tubes, shake all four tubes 10 times to ensure that the entire inner surface of the tube has been coated with the blood. Specimen must be incubated within 16 hours of blood draw.

Serological tests 5 mL blood in GOLD top serum separator tube (SST) Also acceptable: 5 mL blood in ORANGE top rapid serum tube (RST) or RED TOP tube.