Guidelines for the collection of Upper Respiratory Tract Specimens for viral respiratory pathogen

Last updated on April 4th, 2020

Infections of the upper respiratory tract usually involve the ears, the mucus membranes lining the nose and throat above the epiglottis and the sinuses. Upper respiratory tract specimens should be collected within 3 days of symptom onset and no later than 7 days, ideally prior to the initiation of antimicrobial chemoprophylaxis or therapy.

Most infections involving the nose and throat are caused by viruses. Oropharyngeal (OP) and nasopharyngeal (NP) swabs and nasopharyngeal wash/aspirate are the common upper respiratory tract specimens submitted for virologic assays.  Nasopharyngeal wash/aspirate is the preferred sample. Use mask, gloves and eye protection while collecting the specimen.

Oropharyngeal (OP) and nasopharyngeal (NP) swabs

Only sterile dacron or rayon swabs with plastic shafts are appropriate for oropharyngeal and nasopharyngeal swabs.

DO NOT use calcium alginate swabs or swabs with wooden sticks, as they may contain substances that inactivate some viruses and inhibit some molecular assays. 

Procedure for the collection of Oropharyngeal (OP) Swab

1. Insert the swab into the posterior pharynx and tonsillar areas.
2. Rub swab over both tonsillar pillars and posterior oropharynx and avoid touching the tongue, teeth, and gums.

Procedure for the collection of Oropharyngeal (OP) Swab

1. Insert flexible wire shaft swab through the nares parallel to the palate (not upwards) until resistance is encountered or the distance is equivalent to that from the ear to the nostril of the patient indicating contact with the nasopharynx.
2. Gently, rub and roll the swab. Leave the swab in place for several seconds to absorb secretions before removing.

Place NP and OP swabs immediately into a sterile vial containing 2 ml of viral transport media. Both swabs can be placed in the same vial if desired. Aseptically, cut or break applicator sticks off near the tip to permit the tightening of the cap.

 Procedure for collection of Nasopharyngeal wash/aspirate.

1. Have the patient sit with the head tilted slightly backward.
2. Instill 1 ml-1.5 ml of nonbacteriostatic saline (pH 7.0) into one nostril.
3. Flush a plastic catheter or tubing with 2 ml-3 ml of saline.
4. Insert the tubing into the nostril parallel to the palate (not upwards).
5. Aspirate nasopharyngeal secretions. If permitted, repeat this procedure for the other nostril.
6. Collect nasopharyngeal aspirate in sterile vials

Labeling: Label each specimen container with:

1. Name of the patient
2. Hospital or lab identification number
3. Type of specimen collected
4. Date of collection

Transport and Storage

Send specimens to the lab immediately (testing sensitivity decreases over time). If specimens will be examined within 48 hours after collection, keep specimen at 4^oC and ship on wet ice or refrigerant gel-packs, otherwise store frozen at ≤-70^oC and ship on dry ice.

Viability of some pathogens (e.g. respiratory syncytial virus) from specimens that are frozen and then thawed is greatly diminished and may result in false-negative test results.