AHL Labnote 65 - Avian Influenza Testing Protocol for Practitioners

Emily Martin, Davor Ojkic. Tim Pasma

Please note that if Avian influenza is suspected, you must contact your local CFIA District Office who will advise you on further steps.

CFIA District Office Lookup


CFIA hotline for FAD if unable to reach a district office - 1-877-814-2342

Standard swabbing procedure for PCR

Swabbing technique video:


Swab types:

Viral transport media (VTM) tubes with swabs must be used - do not use wood-handled swabs.

CFIA Method:

Oropharyngeal Swabs (OP): Insert the swab into the pharynx (as far back into the oropharynx as possible – we do not require a tracheal swab) and rotate it three times in each direction. When removing the swab, drag it down the choanal groove of the palate (roof of mouth – opening to sinuses).

Cloacal Swabs (CL): Collect by inserting the dry swab into the bird’s vent and swirling gently, ensuring contact with the mucous membrane.

 Have two tubes of media open and labelled so a cloacal swab and oropharyngeal swab can be collected simultaneously from the same bird.

  • Swab the oropharynx or cloaca with a dry, clean swab. A separate swab must be used for each orifice (if available).
  • Pool swabs from 10 birds into one tube of transport media.
  • Do not mix oropharyngeal and cloacal swabs in the same tube of media. Have one tube for a pool of 10 oropharyngeal swabs and another tube for a pool of 10 cloacal swabs.
  • Swirl each swab in the media, then squeeze out fluid against the side of the tube. Remove the swab and discard. Do not leave the swab in the tube.
  • Repeat 9 more times with same tube to create a pool of ten swabs. Use the same procedure for both cloacal and oropharyngeal swabs.
  • Swabs can only be pooled from birds of the same species.
  • The tube should be labelled an “OP” for oropharyngeal or a “C” for cloacal swabs.
  • Only cloacal swabs are required from waterfowl.

- Ensure the Identification on the swabs matches the Identification information on the submission form so that swabs and form can be matched up. Indicate if the swabs are pooled oropharyngeal/cloacal swabs on the side of the vials.

- Spray the outside of the VTM tubes with disinfectant, double-bag the swabs, and spray outside bag with disinfectant, allowing 15 minute contact time (drip dry).

- The time from which birds are negative to when they can become positive may be as short as 48 hours. Sample turnaround should be as short as possible!

- DO NOT move birds until negative results are available! 

For more detailed information, please contact the lab.

Swab information:

Wooden-handled swabs are not suitable. We recommend using commercial products such as (or equivalent):

(1) BD Universal Viral Transport Kits that are available from Fisher Scientific (Cat # B220531) or

(2) Starplex Multitrans Collection and Transport System (for transportation of Viruses, Chlamydia and Mycoplasma) # S160-100 from VWR (Cat # CA73270-008).

VTM transport kits are available from AHL at cost. Please email ahlinfo@uoguelph.ca if required.

Commercial VTM products have stabilizers and antibiotics to protect samples in case of shipping issues. Other sterile swabs in sterile saline are OK, if samples are “strong” positives. For maximum sensitivity, VTM is highly recommended. Swabs need to be in leakproof, impact-resistant container e.g., red-top tube.

To contact the lab for VTM vials and shipping information via Purolator, contact ahlinfo@uoguelph.ca. Any questions, please call AHL at 519-824-4120 ext 54530.

Our website contains shipping information and submission forms:  https://www.uoguelph.ca/ahl/  

Submission Receiving at AHL

The protocol for receiving of samples for avian influenza (whether monitoring or suspect) has changed during the outbreak. First, for any suspect birds CFIA MUST be contacted. AHL will only accept VTM swabs from suspect birds.  For submitting samples for AI, we ask that you DO NOT ENTER our facility. Please remain in your car and dial 519-824-4120 ext 54530 (Guelph Specimen reception) (in Kemptville 613-258-8320).  A staff member will come to your car and either take your samples. 

All birds for PM (that are not suspect) may be swabbed by AHL staff for AI testing. A negative result is needed before the PM is commenced. This may result in slight delays in reporting postmortem results.

Submissions can still be submitted by courier, we just request that you put a “M” for monitoring or a “S” for suspect on the outside of the box / package, and on the submission form to alert Specimen reception that these samples are for the Avian Influenza stream. Please put the AI samples in a separate courier submission and do not include any other samples.

Tim Pasma

Client Services Veterinarian

tpasma@uoguelph.ca  519-824-4120 ext 54611