Avian Influenza – Real-time PCR

Testing Indications

Contact your local health unit if you suspect avian Influenza and PHO Laboratory Customer Service Centre at 1-877-604-4567 prior to submitting specimens.

Testing may be arranged on weekends if approved by a PHOL microbiologist. Contact the PHOL After-hours Emergency Duty Officer at 416-605-3113 for after-hours consultation.

The following specimens should be collected on all patients being tested for avian influenza:

  • Respiratory tract samples (e.g., nasopharyngeal (NP) swab plus bronchoalveolar lavage (BAL) when possible); lung tissue if obtained (e.g. biopsy, post-mortem)

Serology testing is not recommended for influenza diagnosis, including avian influenza, and is not available for clinical testing in Canada.

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit

Avian Influenza

Nasopharyngeal swab

Swab in viral transport media provided in kit

Virus Respiratory Collection Kit (Order number 390082)

Avian Influenza

Nasopharyngeal aspirate

2.0 ml aspirate

Virus Respiratory Collection Kit (Order number 390082)

Avian Influenza

Throat swab2

Swab in viral transport media provided in kit

Virus Respiratory Collection Kit (Order number 390082)

Avian Influenza


2.0 grams

Virus Enteric Collection Kit (sterile container, Order number 390087)

Avian Influenza

Plasma in EDTA3

0.5 ml

Lavender top tube

Submission and Collection Notes


Travel history and clinical information must be provided on the General Test Requisition Form. Indicate the following: travel to farms or areas experiencing avian influenza; symptoms  including pneumonia; high risk status for respiratory viral infection complications; patient setting; admission status at time of collection (if known). 


Viral throat swab in viral transport media should also be collected on all hospitalized patients.


Stool and plasma are not routinely tested for avian influenza but may be tested if avian influenza is detected in respiratory specimens. Submission of stool and plasma in EDTA requires approval of the PHOL microbiologist.

Preparation Prior to Transport

Label the specimen container with the patient’s full name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. Failure to provide this information may result in rejection or testing delay.

Special Instructions

Place specimen in biohazard bag and seal. Specimens should be stored at 2-8°C following collection. Package and ship primary clinical samples to the local PHOL in accordance with the Transportation of Dangerous Goods Regulations.

Mark the outer packaging containing avian Influenza specimens: ‘Attn: Molecular Diagnostics’.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Influenza A testing is performed Monday to Friday. 

Turnaround time is up to 5 days from receipt by PHO Laboratory.

Preliminary subtyping will be completed within 2-3 days from specimen receipt at testing site.

Positive samples will be forwarded to the National Microbiology Laboratory (NML) for confirmation.

The TAT for rapid respiratory virus culture (R-Mix TOO) is up to 4 days.


Results are reported to the ordering physician or health care provider as indicated on the requisition.

Specimens that are positive for avian Influenza are reported to the Medical Officer of Health as per Health Protection and Promotion Act.

Test Methods

Specimens will be initially tested for Influenza A and B by a CDC in-house Real Time PCR assay. 

Influenza A positive specimens will be tested for H1N1pdm09, Human H3, avian H5, avian H7, and N9 subtypes. Specimens that are Not Detected for Influenza PCR testing will be tested for other respiratory viruses by Rapid Respiratory Virus Culture.

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Updated 7 Jan 2019