Avian Influenza – Real-time PCR
Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.
Background
This page provides molecular testing information for avian influenza at Public Health Ontario (PHO). For information regarding other testing options, refer to the following PHO webpages:
Updates
- Added clarification of recommended and acceptable specimen types in response to H5N1 detection in cattle in the US
- Added information on testing sites
Testing Indications
PHO is currently responding to cases of highly pathogenic avian influenza (H5N1) in birds across Ontario. In addition, H5N1 was detected in a number of dairy cows in several farms in the United States. The investigation number ONT-2022-00001 should be included on all requisitions for local exposures related to infected birds or other animals. Testing for symptomatic individuals will include COVID-19, avian influenza and multiplex respiratory virus PCR.
Contact your local public health unit if there is a suspected avian Influenza infection.
Acceptance/Rejection Criteria
Serology testing is not recommended for influenza diagnosis, including avian influenza, and is not available for clinical testing in Canada.
Specimen Requirements
| Test Requested | Required Requisition(s) | Specimen Type | Minimum Volume | Collection Kit |
Avian Influenza |
Nasopharyngeal swab, AND throat swab |
1 swab in the collection kit media for each collection site |
Virus-Respiratory Collection Kit: order# 390082 |
|
Avian Influenza |
Bronchoalveolar Lavage (BAL), bronchial wash (BW) or pleural fluid |
2.0 ml |
Sterile container |
|
Avian Influenza |
Respiratory tract tissue |
1.0 g |
Sterile container |
|
Avian Influenza |
Conjunctival swab (Do not submit until approved by a PHO microbiologist) |
1 swab in the collection kit media (UTM) |
Virus-Respiratory Collection Kit: order# 390082 |
Submission and Collection Notes
Prior to specimen submission, contact PHO’s Laboratory Customer Service Centre at 416-235-6556 or 1-877-604-4567 or after-hours Emergency Duty Officer at 416-605-3113 for further instructions and testing approval. Weekend testing is available and must be approved by a PHO microbiologist or designate.
Complete all fields of the PHO’s General Test Requisition Form, including:
- Tests requested (Avian Influenza, COVID-19 PCR, and Multiplex Respiratory Virus PCR/MRVP) and reason for test
- Patient setting, specimen types and sites
- Outbreak investigation number ONT-2022-00001
- Travel history, exposure history and clinical information (see special instructions section below)
Label the specimen container(s) with the patient’s first and last 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.
Upper respiratory tract samples, including nasopharyngeal (NP) swab and throat swab in universal or viral transport medium (UTM/VTM) are recommended for all symptomatic patients being investigated for avian influenza.
Lower respiratory tract samples - e.g. bronchoalveolar lavage (BAL), bronchial wash, and/or lung tissue if obtained (e.g. biopsy, post-mortem) are recommended for severe cases with lower respiratory tract infection
Sample types other than respiratory, such as swabs from other potentially infected anatomical sites (e.g. conjunctival swabs from patients with conjunctivitis and potential occupational exposure), require approval by a PHO microbiologist.
Stool and blood are not routinely tested for avian influenza but may be tested if avian influenza is detected in respiratory specimens. Contact PHO for approval by a PHO microbiologist before you submit these specimens.
Serology testing is not recommended for influenza diagnosis, including avian influenza, and is not available for clinical testing in Canada.
Storage and Transport
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 PHO location in accordance with the Transportation of Dangerous Goods Regulations.
Special Instructions
Complete all fields of the PHO General Test Requisition Form.
Under Test(s) Requested, order avian influenza, COVID-19 PCR and multiplex respiratory virus PCR (MRVP) (See example below)
Travel history and clinical information must be provided. 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).
Test Frequency and Turnaround Time (TAT)
|
Test |
Turnaround Time |
Test Location |
Frequency |
|---|---|---|---|
|
Avian Influenza subtyping - H5 target only 1 |
Up to 2 business day(s) from specimen receipt at PHO |
Ottawa Timmins |
Monday to Friday |
|
Avian Influenza subtyping – full panel |
Up to 2 business day(s) from specimen receipt at PHO |
Toronto |
Monday to Friday |
1 Specimen will be forwarded to Toronto for full panel typing after H5 typing is completed at one of the regional testing laboratories.
Positive avian influenza specimens will be forwarded to the National Microbiology Laboratory (NML) for confirmation and TAT to receive results is up to 14 days from receipt of specimens at NML
STAT and Critical Specimens Testing
STAT testing is not available.
Priority testing is available outside of regular hours upon approval from a PHO microbiologist for symptomatic individuals (all patient settings) with potential exposure to poultry, wild birds, livestock, or other animals. Please contact PHO’s Laboratory Customer Service at 416-235-6556/1-877-604-4567 or after-hours Duty Officer at 416-605-3113 for consultation.
Priority specimens must be shipped separately from routine specimens with the outer package clearly labelled ‘priority’. It must be handled in accordance with the Canadian Biosafety Standards and shipped in accordance with the Transportation of Dangerous Goods Regulations. Failure to ship separately will delay testing.
Influenza A and B are tested with CDC in-house Real Time PCR assay.
Influenza A positive specimens will be subtyped with real time RT-PCR.
Algorithm
Specimens received in Toronto, will be initially tested for Influenza A and B. Influenza A positive specimens will be further tested for full Avian Influenza panel typing (H1N1pdm09, Human H3, avian H5, avian H7, and N9).
Specimens received in one of the regional laboratories, will be initially screened for H5 and will be forwarded to Toronto for full Avian Influenza panel typing.
Positive avian influenza specimens will be forwarded to NML for confirmation.
Reporting
Results are reported to the physician, authorized health care provider (General O. Reg 45/22, s.18), or submitter as indicated on the requisition.
Specimens that are positive for avian Influenzaare reported to the Medical Officer of Health as per Health Protection and Promotion Act.
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