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 acceptable specimen types in response to H5N1 detection in cattle in the US.
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, or throat swab |
1 swab in the collection kit media |
Virus-Respiratory Collection Kit: order# 390082 |
|
Avian Influenza |
Bronchial Alveolar Lavages (BAL), 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 PHOL microbiologist)5 |
1 swab in the collection kit media (UTM) |
Virus-Respiratory Collection Kit: order# 390082 |
|
Avian Influenza |
Stool (Do not submit until approved by PHOL microbiologist)5 |
2.0 grams |
Sterile container |
|
Avian Influenza |
Blood/Serum (Do not submit until approved by PHOL microbiologist)5 |
5 ml whole blood or 1.0 ml serum |
Serum separator tubes (SST) |
Submission and Collection Notes
Prior to specimen submission, contact PHO’s Laboratory Customer Service Centre at 416-235-6556 or 1-877-604-4567 for further instructions and approval.
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.
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)
- a viral throat swab in viral transport media should also be collected on all hospitalized patients.
Sample types other than nasopharyngeal swabs, nasopharyngeal aspirates, bronchial washes (if available) or throat swabs require approval by a PHO microbiologist.
Swabs from potentially infected anatomical sites, such as conjunctival swabs from patients with conjunctivitis and potential occupational exposure, should be approved before submission.
Stool and blood are not routinely tested for avian influenza but may be tested if avian influenza is detected in respiratory specimens. Submission requires approval of a PHO microbiologist.
Serology testing is not recommended for influenza diagnosis, including avian influenza, and is not available for clinical testing in Canada.
Testing may be arranged on weekends if approved by a PHO microbiologist. Contact the After-hours Emergency Duty Officer at 416-605-3113 for after-hours consultation.
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 laboratory 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)
Influenza A testing is performed Monday to Friday.
The TAT for influenza typing is up to 2 business day(s) from specimen receipt at PHO.
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
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 will be initially tested for Influenza A and B; and Influenza A positive specimens will be further tested for H1N1pdm09, Human H3, avian H5, avian H7, and N9 subtypes.
Positive avian influenza specimens will be forwarded to NML for confirmation.
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