Respiratory Viruses (including influenza)

Testing Indications

Public Health Ontario (PHO) Laboratory utilizes a testing algorithm for influenza and other respiratory viruses.

Refer to the current labstract Respiratory Virus Testing Algorithm LAB-SD-121 for detailed information about what testing will be performed based on patient setting.

Preparation Prior to Transport

For outbreak specimens follow the Respiratory Outbreak Testing Prioritization Protocol

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.

Place the specimen container in the biohazard bag and seal the bag; insert the completed requisition in the pocket on the outside of the sealed biohazard bag. To maintain optimal viability of the virus, specimens should be stored at 2-8°C following collection and transported to PHO laboratory on ice packs within 72 hours of collection. If longer storage/transit time is anticipated, specimens should be frozen at -70°C or lower and transported on dry ice.

Special Instructions

Complete all fields of the COVID-19 Test Requisition (the preferred PHO Laboratory Requisition for respiratory virus testing during the COVID-19 pandemic), include the requesting healthcare provider's CPSO#, complete mailing address, telephone, and fax number, and the patient’s full name, date of birth, Health Card Number (must match the specimen label). Failure to do so may result in rejection or testing delay.

Test Frequency and Turnaround Time (TAT)

The TAT for the Direct Antigen Test for Influenza (Influenza rapid) is within 1 day after receipt at any PHO Laboratory site.

The TAT for seasonal respiratory virus testing, is up to 4 days after receipt by PHO Laboratory.

Reporting

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

Specimens that are positive for COVID-19 or influenza or specimens from outbreaks are reported to the Medical Officer of Health as per Health Protection and Promotion Act.

PHO Laboratory utilizes a testing algorithm for influenza and other seasonal respiratory viruses which is based on patient setting.

Respiratory virus testing is available at PHO Laboratory according to the following table:

Table 1a: Eligibility criteria for respiratory virus testing available at PHO’s laboratory by patient setting and outbreak status Symptomatic Patients: 

Table 1b SARS-CoV-2 testing for asymptomatic patients.

Only SARS-CoV-2 testing will be performed on asymptomatic patients, regardless of patient setting

Table footnotes:

1. The specific test being requested AND patient setting must also appear on the requisition to help with appropriate test assignment and triaging of specimens. If patient setting is not provided, the specimen will only be tested for SARS-CoV-2. For outbreaks or investigations, the requisition must include the assigned outbreak or investigational number.
2. ICU - Intensive Care Unit; CCU - Critical Care Unit.
3. FLUVID detects: influenza A, influenza B, SARS-CoV-2 (COVID-19), and respiratory syncytial virus (RSVA + B).
4. Specimens first received at Hamilton, Kingston and Thunder Bay PHO Laboratory sites for MRVP testing will first undergo FLUVID testing, and will be forwarded to one of the MRVP testing sites (Toronto, London, Ottawa and Timmins) for MRVP testing. Specimens received at Orillia, Peterborough or Sudbury sites will be forwarded to another PHO Laboratory site for molecular (PCR) testing.
5. MRVP detects: influenza A, influenza A H3 subtype, influenza A H1 (pdm09) subtype, influenza B, respiratory syncytial virus (RSV A/B), parainfluenza (1 – 4), adenovirus, enterovirus, seasonal human coronavirus (OC43, 229E, NL63, HKU1), rhinovirus and human metapneumovirus.
   Note: The assay detects the different RSV, parainfluenza and seasonal human coronaviruses named above but does not differentiate between them. It does not detect or cross-react with SARS-CoV-2.
6. A separate cytomegalovirus (CMV) PCR is available upon request (indicate on the requisition) for bronchoalveolar lavage (BAL)/bronchial wash/pleural fluid.
7. A limit of four outbreak specimens are routinely accepted for seasonal respiratory virus testing if ordered on the PHO Laboratory requisition. For requests for additional testing in outbreak settings, contact PHO Laboratory’s Customer Service Centre. Respiratory outbreak spceimens should be submitted following the Respiratory Outbreak Testing Prioritization Protocol.
8. Caution: influenza rapid testing can only be performed if specimen is received in suitable media. See Submission and Collection Notes above.
9. Influenza rapid antigen testing will be performed on the first four outbreak specimens from symptomatic patients if influenza PCR testing (e.g. FLUVID) commencement is delayed to >24 hours from specimen receipt at PHO Laboratory.
10. To assist with patient management when respiratory virus testing is not available, healthcare providers are encouraged to refer to PHO’s respiratory surveillance reports for information on respiratory pathogen activity in Ontario.

Table 2: Respiratory virus testing conducted at PHO Laboratory sites

Labstracts

LAB-SD-121 (Respiratory Viral Testing Algorithm and Enhanced Surveillance - Update)