Respiratory Viruses (including influenza)

Testing Indications

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

Refer to the current labstract on respiratory viral testing titled: LAB-SD-121 (Respiratory Viral Testing Algorithm) for detailed information about the testing method that will be performed based on patient setting.


Changes to Respiratory Virus Specimen Testing / Modification liée aux analyses d’échantillons lors d’une éclosion

Specimen Collection and Handling

Specimen Requirements

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

Respiratory Virus (Molecular)

Nasopharyngeal, throat, or conjunctival swab

1 swab in the collection kit media

Virus-Respiratory Collection Kit: order# 390082

Respiratory Virus (Molecular)

Bronchial Alveolar Lavages (BAL), or pleural fluid

2.0 ml

Sterile container

Respiratory Virus (Molecular)

Respiratory tract tissue

1.0 g

Sterile container

Submission and Collection Notes


Follow the instructions on the Virus-Respiratory Collection Kit.


Complete the following fields of the General Test Requisition Form. Ensure the following fields are completed if diagnostic testing is requested:

  • patient setting
  • symptoms
  • onset date

Patient setting must be provided to help triage specimens. If patient setting is not provided, the specimen will not be tested.


CMV PCR is available upon request (indicate on the requisition) for bronchoalveolar lavage (BAL)/bronchial wash/pleural fluid.

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.

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 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 PHO General Test Requisition Form: 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.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Respiratory virus testing is performed daily Monday to Saturday.

The TAT for the Direct Antigen Test for Influenza is within 1 day after receipt.

The TAT for multiplex respiratory virus PCR (MRVP) is up to 3 days after receipt by PHO Laboratory.

Samples tested by traditional virus culture are observed for a minimum of 17 days prior to reporting a negative culture result; samples that are positive can be observed at any point during this period.

TAT for traditional virus culture is up to 18 days.

TAT will vary during the winter months.


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

Specimens that are positive from Outbreaks are reported to the Medical Officer of Health as per Health Protection and Promotion Act.

Test Methods

Public Health Ontario Laboratory (PHOL) utilizes a testing algorithm for influenza and other respiratory viruses which is based on patient setting.

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

Patient Setting1


In-patient (ICU/CCU2 or ward)

Institutions (non-outbreak)

MRVP 3,4


Institutional Respiratory Infection Outbreaks

Influenza Rapid testing followed by MRVP 3 for up to 45 outbreak samples. See footnote #5.

Emergency Room patients6

Testing not available7

Ambulatory , including ambulatory influenza high risk patients6

Testing not available7

Not specified on requisition

Testing not available7

Table footnotes:

  1. Patient setting must be provided on the requisition to help triaging of specimens. If patient setting is not provided, the specimen will NOT be tested.
  2. ICU - Intensive Care Unit; CCU - Critical Care Units.
  3. MRVP detects: Panel 1: influenza A, influenza A H3 subtype, influenza B, and respiratory syncytial virus (RSV NA/B); Panel 2: parainfluenza (1 – 4), adenovirus, enterovirus and influenza A H1 (pdm09) subtype; Panel 3: Seasonal human coronavirus (OC43, 229E, NL63, HKU1), rhinovirus and human metapneumovirus.
    Note: The assay detects the different RSV, parainfluenza  and season human coronaviruses listed but does not differentiate between them.
  4. CMV PCR is available upon request (indicate on the requisition) for bronchoalveolar lavage (BAL)/bronchial wash/pleural fluid.
  5. A limit of 4 outbreak specimen are routinely accepted for testing. For outbreaks with special concerns, including requests for additional testing, contact PHO Laboratory’s Customer Service Centre.
  6. Respiratory virus swab collection kits will not be supplied for these patient settings.
  7. To assist with patient management, in particular 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.

Data and Analysis

Additional Information

For Outbreaks, contact your local Health Unit

contact lab

Contact Laboratory Customer Service

Laboratory Services

Updated 9 March 2020