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.

For information on COVID-19 testing see the COVID-19 Test Information Sheet (TIS)

Specimen Collection and Handling

Specimen Requirements

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

Respiratory Virus (Molecular)

Upper respiratory tract: Nasopharyngeal swab (NPS)

Nasopharyngeal swab in 3 ml universal transport media (UTM)

Virus-Respiratory Collection Kit: order# 390082

Respiratory Virus (Molecular)

Deep Nasal swab

Deep Nasal swab in 3 ml media provided with the collection kit

See table of acceptable alternative kits

Respiratory Virus (Molecular)

Viral throat swab (see Submission and Collection Notes below)

Swab in 3 ml universal transport media (UTM)

Virus Culture Kit order#: 390081

Respiratory Virus (Molecular)

Lower respiratory tract (when possible): sputum, BAL, bronch wash, pleural fluid, lung tissue, tracheal aspirate (see Submission and Collection Notes below)

1.0 ml

Sterile container; Tuberculosis Kit order#: 390042

Submission and Collection Notes


When respiratory virus testing is requested check ‘Respiratory Viruses’ box in Section 5 of the COVID-19 Test Requisition (the preferred requisition during the COVID-19 pandemic)


PHO Laboratory has done a limited evaluation on several COVID-19 specimen collection kits. These can be used for collection of upper respiratory specimens as indicated for COVID-19 testing. The same specimen can be used for seasonal respiratory testing (e.g. MRVP) provided suitability criteria are met.


Complete all fields of the COVID-19 Test Requisition . Ensure the following fields are completed if diagnostic testing is requested:  

  • Patient setting
  • Symptoms
  • Onset date

Patient setting (including outbreak or investigational number, if applicable) must be provided to help triage specimens. If patient setting is not provided, the specimen will only be tested for COVID-19.


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


Respiratory outbreak specimens should be submitted following the Respiratory Outbreak Testing Prioritization Protocol

CAUTION: “molecular transport media” (media containing guanidine) is unsuitable for influenza rapid testing. Specimens which are not suitable for rapid testing will not be tested by rapid test and will be sent directly for FLUVID or MRVP testing.

Check the expiry dates of both the collection swabs and transport media (tube), as specimens collected using expired swabs or tubes will be rejected. In addition, specimens must meet the Criteria for Acceptance of Patient Specimens.

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.

Requisitions and Kit Ordering

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.


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.

Test Methods

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: 

Testing Dictated by Patient Setting1
(See below for testing of asymptomatic patients.)


ICU/CCU inpatients2


Remote communities

FLUVID3,4 followed by MRVP4,5,6
SARS-CoV-2 and MRVP4,5,6
(Both combinations wil provide testing for the same viruses.)

Institutional and other public health unit declared respiratory infection outbreaks (including school outbreaks)

Up to 4 outbreak specimens7:

Influenza rapid testing8 (
will be done if PCR testing is delayed >24 hours

SARS-CoV-2 followed by FLUVID

Additional specimens will be tested for SARS-CoV-2 only.7

Ward (non-ICU/CCU) inpatients

Institutions (non-outbreak) (e.g. long-term care homes, correctional facilities, congregate living settings)

SARS-CoV-2 followed by FLUVID

Emergency room patients


Ambulatory/outpatient settings, assessment centres, including ambulatory influenza high risk patients


Not specified on requisition



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

Asymptomatic Patients


All patient settings


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

PHO Laboratory Sites

Testing conducted

Management of specimens

Toronto, London, Ottawa, Timmins


Specimens will be tested at receiving site


Rapid Flu, SARS-CoV-2

Specimens transferred to Toronto or London, if FLUVID or MRVP needed

Kingston, Thunder Bay

Rapid Flu, SARS-CoV-2, FLUVID

Specimens transferred to Toronto, London, Ottawa or Timmins if MRVP needed

Orillia, Peterborough, Sault Ste. Marie, Sudbury

Rapid Flu, no molecular testing

Specimens transferred to one of the above laboratory sites

Data and Analysis

Additional Information

For Outbreaks, contact your local Health Unit

Mis à jour le 4 mars 2021