Respiratory Viruses (including influenza)

Conformément au Règlement de l’Ontario 671/92 de la Loi sur les services en français, les renseignements d’analyses de laboratoire liés à la présente page ne sont offerts qu’en anglais parce qu’ils sont de nature scientifique ou technique et destinés uniquement à l’usage des fournisseurs de soins de santé qualifiés et non aux membres du public.

This page provides information on molecular testing for respiratory viruses at Public Health Ontario’s (PHO) laboratory.

PHO’s laboratory utilizes a testing algorithm for influenza and other respiratory viruses that is based on patient settings.

For information regarding other testing options, refer to the following PHO webpages:

PHO’s laboratory has expanded eligibility testing criteria for high risk ambulatory and emergency department (ED) patients and there has been operational changes in testing sites.

Please see the “Testing Indications” and “Test Algorithm – Table 2” sections for more information.

Testing Indications

PHO’s laboratory provides testing using 2 different respiratory test panels – these are multiplex respiratory virus PCR (MRVP) and FLUVID

MRVP testing is performed on the following eligible persons:

  1. Symptomatic children (<18 years) seen in the Emergency Department (ED)
  2. Symptomatic hospitalized patients (ward and ICU/CCU)
  3. Symptomatic residents in institutional settings (non-outbreak)
  4. Specimens from the first four symptomatic individuals (including healthcare workers/staff) in an outbreak setting that requests respiratory virus testing

FLUVID testing is performed on the following eligible persons:

  1. Symptomatic residents and healthcare workers/staff in the institutional settings in an outbreak setting requesting COVID-19 and respiratory virus testing BUT only after the first four have already been tested for SARS-CoV-2 and MRVP
  2. Symptomatic individuals at risk for severe disease/outcome in whom care or treatment decisions may be impacted by test results

Respiratory virus test requests for patients with acute respiratory illness (ARI) in the settings described above should be clearly indicated on the COVID and Respiratory Virus Test Requisition by selecting “Respiratory Viruses” or “COVID-19 Virus AND Respiratory Viruses” as appropriate in section “5 – Test(s) Requested” on the requisition. Only select one of the three test request options. SEE NOTE #1 below.

In addition, the patient’s setting and symptoms should be clearly indicated on the requisition.

NOTE: See “TEST ALGORITHM AND METHODS” Table footnote 3 for FLUVID targets and footnote 4 for MRVP targets.

Acceptance/Rejection Criteria

Label the specimen container with the patient’s first AND last name, AND date of collection, AND one other unique identifier such as the patient’s date of birth or Health Card Number. See Criteria for Acceptance of Patient Specimens.

Asymptomatic patients (or requisitions with no symptoms checked off) will not be tested for respiratory viruses.

Specimens collected using expired swabs or transport media tubes will be rejected.

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 universal transport media (UTM)

Virus-Respiratory Collection Kit: order# 390082

Respiratory Virus (Molecular)

Deep Nasal swab

Deep Nasal swab in 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 universal transport media (UTM)

Virus-Respiratory Collection 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


To request respiratory virus testing only, check the “Respiratory Viruses” box in Section 5 of the COVID-19 and Respiratory Virus Test Requisition (the preferred requisition during the COVID-19 pandemic).

To request COVID-19 AND respiratory virus testing, check the “COVID-19 Virus AND Respiratory Virus” box in Section 5 of the requisition.

Only check one of the three boxes.


NPS is the most sensitive specimen type for respiratory virus testing. Apart from neat saliva and mouth rinse/swish and gargle, these collection kits and associated specimen sources can also be used for seasonal respiratory testing (e.g. MRVP) provided suitability criteria are met, if the specimen is also being tested for COVID-19.

Note: Saliva and mouth rinse/swish and gargle specimens have not been validated for seasonal respiratory virus testing at PHO’s laboratory and will not be accepted for testing respiratory viruses other than SARS-CoV-2.


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

  • Patient setting
  • Symptoms (indicate all symptoms)
  • Onset date
  • Requesting healthcare provider’s CPSO#,
  • Complete mailing address, telephone, and fax number
  • Patient’s full name and address, date of birth, health card number (must match the specimen label)

Failure to do so may result in rejection or testing delay.


Patient setting (including outbreak or investigation 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.


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


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

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.

NOTE: “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 MRVP or FLUVID testing.

Storage and Transport

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 specimen integrity, specimens should be stored at 2-8°C following collection and should transported to PHO’s 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.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

The TAT for MRVP testing is up to 4 days after receipt by PHO’s laboratory .

FLUVID testing is performed 6 days a week.

  • TAT: 60% of results are available within 24 hours and 80% are available within 48 hours from receipt at a PHO testing laboratory .
  • Turnaround time may vary according to geographical location and proximity to a PHO testing laboratory.

NOTE: When performed, TAT for the Direct Antigen Test for Influenza (Influenza rapid) is within 1 day after receipt at any PHO’s laboratory site.

Test Methods


  • Laboratory developed test (LDT) validated at PHO’s laboratory
  • Detects Influenza A, B; RSV (A/B) and SARS CoV-2 (COVID-19) by multiplex nucleic acid amplification testing (NAAT)– see note 3, below

MRVP – Respiratory In House (INH) MPX PCR:

  • Laboratory developed test (LDT) validated at PHO’s laboratory
  • Detects respiratory targets by multiplex NAAT – see note 4 below


PHO’s laboratory utilizes a testing algorithm for influenza and other seasonal respiratory viruses that is based on patient setting.

Respiratory virus testing is available according to the following tables:

Table 1a: Eligibility criteria for respiratory virus testing available at PHO’s laboratory for symptomatic (ARI) patients by patient setting and outbreak status (See Table 1b for testing of asymptomatic patients.)

Patient Setting1

Testing Available By Request

Hospitalized (all inpatients)2



SARS-CoV-2 and MRVP4,5
FLUVID3 followed by MRVP4,5

(Both combinations will provide testing for the same viruses.)

Remote communities

SARS-CoV-2 and MRVP4,5
FLUVID3 followed by MRVP4,5

(Both combinations will provide testing for the same viruses.)

Public health unit declared respiratory infection outbreaks (including institutional outbreaks e.g. long-term care homes, correctional facilities, congregate living settings)

Also applicable to healthcare workers/staff in the facility, that are part of the outbreak

SARS-CoV-2 and MRVP4,5

MRVP for up to 4 outbreak related specimens6

Additional specimens from symptomatic individuals will be tested by FLUVID only.5

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

Institutions (non-outbreak) (e.g. long-term care homes, correctional facilities, congregate living settings)10

SARS-CoV-2 and MRVP4,5

Emergency Department (paediatric patients <18 years old)11


SARS-CoV-2 and MRVP4,5

Emergency Department (adult patients), or Ambulatory/outpatient settings, for individuals at risk of severe disease or outcome in whom care or treatment decisions may be impacted by test results9


Not specified on requisition



Table 1b: Eligibility criteria for respiratory virus testing available at PHO Laboratory for asymptomatic patients

Patient Setting


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 investigation number.
  2. All ICU (Intensive Care Unit)/ CCU (Critical Care Unit) and ward inpatients.
  3. FLUVID detects: influenza A, influenza B, respiratory syncytial virus (RSV A/B), and SARS-CoV-2 (COVID-19). This assay may be used as an initial test prior to MRVP to provide earlier results during influenza and RSV seasons.
  4. 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.
  5. A limit of four outbreak specimens are routinely accepted for MRVP testing if ordered on PHO’s laboratory requisition. Additional symptomatic patient samples will be tested using FLUVID test. For requests for additional MRVP testing in outbreak settings, contact PHO’s laboratory Customer Service Centre. Respiratory outbreak specimens should be submitted following the Respiratory Outbreak Testing Prioritization Protocol
  6. Caution: influenza rapid testing can only be performed if specimen is received in suitable media. See Submission and Collection Notes above.
  7. Influenza rapid antigen testing will be performed on the first four outbreak specimens from symptomatic patients if influenza PCR testing (e.g. MRVP, FLUVID) commencement is delayed to >24 hours from specimen receipt at PHO’s laboratory.
  8. To assist with patient management when respiratory virus testing is not available, healthcare providers are encouraged to refer to the Ontario Respiratory Virus Tool for information on respiratory pathogen activity in Ontario.
  9. Testing of ambulatory patient seen in outpatient setting, clinics, or ER is offered to those in whom care or treatment decisions may be impacted by test results and who are at risk for severe outcome and will benefit from treatment.
  10. Schools and daycare centres are not considered institutions for the purpose of sporadic MRVP testing.
  11. Specimens collected from paediatric patients (<18 years old) seen in the Emergency Department (ED) will be accepted for MRVP testing to support enhanced respiratory virus surveillance.

Table 2: Respiratory virus testing conducted at PHO laboratory sites

PHO Laboratory Sites

Testing conducted

Management of specimens

Toronto, London


Specimens will be tested at receiving site

Ottawa, Timmins


Specimens transferred to Toronto if specimen for SARS-CoV-2 only


Rapid Flu, FLUVID

Specimens transferred to Toronto if specimen for SARS-CoV-2 only

Specimens transferred to Ottawa or Toronto if MRVP needed

Thunder Bay

Rapid Flu, SARS-CoV-2, FLUVID

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

Hamilton, Peterborough, Orillia, Sault Ste. Marie, Sudbury

Rapid Flu, no molecular testing

Specimens transferred to one of the above laboratory sites for molecular testing.


When influenza is circulating, laboratory confirmation of influenza is not needed before initiating treatment, as waiting until influenza is confirmed will delay initiation of therapy. Current clinical guidelines recommend that during influenza season, influenza antiviral therapy (e.g., oseltamivir or zanamivir) be started empirically for patients with:

  • Moderate, progressive, severe or complicated influenza, such as individuals who are hospitalized with influenza-like illness; OR
  • Compatible symptoms who are at high risk of influenza complications/severe disease.

Since these patients may require concurrent administration of empiric treatment for COVID-19 they may benefit from testing in order to guide the course of treatment.

For more information, please see Additional Respiratory Virus Testing Services at PHO’s laboratory below.

To understand which seasonal respiratory pathogens are circulating and to assist with influenza antiviral treatment decisions, healthcare providers are reminded to regularly review PHO’s Ontario Respiratory Virus Tool. The tool is updated weekly on Fridays and provides an overview of influenza and other respiratory pathogens circulating in the province. Data on influenza positivity is also presented at the local public health unit level to provide jurisdiction-specific information.


The following table provides possible test results with associated interpretations for FLUVID and MRVP:





Virus not detected

Target virus not detected by real-time PCR


Virus detected

Target virus detected by real-time PCR


Virus Indeterminate

An indeterminate PCR test result may be due to a low level of target genetic material in the specimen, inadequate specimen content, or a non-specific signal. Please resubmit another specimen for testing if clinically indicated.




Test results are invalid due to the failed amplification of the extraction control. Amplification failure may be due to inadequate specimen content, extraction failure, or PCR inhibition. Please resubmit another specimen for testing if clinically indicated .



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

Specimens that are positive for SARS-CoV-2 and/or influenza, and all results from outbreaks, are reported to the Medical Officer of Health as per Health Protection and Promotion Act.


  1. Fred Y Aoki, Upton D Allen, Samira Mubareka, Jesse Papenburg, H Grant Stiver, and Gerald A Evans. Use of antiviral drugs for seasonal influenza: Foundation document for practitioners—Update 2019. JAMMI. 2019 4:2, 60-82. Available at:
  2. AMMI Canada Guidelines. Available at:
  3. Antiviral Medications for Influenza: Information for Healthcare Providers. Available at:
  4. 2020–2021 AMMI Canada guidance on the use of antiviral drugs for influenza in the setting of co-circulation of seasonal influenza and SARS-CoV-2 viruses in Canada. Available at:

Data and Analysis

Additional Respiratory Virus Testing Services at PHO’s Laboratory

  1. Influenza Antiviral Susceptibility Testing
    Currently circulating influenza A subtypes (H1N1pdm09 and H3N2) are universally amantadine resistant. Almost all currently circulating influenza A and B viruses are oseltamivir susceptible; however, resistance has been documented on rare occasions. Conversely, seasonal influenza A/H1N1 that circulated before the influenza pandemic of 2009 was known to be amantadine susceptible, and almost universally oseltamivir resistant, but it has not been detected in Ontario since mid-2009.

    Routine susceptibility testing is not required for clinical care; however, a proportion of influenza-positive samples will be forwarded to the National Microbiology Laboratory (NML) for strain typing and antiviral susceptibility testing. Limited susceptibility testing is also available at PHO.

    Recommended indications for antiviral susceptibility testing in Ontario include:
    • Influenza developing during or soon after completion of influenza antiviral prophylaxis (e.g., oseltamivir or zanamivir).
    • Severely ill patients such as those admitted to an ICU with laboratory-confirmed influenza not responding to influenza antiviral therapy.
    • Fatalities in patients with laboratory-confirmed influenza being treated with influenza antiviral therapy.
    • Persistent influenza viral shedding, defined as a repeat PCR test positive after seven days or more of treatment. Repeat PCR testing could be undertaken for patients who are not responding to antiviral therapy. Immunocompromised patients are at greater risk for more severe disease, persistent viral shedding and development of antiviral resistance.
    • Positive test for influenza A in a traveler returning from an area where resistance is endemic.

To request influenza susceptibility testing for a patient who meets any of the above criteria, please document the request on the laboratory requisition along with any relevant information. To make a request on a sample already submitted to PHO, please contact our Customer Service Centre at 1-877- 604-4567 or 416-235-6556 or your local PHO laboratory.

  1. Avian Influenza Viruses
    PHO’s laboratory conducts testing for avian influenza (e.g., H5N1, H5N2, and H7N9) as required based on the information provided on the test requisition. Samples indicating travel to affected areas or with exposure to known cases of avian influenza, will be tested by real-time influenza A PCR (US CDC protocol) and if positive will be tested first for seasonal subtypes (H3N2, H1N1pdm09). If no seasonal subtype is detected, further testing for avian influenza subtypes will be conducted.

    If you suspect avian Influenza, contact your local health unit and the PHO laboratory Customer Service Centre at 1-877-604-4567 prior to submitting specimens. Refer to the Avian Influenza Test Information Sheet.

  1. Variant (swine origin) Influenza Viruses in Humans
    Testing is available on request for variant influenza viruses, such as H3N2v, in persons who develop acute respiratory illness following direct contact with swine or their environment. Only limited human-to-human transmission has been documented.

    NOTE: Samples that do not subtype for seasonal influenza will be tested for a panel of avian and/or swine influenza viruses.

  1. Testing for Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
    MERS-CoV is a coronavirus that emerged in the Middle East in 2012. Patients with relevant clinical presentation and epidemiological risk factors for MERS-CoV infection, such as travel to certain countries in the Middle East or contact with a confirmed or probable MERS-CoV case, should be considered for MERS-CoV testing. For further information, please see the MERS-CoV Test Information Sheet.
    Note: MRVP detects seasonal human coronavirus but does not detect MERS-CoV.

    Note: MRVP detects seasonal human coronavirus but does not detect MERS-CoV.

  1. Testing for Enterovirus (including EV-D68 and other serotypes)
    EV-D68 circulated in Ontario in the summer and fall of 2014, and to a lesser extent in 2016. More recently several cases of EV-D68 were detected at PHO’s laboratory up to November 2018.

    For information about non-polio enterovirus, including D68, see PHO’s Infectious Disease page for Enterovirus D68.
    For information on specimen collection and testing for enterovirus, see the Enterovirus Test Information Sheet.

  1. Sentinel Practitioner Surveillance Network (SPSN)
    For general information on Ontario’s SPSN and information for practitioners interested in contributing to the network, see Sentinel Practitioner Surveillance Network (SPSN) — Influenza Vaccine Effectiveness Program.

    The SPSN performs molecular respiratory viral testing on patients with influenza-like-illness visiting community-based sentinel health care providers across Ontario. Other provinces also participate in the SPSN. SPSN sentinel heath care providers in Ontario will be able to offer influenza, other seasonal respiratory virus (by MRVP) and COVID-19 testing to patients meeting SPSN testing criteria, which includes outpatients who would not normally be eligible for influenza and other seasonal respiratory virus testing.
Mis à jour le 15 janv. 2024