Respiratory Viruses (including influenza)
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 information on molecular testing for respiratory viruses at Public Health Ontario (PHO). PHO’s testing algorithm for SARS-CoV-2 follow the Test-to-Treat provincial ministry guidance, for influenza and other respiratory viruses is based on patient setting, vulnerable population, and outbreak investigation needs.
For information on influenza A virus subtyping conducted under PHO’s enhanced influenza surveillance program, involving specimens that tested positive for influenza A at non-PHO external laboratories, please refer to the Avian Influenza and Influenza A Subtyping.
For information regarding other testing options, refer to the following PHO webpages:
Updates- Effective August 31, 2026, the Multiple Respiratory Virus PCR (MRVP) has been expanded to include the SARS-CoV-2 (COVID-19) target. Patients meeting testing eligibility criteria can be tested for COVID-19 through the MRVP or FLUVID platforms.
- Both MRVP and FLUVID will be available at the following PHO locations: Toronto, London, Ottawa, Timmins, Hamilton, Kingston, and Thunder Bay.
- For respiratory swab specimen (nasopharyngeal swab - NPS or throat), multiple swabs submitted in a single transport tube will not be accepted for testing. Please ensure that only one swab is submitted per UTM tube.
Testing Indications
PHO molecular tests for respiratory viruses using either multiplex respiratory virus PCR (MRVP) or FLUVID.
PHO uses a respiratory virus testing algorithm that prioritizes testing based on patient care setting, populations at increased risk of severe disease or complications, and outbreak investigation need. Testing is performed using either multiplex respiratory virus PCR (MRVP) or FLUVID, according to the patient eligibility criteria outlined below.
FLUVID testing is offered to individuals exhibiting respiratory symptoms that meet at least one of the following eligibility criteria :
- Residents in congregate living settings (including Long-Term Care, retirement home and correctional facilities) that are not in an outbreak
- Residents of congregate living setting that is in an outbreak beyond the first four specimens tested by MRVP
- Adults admitted to the hospital
- Staff from congregate living setting that are part of an outbreak
- Respiratory symptomatic individuals eligible for COVID-19 testing belonging to any of the following groups:
- people aged 65 years of age and older
- people who are immunocompromised
- people who are at increased risk due to a combination of age and other medical conditions or risk factors, based on an assessment by a health care provider
MRVP testing is offered to individuals exhibiting respiratory symptoms that meet at least one of the following eligibility criteria:
- Hospitalized patients requiring intensive care
- Hospitalized admitted patients that are
- Children < 18 years of age who are at risk of complications, in the presence of community-acquired pneumonia, or
- Immunocompromised or immunosuppressed, or
- Pregnant
- Patients/residents who are part of a hospital or PHU-declared respiratory outbreaks in congregate living settings. (Only the first four symptomatic patients in a respiratory outbreak (subsequent patients will be tested by FLUVID)
Influenza Antiviral Susceptibility Testing for Oseltamivir is available at PHO. Individuals meeting the testing criteria outlined in the "Additional Respiratory Virus Testing Services at PHO " section (at the bottom of this TIS) with the relevant clinical information and test requested on the requisition will have the test performed at PHO.
Acceptance/Rejection Criteria
Asymptomatic patients (or requisitions with no symptoms checked off) and requisitions lacking patient setting will not be tested for respiratory viruses including SARS-CoV-2.
Specimens received in expired kits or transport media tubes and specimens containing multiple swabs in a single transport tube will be rejected.
Influenza Antiviral Treatment and the Role of Respiratory Virus Testing
When influenza is circulating, laboratory confirmation of influenza is not needed before initiating antiviral treatment, early empiric antiviral therapy for high risk groups remains the standard of care. Current clinical guidelines recommend that during influenza season, influenza antiviral therapy (e.g., oseltamivir) 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 illness.
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.
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.
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) |
||
Respiratory Virus (Molecular) |
Viral throat swab |
Swab in universal transport media (UTM) |
||
Respiratory Virus (Molecular) |
Lower respiratory tract (when possible): sputum, BAL, Bronchial wash, pleural fluid, lung tissue, tracheal aspirate |
1.0 ml (if applicable) |
||
Adenovirus |
Upper and lower respiratory tract and viral swabs |
See above for swabs |
Universal transport medium (UTM) for swabs |
|
Adenovirus |
Conjunctival eye swab |
Swab in universal transport media (UTM) |
Universal transport medium (UTM) for swabs |
|
Adenovirus |
Sterile fluid (CSF) |
0.5ml |
Sterile container for fluids |
Submission and Collection Notes
PHO’s General Test Requisition Form must be submitted
Under “Test Requested”, clearly indicate “Respiratory Viruses” as required.
Complete all fields of the General Test Requisition Form. Ensure the following fields are completed to avoid delays:
- Patient setting (mandatory)*
- Symptoms (indicate all symptoms) (mandatory)*
- Testing Indication/Criteria/ (mandatory if applicable)*
- Valid Outbreak Number (if applicable; including an invalid/outdated number may result in test cancellation)*
- Onset date
*MANDATORY INFORMATION IS USED FOR TRIAGING SPECIMENS. FAILURE TO PROVIDE THIS INFORMATION MAY RESULT IN REJECTION OR TESTING DELAY.
Label the specimen container with the below. See Criteria for Acceptance of Patient Specimens.
- The patient’s first AND last name
- Date of collection
- One other unique identifier, such as the patient’s date of birth or Health Card Number
SPECIMENS RECEIVED IN EXPIRED KITS OR TRANSPORT MEDIA TUBES WILL BE REJECTED
Cytomegalovirus (CMV) PCR is available upon request (indicate on the requisition) for Broncho alveolar lavage (BAL)/bronchial wash/pleural fluid/lung tissue.
Respiratory outbreak specimens may be submitted following the Respiratory Outbreak Testing Prioritization Protocol.
For respiratory swabs (NPS, throat), specimens received containing multiple swabs in a single transport tube will not be acceptable for testing. Please ensure one swab per UTM is submitted.
NOTE: “Molecular transport media” (media containing guanidine) is unsuitable for influenza rapid antigen testing. Specimens which are not suitable for rapid testing will not be tested by rapid test and will be sent directly for molecular testing through MRVP or FLUVID.
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 be 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.
Package and ship primary clinical specimens to a PHO location conducting respiratory PCR testing in accordance with the Transportation of Dangerous Goods Regulations
Test Frequency and Turnaround Time (TAT)
- The TAT for MRVP testing is up to 4 days after receipt by PHO
- The TAT for FLUVID testing is up to 3 days after receipt by PHO
- The TAT for Rapid Flu is 1 day after receipt at PHO site.
Note: Turnaround time may vary according to geographical location and proximity to PHO.
Table 1: Test Frequency of Respiratory Testing and PHO Testing Sites
| PHO Testing Site | FLUVID | MRVP | Rapid FluA | Business DaysB |
|---|---|---|---|---|
| Toronto | Year Round | Year Round | n/a | Monday-Sunday |
| Kingston, London, Ottawa, Timmins | Year Round | Year Round | n/a | Monday-Saturday |
| Hamilton, Thunder Bay | Year Round | Year Round | n/a | Monday-Friday |
| Orillia, Peterborough, Sudbury Sault Ste. Marie |
n/a | n/a | September - May | Monday-Friday |
A Rapid Flu (Direct Antigen Test for Influenza) is performed only on the first four outbreak-related specimens, if molecular testing cannot be initiated within 24 hours of receipt by PHO.
B Saturday cut-off for same day testing is 11:00 am. Samples received after 11:00 am will be tested on the next available run.
FLUVID – Respiratory virus quadplex PCR:
- Laboratory developed test (LDT) validated at PHO
- Detects SARS-CoV-2 (COVID-19), influenza A, influenza B, and RSV (A/B) by nucleic acid amplification testing (NAAT)
MRVP – Multiplex Respiratory Virus PCR - In House assay:
- Laboratory developed test (LDT) validated at PHO
- Detects SARS-CoV-2 (COVID-19), influenza A, influenza A H3 (seasonal H3N2) 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 respiratory targets by multiplex NAAT
Note: The assay detects the different RSV, parainfluenza and seasonal human coronaviruses named above but does not differentiate between them. The seasonal human coronavirus does not cross react with SARS-CoV-2.
Algorithm
PHO utilizes a testing algorithm for influenza and other seasonal respiratory viruses that is based on patient setting and vulnerable population at risk, and outbreak investigation needs as indicated above..
SARS-CoV-2 testing is offered to those who meet testing criteria as indicated in the Ministry of Health’s current guidelines through FLUVID or MRVP molecular panels.
Interpretation
The following table provides possible test results with associated interpretations for FLUVID and MRVP:
|
Result |
Interpretation |
Comments |
|---|---|---|
|
Not Detected |
Virus not detected |
Target virus not detected by real-time PCR |
|
Detected |
Virus detected |
Target virus detected by real-time PCR |
|
Indeterminate |
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. |
|
Invalid |
Invalid |
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. |
Reporting
Results are reported to the ordering physician, authorized healthcare provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.
Specimens that are detected for SARS-CoV-2, influenza, and all respiratory viruses detected results from outbreaks, are reported to the Medical Officer of Health as per Health Protection and Promotion Act.
References
- Robyn Harrison, Samira Mubareka, Jesse Papenburg, Tilman Schober, Upton D Allen, Todd F Hatchette, and Gerald A Evans. AMMI Canada 2023 update on influenza: Management and emerging issues. 2023. JAMMI. 2023 Nov 29. Available at: https://utppublishing.com/doi/10.3138/jammi-2023-07-12
- AMMI Canada Guidelines. Available at: https://www.ammi.ca/?ID=122
- Antiviral Medications for Influenza: Information for Healthcare Providers. Available at: https://www.publichealthontario.ca/-/media/documents/q/2019/qa-antiviral-medication-influenza.pdf
- 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: https://doi.org/10.3138/jammi-2020-11-02
Additional Respiratory Virus Testing Services at PHO
- Influenza Antiviral Susceptibility Testing
Currently circulating influenza A subtypes (H1N1pdm09 and seasonal 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.
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. Oseltamivir resistance PCR screen for H275Y mutation from H1N1pdm09 strain is available at PHO if it meets the below criteria, beyond that specimens will be forwarded to NML for full antiviral susceptibility testing
Recommended indications for antiviral susceptibility testing in Ontario include:- Influenza developing after initiation and/or completion of influenza antiviral prophylaxis (e.g., oseltamivir).
- 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.
- Patients who are not responding to full course of antiviral therapy.
- Immunocompromised patients not responding to influenza antiviral therapy being at greater risk for more severe disease, persistent viral shedding and development of antiviral resistance.
- Positive test for influenza A in a person who had close contact with a case with confirmed decreased susceptibility or a traveler returning from an area where resistant strain is circulating.
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 location.
- Avian Influenza Viruses
PHO conducts testing for avian influenza (e.g., H5, H7, and N9) 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’s Customer Service Centre at 1-877-604-4567 prior to submitting specimens. Refer to the Avian Influenza and Influenza A Subtyping – Real-time PCR Test Information Sheet.
- 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 with sufficiently high viral load (equivalent to Ct<30) will be tested for a panel of avian and/or swine influenza viruses.
- 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 SARS-CoV-2 and seasonal human coronavirus but does not detect MERS-CoV.
- Testing for Enterovirus (including EV-D68 and other serotypes)
EV-D68 exhibits biennial circulation pattern with peaks during late-summer and autumn of even-numbered years.
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.
- 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 acute respiratory infection (ARI) or influenza-like-illness (ILI) 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 viruses, other seasonal respiratory viruses (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.
MyPHO
Don’t have a MyPHO account? Register Now