Respiratory Viruses (including influenza)

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.

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.

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.

FLUVID – FLUVID Multiplex (MPX) PCR:

• 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

Algorithm

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.)

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

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

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.

Interpretation

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

Reporting

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.

References

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: jammi.utpjournals.press/doi/10.3138/jammi.2019.02.08
2. AMMI Canada Guidelines. Available at: ammi.ca/?ID=122
3. Antiviral Medications for Influenza: Information for Healthcare Providers. Available at: https://www.publichealthontario.ca/-/media/documents/q/2019/qa-antiviral-medicationinfluenza.pdf
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: https://doi.org/10.3138/jammi-2020-11-02