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Alert Date: 
Tuesday, September 26, 2017 - 3:30pm

September 26, 2017

Due to an unexpected increase in submissions for respiratory viral testing last year, the Public Health Ontario Laboratory (PHOL) revised their algorithm for respiratory viral testing, effective as of September 20, 2017. We would like to take this opportunity to provide a brief update to clinicians and laboratories of what respiratory viral testing is available from Public Health Ontario. The full Labstract update is available from

Notification: Influenza is a mandatory reportable disease, according to the Health Protection and Promotion Act, R.S.O., 1990. All clinically diagnosed and confirmed cases are reportable to the health unit. If the individual presents with a novel or emerging respiratory infection, please report immediately to the Medical Officer of Health.

Respiratory Viral Testing Algorithm as of September 20, 2017

  • For specimen collection and handling, please ensure the following:
  • Patient setting must be provided for triaging of specimens. If setting is not provided, sample will NOT be tested.
  • Indicate travel history or exposure to known cases of novel influenza viruses.
  • Check specimen collection kit expiry dates (both the collection swab and transport media dates as they may not be the same) before use. Expired kits will be rejected.
  • Store and transport specimens to PHOL at 2-8oC within 48 hours of collection. If longer storage/transit time is anticipated, specimens should be frozen at -70oC or lower.
  • Table 1 describes the respiratory viral testing available by patient setting.
Table 1. Respiratory Viral Testing per Patient Setting
Patient Setting Revised Algorithm as of September 20th 2017
In-patient Intensive Care Unit/Critical Care Units Influenza A/B RT PCR (and subtype if flu A is positive).
If flu A or B is positive then no further testing will be performed. If flu A/B is negative, samples will be further tested by Rapid Viral Culture1,2
Inpatient ward/Institutions Influenza A/B RT PCR (and subtype on a selection of flu A-positive specimens).
If flu A or B is positive then no further testing will be performed. If flu A/B is negative, samples will be further tested by Rapid Viral Culture1,2
Institutional Respiratory Infection Outbreaks Influenza Rapid Testing up to 4 outbreak samples.
Influenza A/B RT PCR (1 sample from each flu A- positive outbreak will be subtyped).
If flu A or B is positive then no further testing will be performed. If flu A/B is negative, samples will be further tested by Rapid Viral Culture1
Emergency Room Patients Testing not available3
Ambulatory – Influenza High Risk Patients Testing not available3
Ambulatory – Patients NOT Influenza High Risk Testing not available3

1 The Rapid Viral Culture system (R-Mix Too) detects adenovirus, influenza A, influenza B, respiratory syncytial virus (RSV), parainfluenza 1, 2 and 3, and human metapneumovirus.

2 CMV culture for bronchial alveolar lavage (BAL)/bronchial wash/pleural fluid will be done if requested on the requisition.

3 To assist with patient management when respiratory viral testing is not available, health care providers are encouraged to refer to PHO’s respiratory surveillance reports for information on respiratory pathogen activity in Ontario.

Note: Adapted from Labstract – September 2017: Respiratory Viral Testing Algorithm – Update for Fall and Winter 2017-2018, by Public Health Ontario, 2017, retrieved from

Public Health Ontario Laboratory is available for consultation on laboratory testing with health care providers as needed at (toll free) 1-877-604-4567.

Influenza Antiviral Therapy and Susceptibility Testing

Current clinical guidelines recommend, during influenza season, that influenza antiviral therapy (e.g., oseltamivir or zanamivir) be started empirically for patients with:

  • severe acute respiratory illness (e.g., requiring hospitalization), or
  • high risk of influenza complications/severe disease.

For more information, refer to the AMMI Canada Guideline at the end of this document.

The currently circulating influenza A subtypes (H1N1pdm09 and H3N2) are universally amantadine resistant. Almost all currently circulating influenza A and B viruses are susceptible to oseltamivir, with rare occasions of documented resistance. Routine susceptibility testing is not required for clinical care. However, a portion of influenza-positive samples will be sent to the National Microbiology Laboratory for strain typing and antiviral susceptibility testing.  Limited susceptibility testing is also available at PHO.

The recommended criteria for antiviral susceptibility testing in Ontario, as outlined in the Labstract, are:

  • Influenza developing during or soon after influenza antiviral prophylaxis (e.g., oseltamivir or zanamivir)
  • Severely-ill patients (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 7 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.
  • Influenza A(H1N1)pdm09-positive outbreak samples (will be routinely tested at PHO)
  • Positive test for influenza A in a traveller returning from an area where resistance is endemic

To request influenza susceptibility testing for a patient who meets any of the above criteria, please provide the relevant information on the laboratory requisition. To make a request on a sample already submitted to PHO, please contact PHOL’s Customer Service Centre at 1-877-604-4567.

Surveillance Reports

Public Health Ontario (PHO) and the Health Unit conduct routine surveillance, and the reports are available at:

The Sentinel Practitioner Surveillance Network (SPSN) performs molecular viral testing on patients with influenza-like-illness visiting community-based sentinel health care providers across Ontario and other provinces.  These SPSN sentinels are the only community practitioners who are exempt from laboratory testing restrictions.  More information about SPSN and for practitioners interested in contributing to the network can be found here.

Our website ( is a reference for health care providers and patients.  For additional information or consultation, please call the Health Unit during regular office hours at 519-258-246 ext. 1420. During after hours and weekends, please call 519-973-4510.

For more information, visit:

  • Aoki, F.Y., Allen, U.D., Stiver, H.G., & Evans, G.A. (2013). Association of Medical Microbiology and Infectious Disease (AMMI) Canada Guideline The use of antiviral drugs for influenza: A foundation document for practitioners - View here.
  • Public Health Ontario Laboratories Labstract: Respiratory Viral Testing Algorithm – Update for Fall and Winter 2017-2018