Co-circulation of Seasonal Influenza and SARS-CoV-2 – Considerations for Outbreak Identification and Management

Advisory Alert

May 11, 2022

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To: Local Long-term Care Homes, Retirement Homes and Congregate Living Settings


Outbreak Prevention, Testing and Treatment Considerations for Suspected Respiratory Outbreaks

As you are aware, influenza A activity has been confirmed and is increasing in the Public Health Sudbury & Districts’ service area. This trend is occurring across Canada. Influenza A is currently the dominant type and influenza A(H3N2) is the dominant subtype.

As COVID-19 continues to circulate locally at high levels it is important for highest risk settings to identify organisms causing intra-facility respiratory symptoms among residents and staff, where possible, to assist in implementing timely and effective infection prevention and control measures including initiating anti-viral prophylaxis and treatment where recommended.

Influenza and COVID-19 cannot be reliably differentiated on the basis of clinical presentation because both viruses cause a range of overlapping respiratory and systemic symptoms. In addition, co-infection with both influenza virus A or B and SARS-CoV-2 may occur.1

The below recommendations for respiratory outbreak prevention, surveillance and reporting, testing, treatment and prophylaxis apply to all long-term care homes, retirement homes and other institutions/congregate living environments such as supported group living residences and intensive support residences.

Outbreak Prevention, Surveillance and Reporting

Facilities should make every effort possible to prevent respiratory infection outbreaks from occurring, with immunization as a key strategy for infection prevention and control. Immunization is recommended for unvaccinated individuals when influenza is circulating in the community and may be given when homes are in outbreak. All individuals are encouraged to maintain their COVID-19  and influenza vaccination up to date. The Outbreak Checklist found on the PHSD line list, can be used to identify any gaps that may be noted in your institutions policies, procedures, and practices. Of particular importance are staff exclusion policies for individuals who refuse influenza immunization during outbreaks and are not taking antiviral medication.

Ongoing surveillance for signs and symptoms of respiratory infection occurring in facilities is important for prevention of spread of infection. Facilities meeting the surveillance case definition for suspected or confirmed acute respiratory infection (ARI) outbreaks must report to Public Health Sudbury & Districts immediately while awaiting test results.

Confirmed respiratory infection outbreak:

Two cases of acute respiratory infections (ARI) within 48 hours with any common epidemiological link (e.g., unit, floor), at least one of which must be laboratory-confirmed;


Three cases of ARI (laboratory confirmation not necessary) occurring within 48 hours with any common epidemiological link (e.g., unit, floor).

Suspect Outbreak Definition Suspect respiratory infection outbreak:

Two cases of ARI occurring within 48 hours with any common epidemiological link (e.g., unit, floor);


One laboratory-confirmed case of influenza.

Further information on outbreak prevention and control measures can be found in the Control of Respiratory Infection Outbreaks in Long-Term Care Homes guidance document.


Specimens should be sent to Public Health Ontario laboratories to ensure testing occurs via Multiplex Respiratory Virus Molecular Panel, for multiple respiratory viruses including influenza and COVID-19. Be sure to check off the Respiratory Panel box on the requisition for testing. Swabs sent to HSN will only be tested for COVID-19.


People of any age who are residents of long-term care homes, retirement homes or other institutions/congregate living environments such as supported group living residences and intensive support residences would benefit from early empiric antiviral therapy for influenza. With late season onset of influenza, current protection from fall vaccination is expected to be low due to waning immunity.

For influenza A only

The standard adult dose of oseltamivir is 75 mg orally twice per day and should be started within 48hrs of symptom onset or as soon as possible. Oseltamivir dose regimens need to be adjusted for individuals with renal insufficiency. Resistance to oseltamivir in circulating viruses in Canada during the 2019–2020 influenza season was very low.

Among residents with mild uncomplicated influenza illness, the recommended duration of oseltamivir therapy is 5 days. The optimal duration of therapy for individuals with laboratory-confirmed influenza without or with concurrent SARS-CoV-2 infection who are hospitalized or have severe, progressive, or complicated disease has not been established. If treatment is being continued for longer than 5 days among severely ill individuals, consultation with an expert in infectious disease should be considered.1

Among residents whose influenza test is negative and whose SARS-CoV-2 virus test is positive, influenza antiviral therapy should be stopped. Among patients for whom tests for both influenza and SARS-CoV-2 are negative but respiratory disease is continuing or progressing, further diagnostic testing and expert input from an infectious disease specialist should be considered before influenza antiviral therapy is discontinued.1

For co-infections with influenza A and COVID-19

As per the 2021–2022 Association of Medical Microbiology  and Infectious Disease Canada (AMMI) guidance on the use of antiviral drugs for influenza in the COVID-19 pandemic setting in Canada, if the resident meets the criteria for use of antivirals for influenza AND the criteria for use of antivirals for treatment of COVID-19, then they can be used concomitantly.  There are no expected drug-drug interactions between oseltamivir and either nirmatrelvir/ritonavir (Paxlovid) or remdesivir.1

Further information on the availability and use of anti-virals for the treatment of COVID-19 infection can be found at: COVID-19 Health System Response Materials | Ontario Health and Clinical Practice Guideline Summary: Recommended Drugs and Biologics in Adult Patients with COVID-19 – Ontario COVID-19 Science Advisory Table (


When influenza and COVID-19 are circulating in the community, it is recommended that prophylaxis be initiated during an influenza confirmed outbreak as per institutional outbreak management protocols1. This recommendation applies to long term care homes, retirement homes and other institutions/congregate living environments such as supported group living residences and intensive support residences.  Guidance for prophylaxis can be found in the current Control of Respiratory Infection Outbreaks in Long-Term Care Homes, 2018.


  1. 2021-2022 AMMI Canada Guidance on the use of Antiviral Drugs for Influenza in the COVID-19 Pandemic Setting in Canada.

For questions related to the testing and treatment of respiratory infections in highest risk settings please contact the Control of Infectious Diseases Program at 705.522.9200, ext. 772 or toll-free at 1.866.522.9200.


Original Signed By

Dr. Penny Sutcliffe
Medical Officer of Health and Chief Executive Officer

NOTE: All Advisory Alerts are found on our website.

This item was last modified on May 11, 2022