Respiratory virus monitoring in Canada

1. Rapidly detect emerging or re-emerging respiratory virus outbreaks and other events.
2. Assess transmissibility, risk factors for transmission and extent of population exposure from an emerging or re-emerging respiratory virus.
3. Describe clinical presentation and risk factors for severe outcomes associated with an emerging or remerging respiratory virus.

1. Monitor activity and assess epidemiologic and clinical characteristics of respiratory illness over time.
2. Monitor virologic and genetic characteristics of circulating respiratory viruses.
3. Monitor and assess activity of respiratory viruses in high-risk settings and populations in situations of vulnerability.
   • ‘Populations living in situations of vulnerability’ refers to populations, groups and communities who are at higher risk of exposure to, severe disease from, or poor health outcomes resulting from infections with respiratory viral pathogens.
     • This will depend on the pathogen, immunity of the host, and context, and is a result of systemic barriers, social determinants of health, and discrimination including but not limited to racism. 
4. Monitor impact on and coping abilities of health care systems.

1. Monitor the impact of non-medical interventions in the population.
2. Monitor vaccine coverage, effectiveness, impact and cost-effectiveness.
3. Monitor adverse events to vaccines and therapeutics.
4. Support other public health and clinical activities as necessary.

Activity levels describe the intensity and geographic spread of respiratory virus circulation in a specific region for a given time period. Provincial and territorial public health partners use multiple data sources to provide a weekly assessment of influenza and COVID-19 virus activity in Canada, including:

• laboratory-confirmed detections
• outbreaks
• syndromic surveillance data
• wastewater monitoring data

Methods for deriving activity levels for influenza and COVID-19 are different and are described in the Canadian Respiratory Virus Surveillance Report.

Canadian respiratory virus surveillance report

Data on outbreaks of test-confirmed COVID-19, influenza, and RSV in high-risk settings are reported from provinces and territories. High-risk settings include:

• long-term care facilities
• acute care facilities
• retirement facilities
• remote and isolated communities
• other settings, such as correctional facilities and group homes

FluWatch+ uses outbreak data to monitor activity of respiratory viruses in high-risk settings in the community in order to:

• measure and assess the impact of respiratory viruses within various closed settings and at-risk populations
• assess epidemiologic and clinical characteristics of respiratory illness over time
• provide a timely, sensitive measure of early respiratory virus activity

Syndromic surveillance for respiratory diseases uses the reports of influenza-like illness (ILI) to detect early signals of respiratory illness activity in the community. These include symptoms such as cough and fever. Early reports are gathered before respiratory virus cases get confirmed and reported to public health agencies.

Data collected through syndromic surveillance are not specific to any one respiratory pathogen and are used with other surveillance data to obtain a more complete and accurate picture of respiratory virus activity in Canada.

FluWatch+ syndromic surveillance consists of 2 data sources:

1. Sentinel Primary Care ILI Surveillance: a program consisting of primary care providers across Canada who report the proportion of patients seen in their clinic each week with ILI
2. FluWatchers: a program consisting of volunteers across Canada who report each week if they had cough or fever via an online questionnaire
   • anyone in Canada can be a volunteer FluWatcher

About FluWatchers

FluWatch+ uses syndromic data to monitor activity and assess epidemiologic and clinical characteristics of respiratory illness over time in order to:

• assess transmissibility, risk factors for transmission and extent of population exposure from an emerging or re-emerging respiratory virus
• measure health-seeking behaviour among ILI cases in the community
• estimate the impact and burden of mild disease associated with respiratory illness in the community
• rapidly detect emerging or re-emerging respiratory virus activity

Data on laboratory-confirmed respiratory virus detections are reported to FluWatch+ through the Respiratory Virus Detection Surveillance System (RVDSS). RVDSS is a sentinel laboratory surveillance system that consists of:

• provincial, territorial and regional public health laboratories
• some hospital laboratories

They report the number of tests and positive detections for up to 8 respiratory viruses:

1. influenza
2. COVID-19
3. RSV
4. human parainfluenza virus
5. adenovirus
6. human metapneumovirus
7. enterovirus and rhinovirus
8. human coronavirus

FluWatch+ uses laboratory data to monitor and analyze patterns of respiratory circulation in Canada in order to assess:

• respiratory virus activity, including signals for the start, progression and end of seasonal epidemics
• respiratory virus transmission patterns by person, place and time
• the intensity of respiratory virus transmission across time periods

PHAC’s National Microbiology Laboratory (NML) conducts genetic and antigenic characterization on a proportion of laboratory-confirmed influenza and SARS-CoV-2 isolates collected across Canada. A temporal distribution of isolates is needed to accurately represent the season, which include a proportion of early-season, peak-season, and late-season isolates.

The purpose of virus characterization is to:

• identify the specific influenza or SARS-CoV-2 strains and lineages circulating in Canada each season
• compare the relatedness of circulating influenza or SARS-CoV-2 isolates to the current vaccine strains and lineages used in their respective vaccines  
• monitor influenza and SARS-CoV-2 evolutionary changes occurring in viruses circulating in humans

The NML also tests a proportion of influenza and SARS-CoV-2 isolates for susceptibility to antivirals, specifically:

• amantadine
• oseltamivir
• zanamivir for influenza
• remdesivir, nirmatrelvir and ritonavir for SARS-CoV-2

Participating provincial and territorial partners provide weekly data on influenza, COVID-19 and RSV hospitalizations, and ICU admissions by age group.

This data provides timely population-based trends of severe outcomes associated with these respiratory virus

Sentinel hospital networks consist of groups of selected hospitals that conduct enhanced surveillance on severe respiratory cases in adult or pediatric population. These hospitals collect detailed case-level information that is not provided by provinces and territories, such as:

• age
• virus subtyping
• sex
• underlying medical conditions
• vaccination status and treatment

The Surveillance Program for Rapid Identification and Tracking of Infectious Diseases in kids (SPRINT-KIDS) is a sentinel surveillance network consisting of 15 pediatric hospitals across 8 provinces in Canada.  

Learn more:

• SPRINT-KIDS (University of Calgary)

Vaccine coverage is a measure of the uptake of vaccines in the population.

Vaccination coverage is measured as the percentage of people who reported receiving the influenza vaccine in a specific influenza season. Data on influenza vaccine coverage is collected annually through surveys. Data on vaccine coverage for COVID-19 is no longer being collected but archived reports are available.

Learn more:

• COVID-19 vaccination: Vaccination coverage
• Influenza vaccine monitoring: Canadian respiratory virus surveillance report

Vaccine effectiveness is a measure of how well a vaccine is able to prevent infections. Throughout the respiratory virus season, surveillance networks estimate how well the vaccine is working. Estimates can vary depending on the:

• study methods used
• population
• setting
• outcomes that are being studied
• type and mix of vaccine products
• stage of the season
• kinds of influenza viruses that are circulating when the study is conducted

Estimates are usually available in February or March, and are included in the Canadian Respiratory Virus Surveillance Report once available.

Canadian respiratory virus surveillance report

PHAC also keeps track of adverse events following immunization for all vaccines, including the influenza, RSV and COVID-19 vaccine through the Canadian Adverse Events Following Immunization Surveillance System (CAEFISS). These data are not included in the weekly Canadian Respiratory Virus Surveillance Report. However, reports with this data are available.

Canadian Adverse Events Following Immunization Surveillance System

Canadian Nosocomial Infection Surveillance Program (CNISP): A sentinel hospital-based surveillance network that conducts surveillance on healthcare-associated infections, antimicrobial resistant organism and viral respiratory illness.

Respiratory virus wastewater monitoring dashboard: A pan-Canadian network to track the levels of COVID-19, influenza, and RSV through community wastewater samples. The wastewater monitoring network aims to track the spread of respiratory viruses to:

• provide an early warning of disease activity in communities across Canada
• inform the public about potential public health risks so they can take steps to protect their health

COVID-19 and animals: Provides links to national and global surveillance data on the detection of SARS-CoV-2 in animals.

Influenza in animals, avian influenza: Presents the latest information, including surveillance data, on avian influenza A(H5N1).

• Annual FluWatch reports (archive)
• Hospital burden of influenza, respiratory syncytial virus, and other respiratory viruses in Canada, seasons 2010/2011 to 2018/2019 (2025) [European Association for Predictive, Preventive and Personalised Medicine]
• Establishing pandemic influenza severity assessment parameters and thresholds for Canada's FluWatch program (2023)
• Does the Australian influenza season predict the Canadian influenza season? A qualitative comparison of seasons, 2014–2020 (2023)
• Syndromic surveillance performance in Canada throughout the COVID-19 pandemic, March 1, 2020 to March 4, 2023 (2023)
• Crowdsourced disease surveillance success story: The FluWatchers program (2021)
• FluWatchers: Evaluation of a crowdsourced influenza-like illness surveillance application for Canadian influenza seasons 2015–2016 to 2018–2019 (2021)
• Representativeness of the FluWatchers Participatory Disease Surveillance Program 2015–2016 to 2018–2019: How do participants compare with the Canadian population? (2021)
• Impact of nonpharmaceutical interventions on laboratory detections of influenza A and B in Canada (2021)