Infectious Diseases

Technical Notes and Definitions

COVID-19 cases represent people whose residential address is in Simcoe Muskoka at the time of their investigation, not the location of the hospital. Cases whose residence is outside of Ontario are assigned to the health unit that is actively following up with the individual. Cases only include those that meet the definition for confirmed case classification as per the Ministry of Health Case Definition Coronavirus Disease (COVID-19) document.

Please note that confirmed re-infections, that is, where an individual has had more than one COVID-19 infection upon public health investigation, are counted as separate cases.

COVID-19 hospitalizations represent cases whose residential address is in Simcoe Muskoka regardless of where they are hospitalized, and who are being managed by Simcoe Muskoka District Health Unit. Cases who are residing and hospitalized outside of Simcoe Muskoka but who have been transferred to a local hospital, are excluded if they are not investigated by our health unit.

For surveillance purposes, a COVID-19 death is defined as a death resulting from a clinically compatible illness in a confirmed COVID-19 case, where no period of complete recovery from illness occurred, or the cause of death was determined to be COVID following recovery as per the death certificate. This includes all cases who died from COVID-19-related illness as per the death certificate or other official documentation, fatalities among COVID-19 cases where there is no alternative cause of death, and deaths that occurred in cases who were actively infected (i.e., symptomatic, self-isolating and/or continued to experience residual effectors or complications from the COVID-19 infection). Deaths due to an unrelated cause or trauma, such as a motor vehicle accident, are typically excluded. For more information on deaths, please see Additional Death Notes and Definitions below.

Hospital occupancy data included in the SMDHU Monitoring Dashboard represent all people who are admitted to local hospitals regardless of whether their residential address is in Simcoe Muskoka or not. People residing in Simcoe Muskoka who are admitted to hospitals outside of our region are excluded. This is different from the COVID-19 hospitalization numbers, which count hospitalizations among people who reside in Simcoe Muskoka regardless of where they are hospitalized.

Please note that 95% confidence intervals are not included on the charts and tables for simplicity; however, statistical significance between groups (e.g. geographic areas and age groups) was determined by non-overlapping confidence intervals.

Data Sources:

Confirmed COVID-19 cases: Public Health Case and Contact Management (CCM) Solution
Confirmed COVID-19 outbreaks: Public Health Case and Contact Management (CCM) Solution and the Integrated Public Health Information System (iPHIS).
COVID-19 testing data: Ontario Laboratories Information System (OLIS).
COVID-19 vaccinations: COVaxON
Hospital occupancy: Daily Bed Census Summary for acute care capacity and the CRITICALL Ontario Critical Care Information System (CCIS) for ICU and ICU-ventilated bed capacity.
COVID-19 local impact survey result: an online survey to learn about the financial, mental, physical and social impacts of the pandemic on the local population.
COVID-19 Wastewater Surveillance: Ontario Tech University and Ontario Wastewater Surveillance Initiative.

Terminology/ Definitions

Case Fatality Rate (CFR): The percentage of people diagnosed with a disease that die within a certain time after diagnosis (usually prior to recovery).

Median Reproductive Number (Rt): The average number of secondary cases that each infected individual would infect if the conditions remained as they were at time ‘t’. R(t) is presented as a 7-Day Rolling Average of Median value of R(t), adjusted for reporting lag times. It is calculated using symptom onset date. A reproduction number greater than 1 means that the epidemic is growing, while a reproduction number less than 1 means the epidemic is slowing and containment/mitigation efforts may be working to keep control of epidemic.

Percent Positivity: Percent positivity represents the percentage of completed COVID-19 tests that are positive for the COVID-19 virus, over a defined period of time. A low percent positivity rate indicates the outbreak is under control, given more testing is finding a smaller proportion of positives.

Variant Definitions

Variant: Variant of Concern cases and Positive Screen cases as combined.

Variant of Concern (VOC): A confirmed case of COVID-19 with whole-genome sequencing (WGS / genomic analysis) results matching it to a known variant of concern, or has tested positive for a specific combination of mutations that are highly correlated with a known variant of concern (i.e. presumptive).

Variants of concern have one or more mutations in the COVID-19 virus (SARS-CoV-2) that differentiates it from other versions of the virus that are being spread in the community and have specific traits that are concerning for human health. Currently, the health unit reports on four variants of concern: Alpha (B.1.1.7), Gamma ( P.1) and Beta (B.1.351), and Delta (B.1.617.2).
Note that all B.1.617 cases are presumed to be Delta (B.1.617.2) as it is the dominant strain of B.1.617 in Ontario.
The count of Alpha (B.1.1.7), Beta (B.1351), Gamma (P.1) includes cases that are presumptive positive for those variants based on specific mutation combinations, as show below:
- Alpha (B.1.1.7) presumptive = positive for N501Y and negative for E484K mutation
- Beta (B.1.3.51) presumptive = positive for the following three mutations: K417N, N501Y and E484K
- Gamma (P.1) presumptive = positive for the following three mutations: K417T, N501Y and E484K
- Delta (B.1.617.2) presumptive = negative for both the N501Y and the E484K mutations.
Variants of concern for COVID-19 to date have shown one or more of the following traits:
- Increases in how easily the virus can be spread
- Increased disease severity
- Changes in our ability to diagnose (test) for the virus
- Decreased effectiveness of treatments and/or vaccines

Note: Changes in the genetic makeup of the COVID-19 virus (SARS-CoV-2) is expected and have been emerging and circulating throughout the world throughout the pandemic.

More information on variants of concern can be found on our website here.

Positive screen: A confirmed case of COVID-19 that has been tested for mutations known to be found in one or more identified variants of concern (see variant of concern above). Subsequent testing is required to identify the specific variant of concern. Locally, mutations of interest that are routinely tested for are N501Y and E484K.

Starting on March 26, 2021 due to changes in testing methods at Public Health Ontario, Alpha (B.1.1.7) cases will include confirmed Alpha (B.1.1.7) lineage based on whole genome sequencing, and presumed Alpha (B.1.1.7) cases based on a positive PCR test for the N501Y mutation and a negative PCR test for the E484K mutation. This resulted in a large number of cases previously reported as screened positive being re-assessed as Alpha (B.1.1.7) variant cases. This aligns with reporting being done by Public Health Ontario.

For cases reported on or after May 23, 2021, Delta (B.1.617.2) cases will include confirmed B.1.617 lineage based on whole genome sequencing, and presumed Delta (B.1.617.2) cases based on negative PCR tests for both the N501Y and E484K mutations.

Additional details about Variant of Concern testing are available from Public Health Ontario.

Screening Practices: Screening practices for VOCs and mutations of interest may vary at the discretion of Public Health Ontario, based on public health priorities and public health lab capacity.

From December 9, 2022, the provincial COVID-19 sequencing strategy increased screening of eligible specimens to 100%.
From November 23, 2022 the provincial COVID-19 sequencing strategy increased screening of eligible specimens to 75%.
From August 24, 2022 the provincial COVID-19 sequencing strategy increased screening of positive specimens for VOCs and mutations of interest to 50%.
From July 22, 2022 the provincial COVID-19 whole genome sequencing strategy decreased screening of eligible samples to 20%
From July 8, 2022 the provincial COVID-19 whole genome sequencing strategy decreased screening of eligible samples to 50%.
From June 10, 2022 the provinicial COVID-19 whole genome sequencing strategy increased screening of eligible samples to 100%.
From May 12, 2022 the provincial COVID-19 whole genome sequencing strategy increased screening of eligible samples to 25%.
From April 13, 2022 the provincial COVID-19 whole genome sequencing strategy decreased screening of eligible samples from 25% to 10%.
From March 30, 2022 the provincial COVID-19 whole genome sequencing strategy decreased screening of eligible specimens to 25%.
From March 9, 2022, the provincial COVID-19 whole genome sequencing strategy increased screening of eligible specimens from 20% to 50%.
From February 16, 2022 the provincial COVID-19 whole genome sequencing strategy increased screening of eligible specimens from 5% to 20%.
From December 30, 2021 the provincial COVID-19 whole genome sequencing strategy reduced screening of eligible specimens from 50% to 5%. Mutation screening for the S-gene target failure was also discontinued at this time.
From December 7, 2021, the provincial lab network will be screening all cases for S gene target failure (SGTF), and 50% of eligible cases will be submitted for whole genome sequencing.
From November 5, 2021, the provincial lab network will be screening 100% of eligible samples via genome sequencing.
From September 10, 2021 the provincial lab network reduced to screening 10% of eligible specimens via whole genome sequencing.
Beginning August 27, 2021 the province has returned to a sampling-based strategy where 50% of all eligible positive COVID-19 tests will be submitted for whole genome sequencing.
As of June 14, 2021, the provincial COVID-19 whole genome sequencing strategy sends all eligible positive COVID-19 samples (from the COVID-19 diagnostic test) for whole genome sequencing as part of their surveillance strategy. This strategy will help detect new and emerging variants in a more proactive and timely way.
From May 26 to June 13, 2021 the provincial genome sequencing strategy was a sampling-based method, with 50% of all eligible positive COVID-19 test results being sequenced using whole genome sequencing (WGS), along with targeted samples of specific SARS-CoV-2 cases (e.g. travel, outbreak and coroner requests).
From February 3 to May 25, 2021, Public Health Ontario (PHO) and the Provincial Diagnostic Laboratory Network screened all new positive COVID-19 specimens for known VOCs, to rapidly identify and mitigate against spread of VOCs in Ontario.

Vaccination Status of Cases Definitions

Fully Vaccinated Cases: New positive COVID-19 cases that have had both doses of vaccine (for a 2-dose series), with their second dose administered (or only dose for a single-dose series) at least 14 days prior to the date of onset of their illness (or testing date if asymptomatic).

Partially Vaccinated Cases: New positive COVID-19 cases that have one dose of vaccine (for a 2-dose series) at least 14 days prior to the date of onset of their illness (or testing date if asymptomatic) AND either have not had their second dose or received their second dose less than 14 prior to illness onset (or testing date). Partial vaccination does not apply for single-dose series vaccines.

Unvaccinated Cases: New positive COVID-19 cases that have not had a dose of vaccine (either for a 2-dose or single-dose series), OR have had a single dose of vaccine (either for a 2-dose or single-dose series) less than 14 days prior to the date of onset of their illness (or testing date if asymptomatic), including receiving a vaccine after illness onset (or testing).

Note: vaccination status of cases is only reported for cases with date reported to public health of December 22, 2021 or later.

Vaccination Definitions

Completed primary series: individuals that have received: one dose of the Janssen (J&J) vaccine OR two-dose a Health Canada (HC) authorized vaccine series including mixed vaccine products OR one dose of a non-HC authorized vaccine and one dose of a HC-authorized vaccine (regardless of the order) OR three doses of a non-HC authorized vaccine product OR one dose of HC-authorized and two doses of non-HC-authorized products (regardless of the order).

Completed primary series with at least one booster dose: individuals that have completed a primary series (as per the definition above) and have received at least one booster dose of a HC-authorized vaccine. A dose of non-HC authorized vaccine is not considered a booster dose. For indicators reporting booster vaccination less than six-months, the six-month interval is calculated as 168 days from the report date to the date of the last booster dose the client received.

Partially vaccinated: individuals with only one dose of a HC-authorized two-dose series.

Unvaccinated: individuals with zero dose of HC-approved vaccine AND less than three doses of non-HC vaccine. Unvaccinated individuals are estimated by subtracting the number of individuals considered at least partially vaccinated (i.e., at least one dose of a HC-approved vaccine OR three or more doses of a non-HC approved vaccine) from the estimated population.

As of December 15th, 2021 vaccine coverage estimate calculations will exclude all individuals that are currently deceased (as recorded in the COVaxON database). In addition, age-specific coverage rate calculations are now based on the age of the client at the time the report was run. Previously, the age-specific estimates were based on the age of the client at the time they received their first dose of vaccine.

Hospital Occupancy Definitions

Acute Care: The percent of all acute care beds in Simcoe Muskoka hospitals that are occupied on the most recent reporting date. This includes occupied beds that have been opened for use in the Pandemic Response Unit at Royal Victoria Regional Health Centre.

Intensive Care Unit (ICU) beds: The percent of all intensive care unit (ICU) beds in Simcoe Muskoka hospitals that are occupied on the most recent reporting date. This is restricted to medical, surgical and cardiovascular ICU units, and excludes neonatal and incremental (surge) ICU beds. The number of ICU beds at a hospital includes both ventilated and non-ventilated beds.

ICU-Ventilated Beds: The percent of all ventilated beds in intensive care units (ICU) in Simcoe Muskoka hospitals that are occupied on the most recent reporting date. This is restricted to medical, surgical and cardiovascular ICU units, and excludes neonatal and incremental (surge) ICU beds.

Case Type Definitions

Active cases are confirmed COVID-19 cases that are currently self-isolating, are under isolation precautions or are in hospital (including those in an ICU bed or on a ventilator). Excludes those with unknown status.

Sporadic cases are those not associated with an outbreak at an institution, workplace, community setting, educational setting or congregate setting in Ontario. These infections are usually acquired from travel, within the community or from close contact with a known case.

Institutional outbreak cases are COVID-19 cases that are linked to long-term care homes, retirement homes, hospitals or, correctional facilities.Applies to residents, staff, volunteers and third-party service providers.Institutions may be located in Simcoe Muskoka or in other health unit jurisdictions. The health unit is only able to comment on institutional outbreaks in our area.

Workplace outbreak cases are confirmed COVID-19 cases that are linked to a place of employment that is not open to the public (e.g., farms, food processing plants, manufacturing). Excludes institutions, congregate settings, educational settings and community setting workplaces.Applies to employees and employers. Based on epidemiological investigation of cases in employees of a workplace who worked in proximity and at the same time of other confirmed cases. Workplaces may be located in Simcoe Muskoka or in other health unit jurisdictions. The health unit is only able to comment on workplace outbreaks in our area.

Community outbreak cases are confirmed COVID-19 cases linked to workplaces that are open to the public (e.g., restaurants, bars, funeral homes, gyms, community centres, personal service settings etc.), community events (e.g., concerts), recreational camps (day or overnight) or social gatherings.Based on epidemiological investigation of cases that were in close proximity and at the same time of other confirmed cases at the facility, event or gathering. These community settings may be located in Simcoe Muskoka or in other health unit jurisdictions. The health unit is only able to comment on community setting outbreaks in our area.

Congregate settings outbreak cases are confirmed COVID-19 cases linked to settings in which people temporarily or permanently reside such as group homes, supportive housing or shelters.Applies to residents and staff. Based on epidemiological investigation of cases in residents/staff of a congregate setting who were in proximity and at the same time of other confirmed cases. Congregate settings may be located in Simcoe Muskoka or in other health unit jurisdictions. The health unit is only able to comment on congregate setting outbreaks in our area.

Educational settings outbreak cases are confirmed COVID-19 cases linked to child care centres, elementary and secondary schools as well as trades school, college and university. Applies to students and staff. Based on epidemiological investigation of cases in students/staff of an educational setting who were in proximity and at the same time of other confirmed cases. Educational settings may be located in Simcoe Muskoka or in other health unit jurisdictions. The health unit is only able to comment on educational setting outbreaks in our area.

For all of the above, only cases where the Simcoe Muskoka District Health Unit is the investigating health unit (previously referred to as responsible health unit) are included.

Acquisition definitions

Travel: most likely acquisition of illness is from travel outside of Ontario.

Close Contact: most likely acquisition of illness is from close contact with another confirmed COVID-19 case. Exposures include: close personal contact, shared airspace, and household contact. This excludes anyone with travel history within 14 days of symptom onset.

Community-Acquired: signifies a sporadic case in an individual where most likely acquisition of illness is from somewhere within the community but not associated with a community outbreak. This also excludes transmission due to travel and due to close contact with a known case.

Educational Setting Outbreak-Related: a confirmed COVID-19 case that is a student/attendee or staff of an educational setting (childcare centres, elementary and secondary schools as well as trades schools colleges and universities) where an outbreak has been declared.

Institutional Outbreak-Related: a confirmed COVID-19 case that is a resident or staff member of a long-term care institution, retirement home, correctional facility, or hospital. These types of transmissions are often referred to as nosocomial.

Workplace Outbreak-Related: multiple confirmed COVID-19 cases in employees of a workplace that is not open to the public and who worked in proximity and at the same time of other confirmed cases and, based on epidemiological investigation, a higher level of disease transmission within the workplace than what would be expected given current local COVID-19 activity and incidence in the community.

Community Outbreak-Related: multiple confirmed COVID-19 cases in individuals who attended a community event, a recreational camp or social gathering at the same time of other confirmed cases and, based on epidemiological investigation, were deemed to be potentially infectious during the event or may have acquired the infection while attending the event.

Congregate Setting Outbreak-Related: a confirmed COVID-19 case that is a resident or staff member of facilities in which people temporarily or permanently reside such as group homes, supportive housing or shelters. These cases are not included in either the institutional or workplace outbreak cases.

Undetermined: most likely acquisition of illness is not clear and investigation is complete.

Under Investigation: a confirmed COVID-19 case with current status under investigation at the time of reporting.

Status definitions

Resolved: includes confirmed COVID-19 cases who are not deceased and are no longer being followed by public health (i.e. 14 days past symptom onset if not hospitalized, 20 days past symptom onset if hospitalized), as well as those who are reported as "recovered"

Active - Not Hospitalized: a confirmed COVID-19 case who is currently not in hospital but is being followed by public health and remains under isolation

Active - Hospitalized: a confirmed COVID-19 case that is currently admitted to hospital, but is not currently in an intensive care unit (ICU)

Active Hospitalized in ICU: a confirmed COVID-19 case that is currently admitted to hospital in an intensive care unit (ICU)

Deceased: a confirmed COVID-19 case that has died

Hospitalized Never in ICU: confirmed COVID-19 case that has ever been admitted to hospital but has never been admitted to an intensive care unit nor been on a ventilator in hospital.

Hospitalized - ICU: confirmed COVID-19 case that has ever been admitted to an intensive care unit or been on a ventilator in hospital.

Total Hospitalized: the number of confirmed COVID-19 cases who have ever been admitted to hospital. This includes patients who have ever been admitted to an intensive care unit and those that have ever been on a ventilator in hospital.

Active or Current Hospitalization: a confirmed COVID-19 cases who has not recovered and is currently admitted to hospital. This includes patients who are currently admitted to an intensive care unit and those currently on a ventilator in hospital.

Additional Death Notes and Definitions

Deaths are determined by using the outcome field in CCM.
Deaths include the total number of individuals who died while infected with COVID-19 – this does not mean COVID-19 was the cause of death.
Fatalities among COVID-19 cases are reported to public health from a variety of sources including hospitals and the coroner’s office. This can result in delays in reporting fatalities among cases.
Underlying conditions can have a significant effect on severe COVID-19 outcomes, including death, as summarized by the European Centre for Disease Control and the US Centre for Disease Control
Deaths are subdivided into the following three categories of type of death:

Contributed to/underlying cause of death: COVID-19 is listed on the death certificate under the cause of death as the immediate, antecedent, or underlying cause in the chain of events leading to death, as well as deaths that were due to pre-existing conditions or new conditions that were exacerbated by COVID-19.
Did not contribute to death: COVID-19 is not listed on the death certificate, but case was infectious and/or symptomatic at time of death and no further information is available on the death.
Pending/Unknown: includes fatalities where the death certificate has yet to be received to determine the cause of death in relation to COVID-19, or it is unclear if COVID-19 illness contributed to the death. This may be due to no official report (e.g. death certificate) available for review by public health, or where COVID-19 was not listed as the cause of death on the death certificate, but where COVID-19 cannot be ruled-out as a cause of death based on additional information provided to public health.

Wastewater Definitions

7-day moving average: The wastewater and reported COVID-19 hospitalization data is transformed into a 7-day midpoint moving average. For the number of cases reported, or viral RNA concentration, this represents the average of any given day and the three previous and the three following days. Also known as a “rolling” average.

7-day moving average of raw viral signal (indexed): This represents the 7-day moving average of the concentration of SARS-CoV-2 viral RNA in copies per L. This value is indexed, meaning it is transformed to fit on the same scale as the reported hospitalization data.

7-day moving average of normalized viral signal (indexed): This represents the 7-day moving average of the number of SARS-CoV-2 viral RNA copies per copy of the Pepper Mottle Mild Virus (PPMoV), a biomarker. This value is indexed, meaning it is transformed to fit on the same scale as the reported hospitalization data.

Indexed Viral Signal: For easier visual comparison of changes in viral signal compared to changes in reported cases in humans, the raw and normalized viral RNA values (gene copies per mL in raw data, copies per copy for normalized data) are transformed to allow comparison on the same scale as reported hospitalizations. The value of the indexed viral signal for raw or normalized values is not meaningful. The actual data values can be accessed by clicking “Get the Data” on each datawrapper object.

Normalized Viral Signal: Concentrations of a biomarker (Pepper Mild Mottle Virus, PPMoV) are used to normalize the SARS-CoV-2 viral RNA levels detected in wastewater. This is presented as copies of the SARS-CoV-2 viral RNA per copy of the PPMoV viral RNA. Wastewater treatment plants receive inputs from residential, commercial and institutional sources. The concentration of PPMoV provides information about the relative proportion of the wastewater that is human waste (e.g. feces) compared to other sources (e.g. kitchen sink, commercial discharge). This helps us to interpret whether changes in the SARS-CoV-2 signal are related to changes in virus excretion in the community or changes to the proportion of wastewater that is related to human fecal content.

Raw Viral Signal: This represents concentrations of the SARS-CoV-2 N1 gene, as gene copies per L from the wastewater samples. The raw signal is not normalized to account for changes in other inputs to the wastewater inputs that may affect the concentration of SARS-CoV-2 viral RNA in the samples. As a result the concentration of SARS-CoV-2 may be affected by other pressures on the wastewater system.

Wastewater collection and analysis: Wastewater samples are collected from within the wastewater treatment plants three times (Midland) or five times (Barrie) per week using 24-hour composite samples (meaning a sample is collected once an hour for 24-hours). These samples are transported to Ontario Tech University for analysis. Two regions of the SARS-CoV-2 are assayed (N1 and N2). The data reported here is for the number of gene copies of the N1 gene identified in the wastewater samples. As of April 1, 2023 Bracebridge, Collingwood, Orillia and Penetanguishene are no longer active sampling sites under the Ontario Ministry of the Environment, Conservation and Parks Wastewater Surveillance Initiative.

Page last updated April 6, 2023