This dataset compiles daily snapshots of publicly reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Data includes: * reporting date * reporting Public Health Unit (PHU) * case outcomes (active, resolutions and deaths) The last update of this file will occur on Thursday December 1, 2022. For more information about COVID-19 cases and deaths by public health unit, please consult the Public Health Ontario COVID-19 data tool The methodology used to count COVID-19 deaths has changed to exclude deaths not caused by COVID. This impacts data captured in the columns “RESOLVED_CASES” and “DEATHS” starting with the file posted on March 11, 2022. Two new columns have been added to the file “ARCHIVED_RESOLVED_CASES” and “ARCHIVED_DEATHS” which represent the data that were posted publicly prior to the methodological change. This dataset is subject to change. Please review the daily epidemiologic summaries for information on variables, methodology, and technical considerations.

This dataset compiles daily snapshots of publicly reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Data includes: * approximation of onset date * age group * patient gender * case acquisition information * patient outcome * reporting Public Health Unit (PHU) * postal code, website, longitude, and latitude of PHU This dataset is subject to change. Please review the daily epidemiologic summaries for information on variables, methodology, and technical considerations. ##Additional information This data is no longer available on this page. Information about COVID-19, and other respiratory viruses, is available through Public Health Ontario’s “Ontario Respiratory Virus Tool". On November 30, 2023 the count of COVID-19 deaths was updated to include missing historical deaths from January 15, 2020 to March 31, 2023. This impacts data captured in the column ‘Outcome1’. Due to changes in data availability, the following variables will be removed from this file, effective Thursday April 13, 2023: ‘Case_AcquisitionInfo’, ‘Outbreak_Related’. Also due to changes in data availability, the variable ‘Outcome1’ will be equal to ‘Fatal’ (deaths due to COVID-19) or blank (all other cases) The methodology used to count COVID-19 deaths has changed to exclude deaths not caused by COVID. This impacts data captured in the column ‘‘Outcome1’ starting with data posted to the catalogue on March 11, 2022. CCM is a dynamic disease reporting system which allows ongoing update to data previously entered. As a result, data extracted from CCM represents a snapshot at the time of extraction and may differ from previous or subsequent results. Public Health Units continually clean up COVID-19 data, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes and current totals being different from previously reported cases and deaths. Observed trends over time should be interpreted with caution for the most recent period due to reporting and/or data entry lags. ##Related dataset(s) * Status of COVID-19 cases in Ontario

This dataset compiles daily snapshots of publicly reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Data includes: * date * OH region * current hospitalizations with COVID-19 * current patients in Intensive Care Units (ICUs) due to COVID-related critical Illness * current patients in Intensive Care Units (ICUs) testing positive for COVID * current patients in Intensive Care Units (ICUs) no longer testing positive for COVID * current patients in Intensive Care Units (ICUs) on ventilators due to COVID-related critical illness * current patients in Intensive Care Units (ICUs) on ventilators testing positive for COVID * current patients in Intensive Care Units (ICUs) on ventilators no longer testing positive for COVID **Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool ** ##Additional notes Data for the period of October 24, 2023 to March 24, 2024 excludes hospitals in the West region who were experiencing data availability issues. Daily adult, pediatric, and neonatal patient ICU census data were impacted by technical issues between September 9 and October 20, 2023. As a result, when public reporting resumes on November 16, 2023, historical ICU data for this time period will be excluded. As of August 3, 2023, the data in this file has been updated to reflect that there are now six Ontario Health (OH) regions. This dataset is subject to change. Please review the daily epidemiologic summaries for information on variables, methodology, and technical considerations.

Status of COVID-19 cases in Ontario This dataset compiles daily snapshots of publicly reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Effective April 13, 2023, this dataset will be discontinued. The public can continue to access the data within this dataset in the following locations updated weekly on the Ontario Data Catalogue: * Ontario COVID-19 testing percent positive by age group * Confirmed positive cases of COVID-19 in Ontario * Ontario COVID-19 testing metrics by Public Health Unit (PHU) * Ontario COVID-19 testing percent positive by age group * COVID-19 cases in hospital and ICU, by Ontario Health (OH) region * Cumulative deaths (new methodology) * Deaths Involving COVID-19 by Fatality Type For information on Long-Term Care Home COVID-19 Data, please visit: Long-Term Care Home COVID-19 Data. Data includes: * reporting date * daily tests completed * total tests completed * test outcomes * total case outcomes (resolutions and deaths) * current tests under investigation * current hospitalizations * current patients in Intensive Care Units (ICUs) due to COVID-related critical Illness * current patients in Intensive Care Units (ICUs) testing positive for COVID-19 * current patients in Intensive Care Units (ICUs) no longer testing positive for COVID-19 * current patients in Intensive Care Units (ICUs) on ventilators due to COVID-related critical illness * current patients in Intensive Care Units (ICUs) on ventilators testing positive for COVID-19 * current patients in Intensive Care Units (ICUs) on ventilators no longer testing positive for COVID-19 * Long-Term Care (LTC) resident and worker COVID-19 case and death totals * Variants of Concern case totals * number of new deaths reported (occurred in the last month) * number of historical deaths reported (occurred more than one month ago) * change in number of cases from previous day by Public Health Unit (PHU). This dataset is subject to change. Please review the daily epidemiologic summaries for information on variables, methodology, and technical considerations. ##Cumulative Deaths **Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool ** The methodology used to count COVID-19 deaths has changed to exclude deaths not caused by COVID. This impacts data captured in the columns “Deaths”, “Deaths_Data_Cleaning” and “newly_reported_deaths” starting with data for March 11, 2022. A new column has been added to the file “Deaths_New_Methodology” which represents the methodological change. The method used to count COVID-19 deaths has changed, effective December 1, 2022. Prior to December 1, 2022, deaths were counted based on the date the death was updated in the public health unit’s system. Going forward, deaths are counted on the date they occurred. On November 30, 2023 the count of COVID-19 deaths was updated to include missing historical deaths from January 15, 2020 to March 31, 2023. A small number of COVID deaths (less than 20) do not have recorded death date and will be excluded from this file. CCM is a dynamic disease reporting system which allows ongoing update to data previously entered. As a result, data extracted from CCM represents a snapshot at the time of extraction and may differ from previous or subsequent results. Public Health Units continually clean up COVID-19 data, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes and current totals being different from previously reported cases and deaths. Observed trends over time should be interpreted with caution for the most recent period due to reporting and/or data entry lags. ##Related dataset(s) * Confirmed positive cases of COVID-19 in Ontario

**Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool ** As of January 26, 2023, the population counts are based on Statistics Canada’s 2021 estimates. The coverage methodology has been revised to calculate age based on the current date and deceased individuals are no longer included. The method used to count daily dose administrations has changed is now based on the date delivered versus the day entered into the data system. Historical data has been updated. Please note that Cases by Vaccination Status data will no longer be published as of June 30, 2022. Please note that case rates by vaccination status and age group data will no longer be published as of July 13, 2022. Please note that Hospitalization by Vaccination Status data will no longer be published as of June 30, 2022. Learn more about COVID-19 vaccines. ##Data includes: * daily and total doses administered * individuals with at least one dose * individuals fully vaccinated * total doses given to fully vaccinated individuals * vaccinations by age * percentage of age group * individuals with at least one dose, by PHU, by age group * individuals fully vaccinated, by PHU, by age group * COVID-19 cases by status: not fully vaccinated, fully vaccinated, vaccinated with booster * individuals in hospital due to COVID-19 (excluding ICU) by status: unvaccinated, partially vaccinated, fully vaccinated * individuals in ICU due to COVID-19 by status: unvaccinated, partially vaccinated, fully vaccinated, unknown * rate of COVID-19 cases per 100,000 by status and age group * rate per 100,000 (7-day average) by status and age group All data reflects totals from 8 p.m. the previous day. This dataset is subject to change. Additional notes * Data entry of vaccination records is still in progress, therefore the dosage data may not be a full representation of all vaccination doses administered in Ontario. * The data does not include dosage data where consent was not provided for vaccination records to be entered into the provincial CoVax system. This includes individual records as well as records from some Indigenous communities where those communities have not consented to including vaccination information into CoVax. ##Hospitalizations and cases by vaccination status Hospitalizations * This is a new data collection and the data quality will continue to improve as hospitals continue to submit data. * In order to understand the vaccination status of patients currently hospitalized, a new data collection process was developed and this may cause discrepancies between other hospitalization numbers being collected using a different data collection process. * Data on patients in ICU are being collected from two different data sources with different extraction times and public reporting cycles. The existing data source (Critical Care Information System, CCIS) does not have vaccination status. * Historical data for hospitalizations by region may change over time as hospitals update previously entered data. * Due to incomplete weekend and holiday reporting, vaccination status data for hospital and ICU admissions is not updated on Sundays, Mondays and the day after holidays * Unvaccinated is defined as not having any dose, or between 0-13 days after administration of the first dose of a COVID-19 vaccine. * Partially vaccinated is defined as 14 days or more after the first dose of a 2-dose series COVID-19 vaccine, or between 0-13 days after administration of the second dose * Fully vaccinated is defined as 14 days or more after receipt of the second dose of a 2-dose series COVID-19 vaccine Cases * The cases by vaccination status may not match the daily COVID-19 case count because records with a missing or invalid health card number cannot be linked.

Effective June 7th, 2024, this dataset will no longer be updated.This file contains data for the last 6 weeks on: Weekly counts and rates of Ottawa residents with laboratory-confirmed COVID-19 by episode date (i.e. the earliest of symptom onset, testing or reported date) and age. Weekly counts and rates of Ottawa residents with laboratory-confirmed COVID-19 by reported date. Data are from the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM).

Accuracy: Points of consideration for interpretation of the data: Data are entered into and extracted by Ottawa Public Health from the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM). The COD is a dynamic disease reporting system that allows for ongoing updates; data represent a snapshot at the time of extraction and may differ from previous or subsequent reports.As the cases are investigated and more information is available, the dates are updated. A person’s exposure may have occurred up to 14 days prior to onset of symptoms. Symptomatic cases occurring in approximately the last 14 days are likely under-reported due to the time for individuals to seek medical assessment, availability of testing, and receipt of test results.Confirmed cases are those with a confirmed COVID-19 laboratory result as per the Ministry of Health Public health management of cases and contacts of COVID-19 in Ontario. March 25, 2020 version 6.0.Counts will be subject to varying degrees of underreporting due to a variety of factors, such as disease awareness and medical care seeking behaviours, which may depend on severity of illness, clinical practice, changes in laboratory testing, and reporting behaviours.Surveillance testing for COVID-19 began in long term care facilities on April 25, 2020. Update Frequency: Tuesdays and Fridays

Attributes: Data fields: Week – Date of the first day of the episode week (i.e. the week during which the case first developed symptom, got tested or was reported to OPH – whichever was earliest). Date in format YYYY-MM-DD H:MM. Weekly Rate of COVID-19 by 20-year Age Groupings (per 100,000 pop) and Episode Date – The number of Ottawa residents with confirmed COVID-19 within an age group (e.g. 0-9 years) divided by the total Ottawa population for that age group. This fraction is then multiplied by 100,000 to get a rate of COVID-19 per 100,000 population for that age group.Weekly Total of Cases by Episode Date - number of Ottawa residents with laboratory-confirmed COVID-19 by episode date.Weekly Total of Cases by Reported Date – number of Ottawa residents with laboratory-confirmed COVID-19 by reported date.Weekly Rate of COVID-19 (per 100,000 pop) by Reported Date – number of Ottawa residents with laboratory-confirmed COVID-19 by reported date divided by the total Ottawa population and multiplied by 100,000. Contact: OPH Epidemiology Team | Epidemiology & Evidence, Ottawa Public Health

As of April 15, 2023, there had been over 4.65 million confirmed cases of COVID-19 in Canada. As of this date, the coronavirus had been confirmed in every province and territory, with the province of Ontario having the highest number of confirmed cases.

COVID-19 vaccinations in Canada There have now been seven COVID-19 vaccines approved for use in Canada, the most widely distributed of which is manufactured by Pfizer and BioNTech. Around 63 million doses of the Pfizer/BioNTech vaccine have been distributed across Canada. As of January 1, 2023, around 83 percent of the population in Canada had received at least one COVID-19 vaccination dose.

This dataset compiles daily snapshots of publicly reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. Data includes: * reporting date * reporting Public Health Unit (PHU) * case outcomes (active, resolutions and deaths) The last update of this file will occur on Thursday December 1, 2022. For more information about COVID-19 cases and deaths by public health unit, please consult the Public Health Ontario COVID-19 data tool The methodology used to count COVID-19 deaths has changed to exclude deaths not caused by COVID. This impacts data captured in the columns “RESOLVED_CASES” and “DEATHS” starting with the file posted on March 11, 2022. Two new columns have been added to the file “ARCHIVED_RESOLVED_CASES” and “ARCHIVED_DEATHS” which represent the data that were posted publicly prior to the methodological change. This dataset is subject to change. Please review the daily epidemiologic summaries for information on variables, methodology, and technical considerations.

As of April 15, 2023, there had been a total of around 51,921 deaths attributed to COVID-19 in Canada. As of this time, every province and territory has reported deaths, with Quebec and Ontario reporting the highest numbers.

COVID-19 in Canada Canada has recorded almost 4.65 million coronavirus cases since the first infection in the country was confirmed on January 25, 2020. The number of cases by province shows that Ontario and Quebec have been the most severely affected. The number of daily new cases reached record highs at the end of 2021 and began to decrease as spring arrived in 2022.

COVID-19 vaccinations in Canada Seven COVID-19 vaccines have now been approved for use in Canada and vaccines are widely available. As of January 1, 2023 around 83 percent of the Canadian population had received at least one dose of a COVID-19 vaccine. The provinces with the highest share of people fully vaccinated against COVID-19 are Newfoundland and Labrador and Nova Scotia. However, Ontario and Quebec are the provinces with the highest total number of people vaccinated.

Dataset

This dataset was created by Penny Li

Contents

Every day, schools, child care centres and licensed home child care agencies report to the Ministry of Education on children, students and staff that have positive cases of COVID-19. If there is a discrepancy between numbers reported here and those reported publicly by a Public Health Unit, please consider the number reported by the Public Health Unit to be the most up-to-date. Licensed child care centres and home child care agencies report when a centre or home is closed to the Ministry of Education, using the Child Care Licensing System. Data is taken from the system at 12:00 pm the previous day. This dataset is subject to change. Data is only updated on weekdays excluding provincial holidays Effective June 15, 2022, board and school staff will not be expected to report student/staff absences and closures in the Absence Reporting Tool. The ministry will no longer report absence rates or school/child care closures on Ontario.ca for the remainder of the school year. Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak. ##Summary of cases in licensed child care settings This report provides a summary of COVID-19 activity in: * licensed child care centres * home child care agencies Data includes : * Child care centres and homes with confirmed cases * Child-care related child cases * Child-care related staff cases * Centres closed * Homes closed * Current number of centres with a reported case * Current number of centres closed Note: In some instances the type of cases are not identified due to privacy considerations. ##Licensed child care centres and agencies with active COVID-19 cases This report lists child care centres and home child care agencies that currently have active cases of COVID-19. Data includes : * Child care centre or home child care agency * Municipality * Confirmed child cases * Confirmed staff/provider cases * Total confirmed cases Note: Total number of confirmed cases may include other people (e.g., parents, other people who live at a home child care location), so the number of confirmed cases of children and staff may not equal the total number of confirmed cases.

This dataset reports the daily reported number of the 7-day moving average rates of Deaths involving COVID-19 by vaccination status and by age group.

Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak.

Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool

Data includes:

• Date on which the death occurred
• Age group
• 7-day moving average of the last seven days of the death rate per 100,000 for those not fully vaccinated
• 7-day moving average of the last seven days of the death rate per 100,000 for those fully vaccinated
• 7-day moving average of the last seven days of the death rate per 100,000 for those vaccinated with at least one booster

Additional notes

As of June 16, all COVID-19 datasets will be updated weekly on Thursdays by 2pm.

As of January 12, 2024, data from the date of January 1, 2024 onwards reflect updated population estimates. This update specifically impacts data for the 'not fully vaccinated' category.

On November 30, 2023 the count of COVID-19 deaths was updated to include missing historical deaths from January 15, 2020 to March 31, 2023.

CCM is a dynamic disease reporting system which allows ongoing update to data previously entered. As a result, data extracted from CCM represents a snapshot at the time of extraction and may differ from previous or subsequent results. Public Health Units continually clean up COVID-19 data, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes and current totals being different from previously reported cases and deaths. Observed trends over time should be interpreted with caution for the most recent period due to reporting and/or data entry lags.

The data does not include vaccination data for people who did not provide consent for vaccination records to be entered into the provincial COVaxON system. This includes individual records as well as records from some Indigenous communities where those communities have not consented to including vaccination information in COVaxON.

“Not fully vaccinated” category includes people with no vaccine and one dose of double-dose vaccine. “People with one dose of double-dose vaccine” category has a small and constantly changing number. The combination will stabilize the results.

Spikes, negative numbers and other data anomalies: Due to ongoing data entry and data quality assurance activities in Case and Contact Management system (CCM) file, Public Health Units continually clean up COVID-19, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes, negative numbers and current totals being different from previously reported case and death counts.

Public Health Units report cause of death in the CCM based on information available to them at the time of reporting and in accordance with definitions provided by Public Health Ontario. The medical certificate of death is the official record and the cause of death could be different.

Deaths are defined per the outcome field in CCM marked as “Fatal”. Deaths in COVID-19 cases identified as unrelated to COVID-19 are not included in the Deaths involving COVID-19 reported.

Rates for the most recent days are subject to reporting lags

All data reflects totals from 8 p.m. the previous day.

This dataset is subject to change.

This dataset is no longer updated This dataset compiles daily snapshots of reported data on 2019 Novel Coronavirus (COVID-19) testing in Ontario's Provincial Correctional Institutions. Data includes: * reporting date * institution name * confirmed cases Staff data is not included. Data is only updated on weekdays excluding provincial holidays This dataset is subject to change. ##Related dataset(s) * COVID-19 testing of inmates in Ontario’s Provincial Correctional Institutions * Ontario’s Provincial Correctional Institution locations

Summary of COVID-19 outbreaks in Ottawa healthcare, childcare and educational establishments, based on the most up to date information available in the the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM) .

Accuracy: Points of consideration for interpretation of the data: The data was extracted by Ottawa Public Health from the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM) . The CCM is a dynamic disease reporting system that allows for ongoing updates to data previously entered. The data extracted from The CCM represent a snapshot at the time of extraction and may differ in previous or subsequent reports.Data are for confirmed outbreaks and the number of staff, living in Ottawa, and residents/patients/students with laboratory confirmed COVID-19 associated to each outbreak is provided. Please note, individuals may be linked to multiple outbreaks. All the outbreaks reflect the outbreak definitions at the time they were declared open:Healthcare Institutions: From April 1st 2020, 1 staff or resident case of laboratory-confirmed COVID-19 is considered an outbreak in long-term care homes (LTCH), retirement homes (RH) and other healthcare institutions (e.g. group home, assisted living, group shelter) and declared facility wide. Starting May 10th 2020, 2 staff or patient cases of laboratory-confirmed COVID-19 within a specified hospital unit within a 14-day period where both cases could have reasonably acquired their infection in hospital is considered an outbreak in a public hospital.Childcare & Education: Starting July 2020, 1 child or staff (or household member) case of laboratory-confirmed COVID-19 is considered an outbreak in a childcare establishment. Starting August 26 2020, 2 student or staff (or visitor) cases of laboratory-confirmed COVID-19 within a specified class within a 14-day period where at least one case could have reasonably acquired their infection at school (including transportation and before/after school care) is considered an outbreak in an educational establishment. Update Frequency: Tuesdays and Fridays

Attributes: Data fields: Facility Name – textType of Facility - textLocation in Facility – textReported Date – date the COVID-19 outbreak was openedEnd Date - date the COVID-19 outbreak was closedResident/Patient/Child/Student Cases – number of residents, patients, children, or students with confirmed COVID-19Resident/Patient/Child/Student Cases – number of residents, patients, children, or students with confirmed COVID-19 who diedStaff Cases – number of staff with confirmed COVID-19Staff Deaths – number of staff with confirmed COVID-19 who diedTotal Cases – total number of people with confirmed COVID-19Total Deaths – total number of people with confirmed COVID-19 who died Contact: OPH Epidemiology Team | Epidemiology & Evidence, Ottawa Public Health

This is the Zenodo archive for the manuscript "Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada" (Mucaki EJ, Shirley BC and Rogan PK. F1000Research 2021, 10:1312, DOI: 10.12688/f1000research.75891.1). This study aimed to produce community-level geo-spatial mapping of patterns and clusters of symptoms, and of confirmed COVID-19 cases, in near real-time in order to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals. This archive will contain data and image files from this study, which were too numerous to be included in the manuscript for this study. It also provides all program files pertaining to the Geostatistical Epidemiology Toolbox (Geostatistical analysis software package to be used in ArcGIS), as well as all other scripts described in this manuscript and other software developed (cluster, outlier, streak identification and pairing)..

We also provide a guide which provides a general description of the contents of the four sections in this archive (Documentation_for_Sections_of_Zenodo_Archive.docx). If you have any intent to utilize the data provided in Section 3, we greatly advise you to review this document as it describes the output of all geostatistical analyses performed in this study in detail.

Data Files:

Section 1. "Section_1.Tables_S1_S7.Figures_S1_S11.zip"

This section contains all additional tables and figures described in the manuscript "Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada". Additional tables S1 to S7 are presented in an Excel document. These 7 tables provide summary statistics of various geostatistical tests described in the study (“Section 1 – Tables S1-S4”) and lists all identified single and paired high-case cluster streaks (“Section 1 – Tables S5-S7”). This section also contains 11 additional figures referred to in the manuscript (“Section 1 – Figures S1-S11”) both individually and within a Word document which describes them.

Section 2. "Section_2.Localized_Hotspot_Lists.zip"

All localized hotspots (identified through kriging analysis) were catalogued for each municipality evaluated (Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, Windsor/Essex). These files indicate the FSA in which the hotspot was identified, the date in which it was identified (utilizing 3-day case data at the postal code level), the amount of cases which occurred within the FSA within these 3 dates, the range of cases interpolated by kriging analysis (between 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-50, >50), and whether or not the FSA was deemed a hotspot by Gi* relative to the rest of Ontario on any of the three dates evaluated. Please see Section 4 for map images of these localized hotspots.

Section 3. "Section_3.All-Data_Files.Kriging_GiStar_Local_and_GlobalMorans.2020_2021"

Section 3 – All output files from the geostatistical tests performed in this study are provided in this section. This includes the output from Ontario-wide FSA-level Gi* and Cluster and Outlier analyses, and PC-level Cluster and Outlier, Spatial Autocorrelation, and kriging analysis of 6 municipal regions. It also includes kriging analysis of 7 other municipal regions adjacent to Toronto (Ajax, Brampton, Markham, Mississauga, Pickering, Richmond Hill and Vaughan). This section also provides data files from our analyses of stratified case data (by age, gender, and at-risk condition). All coordinates presented in these data files are given in “PCS_Lambert_Conformal_Conic” format. Case values between 1-5 were masked (appear as “NA”).

Section 4. "Section_4.All_Map_Images_of_Geostat_Analyses.zip"

Sets of image files which map the results of our geostatistical analyses onto a map of Ontario or within the municipalities evaluated (Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, Windsor/Essex) are provided. This includes: Kriging analysis (PC-level), Local Moran's I cluster and outlier analysis (FSA and PC-level), normal and space-time Gi* analysis, and all images for all analyses performed on stratified data (by age, gender and at-risk condition). Kriging contour maps are also included for 7 other municipal regions adjacent to Toronto (Ajax, Brampton, Markham, Mississauga, Pickering, Richmond Hill and Vaughan).

Software:

This Zenodo archive also provides all program files pertaining to the Geostatistical Epidemiology Toolbox (Geostatistical analysis software package to be used in ArcGIS), as well as all other scripts described in this manuscript. This geostatistical toolbox was developed by CytoGnomix Inc., London ON, Canada and is distributed freely under the terms of the GNU General Public License v3.0. It can be easily modified to accommodate other Canadian provinces and, with some additional effort, other countries.

This distribution of the Geostatistical Epidemiology Toolbox does not include postal code (PC) boundary files (which are required for some of the tools included in the toolbox). The PC boundary shapefiles used to test the toolbox were obtained from DMTI (https://www.dmtispatial.com/canmap/) through the Scholar's Geoportal at the University of Western Ontario (http://geo2.scholarsportal.info/). The distribution of these files (through sharing, sale, donation, transfer, or exchange) is strictly prohibited. However, any equivalent PC boundary shape file should suffice, provided it contains polygon boundaries representing postal code regions (see guide for more details).

Software File 1. "Software.GeostatisticalEpidemiologyToolbox.zip"

The Geostatistical Epidemiology Toolbox is a set of custom Python-based geoprocessing tools which function as any built-in tool in the ArcGIS system. This toolbox implements data preprocessing, geostatistical analysis and post-processing software developed to evaluate the distribution and progression of COVID-19 cases in Canada. The purpose of developing this toolbox is to allow external users without programming knowledge to utilize the software scripts which generated our analyses and was intended to be used to evaluate Canadian datasets. While the toolbox was developed for evaluating the distribution of COVID-19, it could be utilized for other purposes.

The toolbox was developed to evaluate statistically significant distributions of COVID-19 case data at Canadian Forward Sortation Area (FSA) and Postal Code-level in the province of Ontario utilizing geostatistical tools available through the ArcGIS system. These tools include: 1) Standard Gi* analysis (finds areas where cases are significantly spatially clustered), 2) spacetime based Gi* analysis (finds areas where cases are both spatially and temporally clustered), 3) cluster and outlier analysis (determines if high case regions are an regional outlier or part of a case cluster), 4) spatial autocorrelation (determines the cases in a region are clustered overall) and, 5) Empirical Bayesian Kriging analysis (creates contour maps which define the interpolation of COVID-19 cases in measured and unmeasured areas). Post-processing tools are included that import these all of the preceding results into the ArcGIS system and automatically generate PNG images.

This archive also includes a guide ("UserManual_GeostatisticalEpidemiologyToolbox_CytoGnomix.pdf") which describes in detail how to set up the toolbox, how to format input case data, and how to use each tool (describing both the relevant input parameters and the structure of the resultant output files).

Software File 2: “Software.Additional_Programs_for_Cluster_Outlier_Streak_Idendification_and_Pairing.zip"

In the manuscript associated with this archive, Perl scripts were utilized to evaluate postal code-level Cluster and Outlier analysis to identify significantly, highly clustered postal codes over consecutive periods (i.e., high-case cluster “streaks”). The identified streaks are then paired to those in close proximity, based on the neighbors of each postal code from PC centroid data ("paired streaks"). Multinomial logistic regression models were then derived in the R programming language to measure the correlation between the number of cases reported in each paired streak, the interval of time separating each streak, and the physical distance between the two postal codes. Here, we provide the 3 Perl scripts and the R markdown file which perform these tasks:

“Ontario_City_Closest_Postal_Code_Identification.pl”

Using an input file with postal code coordinates (by centroid), this program identifies the nearest neighbors to all postal codes for a given municipal region (the name of this region is entered on the command line). Postal code centroids were calculated in ArcGIS using the “Calculate Geometry” function against DMTI postal code boundary files (not provided). Input from other sources could be used, however, as long as the input includes a list of coordinates with a unique label associated with a particular municipality.

The output of this program (for the same municipal region being evaluated) is required for the following two Perl

Summary of COVID-19 community outbreaks in Ottawa based on the most up to date information available in the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM).

Accuracy: Points of consideration for interpretation of the data:

• The data was extracted by Ottawa Public Health from the Ontario Ministry of Health Public Health Case and Contact Management Solution (CCM). The CCM is a dynamic disease reporting system that allows for ongoing updates to data previously entered. The data extracted from The CCM represent a snapshot at the time of extraction and may differ in previous or subsequent reports.

• Data are for confirmed outbreaks and the number Ottawa residents with laboratory confirmed COVID-19 associated to each outbreak is provided. Please note, individuals may be linked to multiple outbreaks.

• All the outbreaks reflect the outbreak definitions at the time they were declared open:

o Community: From April 1st 2020, 2 or more laboratory-confirmed COVID-19 cases with an epidemiological link in the setting within a 14-day period where at least 2 cases could have reasonably acquired their infection in the setting. Examples of epidemiological links in community settings include community organization (e.g. attended same social or volunteer club meeting), religious/spiritual organization (e.g. attended same service), residential (e.g. multi-unit dwelling - from different households in the same apartment building but rode the elevator together, used a common room at the same time), social event (e.g. attended same one-time party, wedding or funeral together), sports and recreation (e.g. attended same sports team practice or fitness class), or workplace (e.g. same work area, same shift).

• Public health is only required to formally declare outbreaks for workplace community settings but has chosen to declare outbreaks in other community settings when there is more risk to the public, there are challenges in contact tracing and/or capacity allows. Since October 2020, OPH has systematically reported outbreaks in other community settings. Please see the definitions for community outbreaks posted on the OPH COVID-19 Dashboard web page for more information.

Attributes: Data fields:

• Outbreak ID

• Setting - text

• Sub-category - text

• Start Date - outbreak start date

• End Date – outbreak end date

• Cases – total number of people with confirmed COVID-19 linked to the outbreak

• Deaths – total number of people with confirmed COVID-19 linked to the outbreak who died

Update Frequency: Daily

Contact: OPH Epidemiology Team

As of May 2, 2023, of 34,206 COVID-19 cases deceased in Canada, around 4,058 were aged 60 to 69 years. This statistic shows the number of COVID-19 deaths in Canada as of May 2, 2023, by age.

This dataset reports the daily reported number of deaths involving COVID-19 by fatality type.

Learn how the Government of Ontario is helping to keep Ontarians safe during the 2019 Novel Coronavirus outbreak.

Effective November 14, 2024 this page will no longer be updated. Information about COVID-19 and other respiratory viruses is available on Public Health Ontario’s interactive respiratory virus tool: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool

Data includes:

• Date on which the death occurred
• Total number of deaths involving COVID-19
• Number of deaths with “COVID-19 as the underlying cause of death”
• Number of deaths with “COVID-19 contributed but not underlying cause”
• Number of deaths where the “Cause of death unknown” or “Cause of death missing”

Additional Notes

The method used to count COVID-19 deaths has changed, effective December 1, 2022. Prior to December 1 2022, deaths were counted based on the date the death was updated in the public health unit’s system. Going forward, deaths are counted on the date they occurred.

On November 30, 2023 the count of COVID-19 deaths was updated to include missing historical deaths from January 15, 2020 to March 31, 2023.

CCM is a dynamic disease reporting system which allows ongoing update to data previously entered. As a result, data extracted from CCM represents a snapshot at the time of extraction and may differ from previous or subsequent results. Public Health Units continually clean up COVID-19 data, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes and current totals being different from previously reported cases and deaths. Observed trends over time should be interpreted with caution for the most recent period due to reporting and/or data entry lags.

As of December 1, 2022, data are based on the date on which the death occurred. This reporting method differs from the prior method which is based on net change in COVID-19 deaths reported day over day.

Data are based on net change in COVID-19 deaths for which COVID-19 caused the death reported day over day. Deaths are not reported by the date on which death happened as reporting may include deaths that happened on previous dates.

Spikes, negative numbers and other data anomalies: Due to ongoing data entry and data quality assurance activities in Case and Contact Management system (CCM) file, Public Health Units continually clean up COVID-19, correcting for missing or overcounted cases and deaths. These corrections can result in data spikes, negative numbers and current totals being different from previously reported case and death counts.

Public Health Units report cause of death in the CCM based on information available to them at the time of reporting and in accordance with definitions provided by Public Health Ontario. The medical certificate of death is the official record and the cause of death could be different.

Deaths are defined per the outcome field in CCM marked as “Fatal”. Deaths in COVID-19 cases identified as unrelated to COVID-19 are not included in the number of deaths involving COVID-19 reported.

"_Cause of death unknown_" is the category of death for COVID-19 positive individuals with cause of death still under investigation, or for which the public health unit was unable to determine cause of death. The category may change later when the cause of death is confirmed either as “COVID-19 as the underlying cause of death”, “COVID-19 contributed but not underlying cause,” or “COVID-19 unrelated”.

"_Cause of death missing_" is the category of death for COVID-19 positive individuals with the cause of death missing in CCM.

Rates for the most recent days are subject to reporting lags

All data reflects totals from 8 p.m. the previous day.

This dataset is subject to change.

This data set contains a compiled list of the best available information on individual COVID-19 Case details. Data from a number of sources are merged with consistent field names and content. Age information is binned into large age ranges. Regional Health district names are aligned with those used in other data sets on this hub. Data Sources:The data comes from multiple sources and is combined. Where a provincial source is available (e.g. BC, AB & ON) we use that. Where there is not, we use the data curated by the COVID-19 Canada Open Data Working Group.Here are the URLs the individual datasets have been pulled from:Ontario:https://data.ontario.ca/dataset/f4112442-bdc8-45d2-be3c-12efae72fb27/resource/455fd63b-603d-4608-8216-7d8647f43350/download/conposcovidloc.csvhttps://data.ontario.ca/dataset/confirmed-positive-cases-of-covid-19-in-ontarioBC:https://www.bccdc.ca/Health-Info-Site/Documents/BCCDC_COVID19_Dashboard_Case_Details.csvhttps://www.bccdc.ca/health-info/diseases-conditions/covid-19/dataAlberta:https://covid19stats.alberta.ca/Everywhere else (COVID-19 Canada Open Data Working Group): https://raw.githubusercontent.com/ishaberry/Covid19Canada/master/cases.csvhttps://github.com/ishaberry/Covid19CanadaOther Notes:The Latitude and Longitude in the table are the cartographic centroid of the reported region (they are not patient locations). So, spatially you can have a large number of points stacked on top of one another.Data is updated every 24 hours, between 11:00PM and midnight (EST) each day.Many provinces do not report case detailCOVID-19 Canada Open Data Working Group Citation:Berry I, Soucy J-PR, Tuite A, Fisman D. Open access epidemiologic data and an interactive dashboard to monitor the COVID-19 outbreak in Canada. CMAJ. 2020 Apr 14;192(15):E420. doi: https://doi.org/10.1503/cmaj.75262Licensed under the Creative Commons Attribution 4.0 International: https://raw.githubusercontent.com/ishaberry/Covid19Canada/master/LICENSE.MD

Daily number of Ottawa residents tested for COVID-19 and the percentage of residents tested with laboratory-confirmed COVID-19. Data are based on information extracted from the Ontario Laboratories Information System (OLIS) on Monday, Wednesday, and Friday.

Accuracy: Points of consideration for interpretation of the data: Not all labs report to OLIS and only patients with health card numbers are included in the OLIS dataset.Once an individual is confirmed positive, subsequent tests for that individual are excluded from the daily totals.Duplicate tests are excluded from the total number of positive tests, including those that arose from multiple tests of cure. Results for patients who placed an OLIS consent block (~50 records province-wide) are excluded.Staff working in long-term care homes are not captured in OLIS.City assignment in OLIS is based on the patient's health card address. Patients living in long-term care homes may not have the correct address associated with their health cards; therefore, not all tests in long-term care homes may be captured.Confirmed cases are those with a confirmed COVID-19 laboratory result as per the Ministry of Health Public health management of cases and contacts of COVID-19 in Ontario. March 25, 2020 version 6.0.The province has had to limit testing to priority groups in the early stages of the pandemic. Since only a small fraction of all the persons who were infected with the COVID-19 virus were tested, the number of reported confirmed community cases underestimates the actual number of infections. Information on overall infection rates in Canada will not be available until large studies on COVID-19 antibody presence in blood serum are conducted. Based on available information, the actual number of infections may lie from 5 to 30 times or more than the reported number of cases (1).Surveillance testing for COVID-19 began in long term care facilities on April 25, 2020. Reference: Richterich P. Severe underestimation of COVID-19 case numbers: Effect of epidemic growth rate and test restrictions. medRxiv. April 2020: 2020.04.13. doi.org/10.1101/2020.04.13.20064220 Update Frequency: Tuesdays and Fridays Attributes: Data fields: Date – date of the test (YYYY-MM-DD).Number of tests – number of Ottawa residents tested for COVID-19Daily % Positivity – number of Ottawa residents tested on that day that received a positive test result for COVID-19 divided by the total number of Ottawa residents tested on that dayNumber of tests in LTCH– number of Ottawa residents in long-term care homes who were tested for COVID-19LTCH Daily % Positivity – number of Ottawa residents in long-term care homes tested on that day that received a positive test result for COVID-19 divided by the total number of Ottawa residents in long-term care homes tested on that day Contact: OPH Epidemiology Team | Epidemiology & Evidence, Ottawa Public Health