COVID-19 Data Holdings

On April 7, 2020, ICES started to receive daily feeds of COVID-19 test orders recorded in the Ontario Laboratories Information System (OLIS) from Ontario Health Digital Services (OHDS). The data received are a minimum dataset extracted from lab orders with COVID-19-specific test request (TR) codes or Logical Observation Identifiers Names and Codes (LOINC) and other TR/LOINC codes indicative of viral or respiratory virus testing. Cleaning, parsing and aggregating of the OLIS COVID-19 data was conducted using Python scripts created at ICES. The scripts process the OHDS original minimum dataset into two research-ready datasets by: 1) parsing lab results pertaining to SARS-CoV-2 and other respiratory viruses, and 2) rolling-up the COVID-19 lab results into more clinically relevant "testing episodes". The original minimum dataset received from OHDS contains identifiers to allow for linkage, in addition to test result information such as patient IDs, order IDs, lab names, TR codes, LOINC codes, test result release times, test result statuses, and test results in free-text. The recommended analytical dataset is derived by aggregating information from the minimum dataset by unique individual + testing date (i.e., testing episode), to represent the overall COVID-19 testing result status for each tested individual on each day. Variables included in this dataset include province, postal code, date of birth, sex, encrypted healthcard number, specimen collection date, result release date, whether a COVID test was done, COVID19 test result (Positive/Presumptive > Indeterminate > Negative > Pending > Cancelled > Rejected). Due to the time required for transportation and processing of specimens, it takes up to six days for approximately 95% of results to be finalized and reported for a given testing date. In other words, the larger the difference between when the dataset was received and the specimen collection date (observationdate), the more likely we have all the results for that specimen collection date.

The COVID-19 Integrated Testing Dataset is derived from 3 data sources: 1) Ontario Laboratories Information System (OLIS) contains COVID-19 testing episodes using standard PCR tests, from January 2020 to current; 2) Distributed testing data from laboratories (DL) within the COVID-19 Diagnostic Network, with results only up to April 13, 2020 (prior to a requirement to report all test results in OLIS, the results of tests performed by laboratories that were part of this network were compiled by PHO in a separate database); and 3) Public Health Case & Contact Management (CCM) Solution, formerly known as the integrated Public Health Information System (iPHIS), a client-level dataset (not testing episodes) for individuals who are confirmed positive for COVID-19 based on the provincial case definition, from January 2020 to current.

Vaccination data includes three separate tables containing vaccination, appointment, and screening information.

The purpose of the Vaccinations data is to provide a weekly update on the number and types of COVID-19 vaccinations that are provided in the province of Manitoba.

The purpose of the Appointments data is to collect and record the COVID-19 vaccination appointments made in the on-line system, including changes/cancellations to appointments.

The purpose of the Screening data is to collect and record screening data on the types of people being vaccinated and specific indicators that are under consideration.

Contains information on COVID-19 vaccination events, including: Date(s) of dose administration; Reason for administration (e.g., health care worker, long-term care resident, other priority groups); Vaccine product information (i.e., manufacturer, lot number, diluent); Location and responsible Public Health Unit for vaccination event; Client information (e.g., date of birth, demographics [age, sex], postal code of residence).

Data containing information on COVID-19 vaccinations for individuals receiving a dose of COVID-19 vaccine in Newfoundland and Labrador.

The Case and Contact Management System (CCM) is a central data repository for COVID-19 case and contact management, and reporting in Ontario. This information is used for local, provincial and national surveillance.