| 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 number of individuals who tested positive in OLIS is ~90% of the cases reported by the Ministry of Health (who use the Integrated Public Health Information System (iPHIS)). Under-reporting may be due to a number of factors, including that early tests were performed at the National Microbiology Laboratory (in addition to Public Health Ontario); some hospital labs did not contribute all or part of their data to OLIS (e.g., Hospital for Sick Children performed tests in March but was not a reporting lab in OLIS until April 20, therefore OLIS likely underestimates the number of children tested); change in the responsibility for reporting of lab results into OLIS (e.g., miscommunication between ordering facility and performing laboratory as to who reports the final result to OLIS); unconsented records (~500 individuals); lab requisitions entered into OLIS without a health card number (HCN) or a medical record number (MRN) that would permit linkage. OHDS links HCNs to test results submitted to OLIS with an MRN if possible; however, as of July 31, 2020, OLIS records for ~4,000 individuals are not in the ICES data feed due to unresolved HCNs. |
