Covid-19 test results
The Second Generation Surveillance System (SGSS) is an application that stores and manages data on laboratory isolates and notifications, and is the preferred method for capturing routine laboratory surveillance data on infectious diseases and antimicrobial resistance from laboratories across England. -- PHE Laboratory Reporting Guidelines, page 6
SGSS data currently available in OpenSAFELY is for SARS-COV-2 test results from the UK's Pillar 1 and Pillar 2 tests. Some SARS-CoV-2 testing info also flows directly into the primary care record from SGSS (see below).
Metadata🔗
- Data provider Public Health England
- Participation / Coverage Unclear, and varies over time
- Provenance PHE and NHS hospital testing labs
- Update frequency in OpenSAFELY Approximately monthly
- Delay between event occurring and event appearing in OpenSAFELY Approximately 1-2 weeks.
- Collected information Earliest specimen date, lab report date, age, sex, county, test result, source ("pillar 2" or "other")
Overview🔗
SGSS contains information on patients receiving a swab test for SARS-CoV-2, from Pillar 1 (NHS and PHE labs) and Pillar 2 (commercial partners).
It includes "earliest specimen date" (when the sample was taken); "lab report date" (when the result was uploaded to SGSS system); pillar 2 or "other"; result (pos/neg); some demographics.
The are two tables, one for positive tests and one for negative tests.
Multiple tests for the same person are treated as a single 'infection episode', no matter how far apart, and so the system will only return the earliest test (sample date and report date), and all subsequent tests are dropped. 'Infection episodes' are split by test results, so SGSS will in theory return data for both the earliest positive test, and the earliest negative test. However, negative testing data appears to be incomplete. Other viruses/organisms may have a finite episode length, so that any tests occurring within say the first 14 days of the first test are dropped, but for coronavirus the episode length is indefinite, though this may change in future.
Negative test data is unreliable — DO NOT USE
SARS-CoV-2 test results from various sources are also coded within SystmOne.