COVID-19 Phenotype Documentation, Version 4.0 (Last updated 3/11/2022)

Objective: To identify lab-confirmed, suspected, and possible cases of COVID-19, and demographically match (on age group, sex, race, and ethnicity) those cases to controls who have tested negative/equivocal for COVID-19, at a ratio of 1:2 (cases:controls).

Note: The phenotype is specifically designed to include criteria that would be queryable in most clinical common data models (CDMs), including OMOP, PCORnet, ACT, and TriNetX. This may not enable inclusion of certain criteria that would otherwise be available (e.g., in a local data warehouse), such as temperature, O2 sat measurements, isolation flags, and information gleaned from clinical notes.

• No age or demographic restrictions.
• Use 1/1/2020 as the start date.
• Patient must have:

  • ONE or more of the lab tests in the Labs table (below), with a positive result. (Different institutions use different terms/values for “positive”; see this article for more details.

    OR

  • ONE or more of the “Strong Positive” diagnosis codes from the ICD-10 or SNOMED tables (below)

    OR

  • TWO or more of the “Weak Positive” diagnosis codes from the ICD-10 or SNOMED tables (below) during the same encounter or on the same date, on or prior to 5/1/2020

• No age or demographic restrictions.
• Use 1/1/2020 as the start date.
• Patient must have ONE or more of the lab tests in the Labs table (below), with a non-positive result.
• Patient must NOT have qualified as a case.
• There must be at least 10 days between patient's minimum and maximum encounter date in the EHR. (Eliminates patients who have only been seen for a COVID test.)

This list has changed significantly from prior versions of the phenotype. As of Phenotype 4.0, we are no longer including labs with a quantitative result, as those labs would never match our “Positive” result criteria and just add to processing time unnecessarily. We also exclude panels, variants, lineage, SARS-related coronavirus tests not specific to SARS-CoV-2. Note that these excluded labs will still flow into N3C–they will just not be used as selection criteria.

**New ICD-10s added in this phenotype version

(“emergency codes” used as placeholders; only applies to OMOP)