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Phenotype 2.2 (deprecated)
empfff edited this page Dec 2, 2020
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1 revision
Covid-19 Phenotype Documentation, Version 2.2 (Last updated 9/14/2020)
Objective: To identify lab-confirmed, suspected, and possible cases of covid-19.
This phenotype will capture patients in four “tiers”: “lab-confirmed positive,” “lab-confirmed negative,” “suspected positive,” and “possible positive.”
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.
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Changelog (from version 2.1)
- Some LOINC codes removed (see strikethroughs in LOINC table), due to the tests not being specific to SARS-CoV-2.
- One new OMOP-only code added
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Phenotype Inclusion Criteria:
- No age or demographic restrictions.
- Use 1/1/2020 as the start date.
- Patient must have:
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ONE or more of the lab tests in the Labs table (below), regardless of result (unless negative and accompanied by a Z11.59; see exclusions)
OR
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ONE or more of the “Strong Positive” diagnosis codes from the ICD-10 or SNOMED tables (below)
OR
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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
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Phenotype Exclusion Criteria:
- Patient was assigned code Z11.59 (viral screening code; used per CDC guidance to indicate asymptomatic covid screening) on or after 4/1/2020, and does NOT also have a record of a positive covid test or a “strong positive” diagnosis code.
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Phenotype Categories for Downstream Analytics and Data Quality Checking:
To identify “lab-confirmed positive cases”:
- Patient must have clear positive result from one or more of the labs listed in the Labs table, below.
To identify “lab-confirmed negative cases”:
- Patient must have a clear negative result from one or more of the labs listed in the Labs table, below.
Note: If patient has both a negative and a positive result within the timeframe of a single “run” of the phenotype, consider them a “lab-confirmed positive” case for the purpose of the phenotype, though both results will appear in the data for use in downstream analytics.
To identify “suspected positive” cases:
- Patient must not be in the “lab-confirmed positive” or “lab-confirmed negative” categories and must have one or more of the following:
- One or more of the “strong positive” diagnosis codes from the Diagnosis table below (ICD or SNOMED)
- OR Unclear (null, uncertain, or incomplete) result from one or more of the labs listed in the Labs table, below.
To identify “possible positive” cases:
- Patient must _not _be in the “lab-confirmed positive,” “lab-confirmed negative,” or “suspected positive” category and must have two or more different “weak positive” diagnosis codes from the Diagnosis table below (ICD or SNOMED), in the same encounter OR on the same date.
A patient should only be in one category at any given point in time but may move between categories. (E.g., a patient could be a “suspected positive” on Monday when their test is sent out and move to “lab-confirmed positive” by Friday when their test result comes back.)
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Labs
| LOINC Code | Name | Provenance |
| 94306-8 | SARS coronavirus 2 RNA panel, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94307-6 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94308-4 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94309-2 | SARS-CoV-2 RNA, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94311-8 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94312-6 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94314-2 | SARS-CoV-2 RdRp gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94316-7 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94500-6 | SARS-CoV-2 RNA, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94503-0 | SARS coronavirus 2 IgG and IgM panel, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94504-8 | SARS coronavirus 2 IgG and IgM panel, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94505-5 | SARS-CoV-2 IgG, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94506-3 | SARS-CoV-2 IgM, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94507-1 | SARS-CoV-2 IgG, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94508-9 | SARS-CoV-2 IgM, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
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| 94510-5 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94511-3 | SARS-CoV-2 ORF1ab region, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94531-1 | SARS coronavirus 2 RNA panel, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94533-7 | SARS-CoV-2 N gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94534-5 | SARS-CoV-2 RdRp gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94547-7 | SARS-CoV-2 IgG + IgM, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94558-4 | SARS-CoV-2 Ag, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94559-2 | SARS-CoV-2 ORF1ab region, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94562-6 | SARS-CoV-2 IgA, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94563-4 | SARS-CoV-2 IgG, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94564-2 | SARS-CoV-2 IgM, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94565-9 | SARS-CoV-2 RNA, nasopharyngeal specimen | https://loinc.org/sars-coronavirus-2/ |
| 94639-2 | SARS-CoV-2 ORF1ab region, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94640-0 | SARS-CoV-2 S gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94641-8 | SARS-CoV-2 S gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94642-6 | SARS-CoV-2 S gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94643-4 | SARS-CoV-2 S gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94644-2 | SARS-CoV-2 ORF1ab region, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94645-9 | SARS-CoV-2 RdRp gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94646-7 | SARS-CoV-2 RdRp gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94660-8 | SARS-CoV-2 RNA, serum/plasma | https://loinc.org/sars-coronavirus-2/ |
| 94661-6 | SARS-CoV-2 antibody interpretation | https://loinc.org/sars-coronavirus-2/ |
| 94720-0 | SARS-CoV-2 IgA, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94745-7 | SARS-CoV-2 RNA, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94746-5 | SARS-CoV-2 RNA, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94756-4 | SARS-CoV-2 N gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 94757-2 | SARS-CoV-2 N gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
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| 94759-8 | SARS-CoV-2 N overall result, nasopharyngeal specimen | https://loinc.org/sars-coronavirus-2/ |
| 94760-6 | SARS-CoV-2 N gene result, nasopharyngeal specimen | https://loinc.org/sars-coronavirus-2/ |
| 94761-4 | SARS-CoV-2 IgG Ab, DBS | https://loinc.org/sars-coronavirus-2/ |
| 94762-2 | SARS-CoV-2 Ab qualitative | https://loinc.org/sars-coronavirus-2/ |
| 94763-0 | SARS-CoV-2, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94764-8 | SARS-CoV-2 whole genome | https://loinc.org/sars-coronavirus-2/ |
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| 94766-3 | SARS-CoV-2 N gene, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94767-1 | SARS-CoV-2 S gene, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94768-9 | SARS-CoV-2 IgA, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94769-7 | SARS-CoV-2 IgA, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 94819-0 | SARS-CoV-2 N gene, unspecified specimen | https://loinc.org/sars-coronavirus-2/ |
| 94822-4 | SARS-CoV-2 RNA, saliva | https://loinc.org/sars-coronavirus-2/ |
| 94845-5 | SARS-CoV-2 RNA, saliva | https://loinc.org/sars-coronavirus-2/ |
| 95125-1 | SARS-CoV-2 RNA, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
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| 95406-5 | SARS-CoV-2 RNA, nose | https://loinc.org/sars-coronavirus-2/ |
| 95409-9 | SARS-CoV-2 N gene, nose | https://loinc.org/sars-coronavirus-2/ |
| 95410-7 | SARS-CoV-2 neutralizing antibody, serum | https://loinc.org/sars-coronavirus-2/ |
| 95411-5 | SARS-CoV-2 neutralizing antibody, serum | https://loinc.org/sars-coronavirus-2/ |
| 95416-4 | SARS-CoV-2 IgM Ab, DBS | https://loinc.org/sars-coronavirus-2/ |
| 95424-8 | SARS-CoV-2 RNA, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 95425-5 | SARS-CoV-2 N gene, saliva | https://loinc.org/sars-coronavirus-2/ |
| 95427-1 | SARS-CoV-2 IgA Ab, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 95428-9 | SARS-CoV-2 IgM Ab, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 95429-7 | SARS-CoV-2 IgG Ab, serum or plasma | https://loinc.org/sars-coronavirus-2/ |
| 95521-1 | SARS-CoV-2 N gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| 95522-9 | SARS-CoV-2 N gene, respiratory specimen | https://loinc.org/sars-coronavirus-2/ |
| NULL* | Upper(Name) LIKE ‘%COVID-19%’ |
*For non-LOINC-coded covid lab tests at your institution, the string pattern to match in the name may be different then the one shown here. We encourage you to try different combinations per the naming practices at your site (“coronavirus,” “ncov,” “sars-cov,” etc.).
**New LOINCs added in this phenotype version
Diagnosis Codes
| ICD-10-CM Code | Diagnosis Name | Provenance (if known) | Confidence Level | Notes |
| B97.21 | SARS-associated coronavirus as the cause of diseases classified elsewhere | PCORnet | Strong positive prior to 4/1/2020; weak positive after 4/1/2020 | |
| B97.29 | Other coronavirus as the cause of diseases classified elsewhere | PCORnet; CDC coding guidance 2/2/2020 | Strong positive prior to 4/1/2020; weak positive after 4/1/2020 | |
| U07.1 | 2019-nCoV acute respiratory disease | PCORnet slide deck; https://www.who.int/classifications/icd/covid19/en/ | Strong positive | Code effective as of 4/1/2020 |
| Z11.59 | Screening for viral diseases | CDC coding guidance 4/1/2020 | Asymptomatic | Code effective for this purpose as of 4/1/2020 (used to code screenings for other viruses as well, so not extremely specific.) |
| Z20.828 | Contact with and (suspected) exposure to other viral communicable diseases | Weak positive | Exposure only | |
| B34.2 | Coronavirus infection, unspecified | Weak positive | CDC 2/2/2020 guidance specifically says NOT to use this code; however, likely appears in EHR code “pick lists” for covid | |
| R50.X | Fever | PCORnet | Weak positive | |
| R05.X | Cough | PCORnet | Weak positive | |
| R06.0.X | Dyspnea | PCORnet | Weak positive | |
| J12.X; J18.X | Pneumonia | PCORnet | Weak positive | |
| J20.X; J40.X | Bronchitis (acute or nonspecified) | PCORnet | Weak positive | |
| J21.X | Acute bronchiolitis | PCORnet | Weak positive | |
| J96.X | Respiratory failure | PCORnet | Weak positive | |
| J22.X | Unspecified acute lower respiratory infection | PCORnet | Weak positive | |
| J06.9 | Acute upper respiratory infection, unspecified | PCORnet | Weak positive | |
| J98.8 | Other specified respiratory disorders | PCORnet | Weak positive | |
| J80.X | Acute respiratory distress syndrome | PCORnet | Weak positive | |
| R43.0 | Anosmia | Weak positive | ||
| R43.2 | Parageusia | Weak positive | ||
| R07.1 | Chest pain on breathing | Weak positive | ||
| R68.83 | Chills (without fever) | Weak positive |
SNOMED codes
| SNOMED Code | Name | Provenance | Confidence Level |
| 840539006 | Disease caused by 2019 novel coronavirus (disorder) | OHDSI | Strong positive |
| 840544004 | Suspected disease caused by 2019 novel coronavirus (situation) | OHDSI | Strong positive |
| 840546002 | Exposure to severe acute respiratory syndrome coronavirus 2 (event) | NIH VSAC | Weak positive |
| 103001002 | Feeling feverish (finding) | NIH VSAC | Weak positive |
| 11833005 | Dry cough (finding) | NIH VSAC | Weak positive |
| 267036007 | Dyspnea (finding) | NIH VSAC | Weak positive |
| 28743005 | Productive cough (finding) | NIH VSAC | Weak positive |
| 36955009 | Loss of taste (finding) | NIH VSAC | Weak positive |
| 426000000 | Fever greater than 100.4 Fahrenheit | NIH VSAC | Weak positive |
| 44169009 | Loss of sense of smell (finding) | NIH VSAC | Weak positive |
| 49727002 | Cough (finding) | NIH VSAC | Weak positive |
| 135883003 | Cough with fever (finding) | Weak positive | |
| 161855003 | Complaining of shivering (finding) | Weak positive | |
| 161939006 | Breathless - moderate exertion (finding) | Weak positive | |
| 161940008 | Breathless - mild exertion (finding) | Weak positive | |
| 161941007 | Dyspnea at rest (finding) | Weak positive | |
| 2237002 | Pleuritic pain (finding) | Weak positive | |
| 23141003 | Gasping for breath (finding) | Weak positive | |
| 247410004 | Painful cough (finding) | Weak positive | |
| 274640006 | Fever with chills (finding) | Weak positive | |
| 274664007 | Chest pain on breathing (finding) | Weak positive | |
| 284523002 | Persistent cough (finding) | Weak positive | |
| 386661006 | Fever (finding) | Weak positive | |
| 409702008 | Hyperpyrexia (finding) | Weak positive | |
| 426976009 | Pain provoked by breathing (finding) | Weak positive | |
| 43724002 | Chill (finding) | Weak positive | |
| 60845006 | Dyspnea on exertion (finding) | Weak positive | |
| 75483001 | Breathing painful (finding) | Weak positive |
OMOP-only codes (“emergency codes” used as placeholders; only applies to OMOP)
| OMOP Concept Code | Name | Provenance/Comment | Confidence Level |
| 756055** (and descendants) | Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) | Only count this if used in the measurement table. | N/A |
| 756023 | Acute bronchitis caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 756031 | Bronchitis caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 756039 | Respiratory infection caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 756044 | Acute respiratory distress syndrome (ARDS) caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 756061 | Asymptomatic infection caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 756081 | Infection of lower respiratory tract caused by severe acute respiratory syndrome coronavirus 2 | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
| 37310285 | Pneumonia caused by 2019 novel coronavirus | https://github.com/OHDSI/Covid-19/wiki/Release | Strong positive |
**New codes added in this phenotype version