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Phenotype 4.0

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empfff edited this page Feb 8, 2023 · 1 revision

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.

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Phenotype Inclusion Criteria:

Cases:

  • 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

Controls:

  • 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.)

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Labs: 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.

LOINC Code Long Common Name LOINC Version
95209-3 SARS-CoV+SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay 2.68
94763-0 SARS-CoV-2 (COVID-19) [Presence] in Specimen by Organism specific culture 2.68
94762-2 SARS-CoV-2 (COVID-19) Ab [Presence] in Serum or Plasma by Immunoassay 2.68
94558-4 SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay 2.68
94562-6 SARS-CoV-2 (COVID-19) IgA Ab [Presence] in Serum or Plasma by Immunoassay 2.68
94768-9 SARS-CoV-2 (COVID-19) IgA Ab [Presence] in Serum, Plasma or Blood by Rapid immunoassay 2.68
95125-1 SARS-CoV-2 (COVID-19) IgA+IgM [Presence] in Serum or Plasma by Immunoassay 2.68
94761-4 SARS-CoV-2 (COVID-19) IgG Ab [Presence] in DBS by Immunoassay 2.68
94563-4 SARS-CoV-2 (COVID-19) IgG Ab [Presence] in Serum or Plasma by Immunoassay 2.68
94507-1 SARS-CoV-2 (COVID-19) IgG Ab [Presence] in Serum, Plasma or Blood by Rapid immunoassay 2.68
94547-7 SARS-CoV-2 (COVID-19) IgG+IgM Ab [Presence] in Serum or Plasma by Immunoassay 2.68
95416-4 SARS-CoV-2 (COVID-19) IgM Ab [Presence] in DBS by Immunoassay 2.68
94564-2 SARS-CoV-2 (COVID-19) IgM Ab [Presence] in Serum or Plasma by Immunoassay 2.68
94508-9 SARS-CoV-2 (COVID-19) IgM Ab [Presence] in Serum, Plasma or Blood by Rapid immunoassay 2.68
94760-6 SARS-CoV-2 (COVID-19) N gene [Presence] in Nasopharynx by NAA with probe detection 2.68
95409-9 SARS-CoV-2 (COVID-19) N gene [Presence] in Nose by NAA with probe detection 2.68
94533-7 SARS-CoV-2 (COVID-19) N gene [Presence] in Respiratory specimen by NAA with probe detection 2.68
94756-4 SARS-CoV-2 (COVID-19) N gene [Presence] in Respiratory specimen by Nucleic acid amplification using CDC primer-probe set N1 2.68
94757-2 SARS-CoV-2 (COVID-19) N gene [Presence] in Respiratory specimen by Nucleic acid amplification using CDC primer-probe set N2 2.68
94766-3 SARS-CoV-2 (COVID-19) N gene [Presence] in Serum or Plasma by NAA with probe detection 2.68
94316-7 SARS-CoV-2 (COVID-19) N gene [Presence] in Specimen by NAA with probe detection 2.68
94307-6 SARS-CoV-2 (COVID-19) N gene [Presence] in Specimen by Nucleic acid amplification using CDC primer-probe set N1 2.68
94308-4 SARS-CoV-2 (COVID-19) N gene [Presence] in Specimen by Nucleic acid amplification using CDC primer-probe set N2 2.68
95411-5 SARS-CoV-2 (COVID-19) neutralizing antibody [Presence] in Serum by pVNT 2.68
94559-2 SARS-CoV-2 (COVID-19) ORF1ab region [Presence] in Respiratory specimen by NAA with probe detection 2.68
94639-2 SARS-CoV-2 (COVID-19) ORF1ab region [Presence] in Specimen by NAA with probe detection 2.68
94534-5 SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Respiratory specimen by NAA with probe detection 2.68
94314-2 SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Specimen by NAA with probe detection 2.68
94565-9 SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with non-probe detection 2.68
94759-8 SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection 2.68
95406-5 SARS-CoV-2 (COVID-19) RNA [Presence] in Nose by NAA with probe detection 2.68
94500-6 SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection 2.68
94845-5 SARS-CoV-2 (COVID-19) RNA [Presence] in Saliva (oral fluid) by NAA with probe detection 2.68
94822-4 SARS-CoV-2 (COVID-19) RNA [Presence] in Saliva (oral fluid) by Sequencing 2.68
94660-8 SARS-CoV-2 (COVID-19) RNA [Presence] in Serum or Plasma by NAA with probe detection 2.68
94309-2 SARS-CoV-2 (COVID-19) RNA [Presence] in Specimen by NAA with probe detection 2.68
94640-0 SARS-CoV-2 (COVID-19) S gene [Presence] in Respiratory specimen by NAA with probe detection 2.68
94767-1 SARS-CoV-2 (COVID-19) S gene [Presence] in Serum or Plasma by NAA with probe detection 2.68
94641-8 SARS-CoV-2 (COVID-19) S gene [Presence] in Specimen by NAA with probe detection 2.68
95825-6 SARS-CoV-2 (COVID-19) Ab [Presence] in DBS by Immunoassay 2.69
95542-7 SARS-CoV-2 (COVID-19) Ab [Presence] in Serum, Plasma or Blood by Rapid immunoassay 2.69
96119-3 SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay 2.69
95425-5 SARS-CoV-2 (COVID-19) N gene [Presence] in Saliva (oral fluid) by NAA with probe detection 2.69
96448-6 SARS-CoV-2 (COVID-19) N gene [Presence] in Saliva (oral fluid) by Nucleic acid amplification using CDC primer-probe set N1 2.69
95824-9 SARS-CoV-2 (COVID-19) ORF1ab region [Presence] in Saliva (oral fluid) by NAA with probe detection 2.69
96120-1 SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Lower respiratory specimen by NAA with probe detection 2.69
96091-4 SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Saliva (oral fluid) by NAA with probe detection 2.69
96123-5 SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Upper respiratory specimen by NAA with probe detection 2.69
95608-6 SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with non-probe detection 2.69
95424-8 SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by Sequencing 2.69
95609-4 SARS-CoV-2 (COVID-19) S gene [Presence] in Respiratory specimen by Sequencing 2.69
96603-6 SARS-CoV-2 (COVID-19) S protein RBD neutralizing antibody [Presence] in Serum or Plasma by sVNT 2.69
95970-0 SARS-CoV-2 (COVID-19) specific TCRB gene rearrangements [Presence] in Blood by Sequencing 2.69
95971-8 SARS-CoV-2 stimulated gamma interferon [Presence] in Blood 2.69
96121-9 SARS-related coronavirus E gene [Presence] in Lower respiratory specimen by NAA with probe detection 2.69
95823-1 SARS-related coronavirus E gene [Presence] in Saliva (oral fluid) by NAA with probe detection 2.69
96122-7 SARS-related coronavirus E gene [Presence] in Upper respiratory specimen by NAA with probe detection 2.69
97097-0 SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay 2.7
96763-8 SARS-CoV-2 (COVID-19) E gene [Presence] in Respiratory specimen by NAA with probe detection 2.7
96957-6 SARS-CoV-2 (COVID-19) M gene [Presence] in Upper respiratory specimen by NAA with probe detection 2.7
96986-5 SARS-CoV-2 (COVID-19) N gene [Presence] in Nose by NAA with non-probe detection 2.7
96958-4 SARS-CoV-2 (COVID-19) N gene [Presence] in Saliva (oral fluid) by Nucleic acid amplification using CDC primer-probe set N2 2.7
97098-8 SARS-CoV-2 (COVID-19) Nsp2 gene [Presence] in Upper respiratory specimen by NAA with probe detection 2.7
96797-6 SARS-CoV-2 (COVID-19) RNA [Presence] in Oropharyngeal wash by NAA with probe detection 2.7
96829-7 SARS-CoV-2 (COVID-19) RNA [Presence] in Specimen from Donor by NAA with probe detection 2.7
96765-3 SARS-CoV-2 (COVID-19) S gene [Presence] in Saliva (oral fluid) by NAA with probe detection 2.7
96752-1 SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method 2.7
98069-8 SARS-CoV-2 (COVID-19) Ab [Presence] in Saliva (oral fluid) by Rapid immunoassay 2.71
98132-4 SARS-CoV-2 (COVID-19) ORF1a region [Presence] in Respiratory specimen by NAA with probe detection 2.71
98494-8 SARS-CoV-2 (COVID-19) ORF1a region [Presence] in Saliva (oral fluid) by NAA with probe detection 2.71
98131-6 SARS-CoV-2 (COVID-19) ORF1b region [Presence] in Respiratory specimen by NAA with probe detection 2.71
98493-0 SARS-CoV-2 (COVID-19) ORF1b region [Presence] in Saliva (oral fluid) by NAA with probe detection 2.71
99596-9 SARS-CoV-2 (COVID-19) N protein IgG Ab [Presence] in Serum or Plasma by Immunoassay 2.72
99597-7 SARS-CoV-2 (COVID-19) S protein IgG Ab [Presence] in Serum or Plasma by Immunoassay 2.72
99772-6 SARS-CoV-2 stimulated gamma interferon [Interpretation] in Blood Qualitative 2.72

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
J12.82 Pneumonia due to coronavirus disease 2019 Strong positive Code effective as of 1/1/2021
M35.81 Multisystem inflammatory syndrome Strong positive Code effective as of 1/1/2021
U09.9 Post-COVID-19 condition, unspecified Strong positive Code effective as of 10/1/2021
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
R06.0X 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

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

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

OMOP Concept Code Name Provenance/Comment Confidence Level
756029 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Respiratory specimen Only count this if used in the measurement table. N/A
756065 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Unspecified specimen Only count this if used in the measurement table. N/A
756084 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Nucleic acid amplification technique in Unspecified specimen Only count this if used in the measurement table. N/A
756055 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Only count this if used in the measurement table. N/A
756085 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Nucleic acid amplification technique in Respiratory specimen 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
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