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Phenotype 1.3 (deprecated)

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empfff edited this page May 8, 2020 · 1 revision

Covid-19 Phenotype Documentation, Version 1.3 (Last updated 4/24/2020)

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.

The University of North Carolina at Chapel Hill is planning to validate this draft phenotype through chart review. Results of this validation effort will be made public once complete. Other sites are also encouraged to validate against patient charts, especially because there may be regional differences in phenotype performance.

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Phenotype Inclusion Criteria:

  • 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), regardless of result

      OR

    • **ONE **or more of the HCPCS/CPT codes in the HCPCS/CPT table (below)

      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.

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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.
    • **OR **One or more of the HCPCS/CPT codes in the HCPCS/CPT table below, without an accompanying result record (may be waiting on result return)

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
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/
94310-0 SARS-like CoV N gene, unspecified specimen https://loinc.org/sars-coronavirus-2/
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/
94313-4 SARS-like CoV N gene, unspecified specimen https://loinc.org/sars-coronavirus-2/
94314-2 SARS-CoV-2 RdRp gene, unspecified specimen https://loinc.org/sars-coronavirus-2/
94315-9 SARS-CoV-2 E gene, unspecified specimen https://loinc.org/sars-coronavirus-2/
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/
94502-2 SARS-related CoV, respiratory specimen 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/
94509-7 SARS-CoV-2 E gene, unspecified specimen https://loinc.org/sars-coronavirus-2/
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/
94532-9 SARS-related CoV + MERS, respiratory specimen https://loinc.org/sars-coronavirus-2/
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/
94647-5 SARS-related CoV, unspecified specimen https://loinc.org/sars-coronavirus-2/
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/
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.).

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
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* Fever PCORnet Weak positive
R05* Cough PCORnet Weak positive
R06.0* Dyspnea PCORnet Weak positive
J12*; J18* Pneumonia PCORnet Weak positive
J20*; J40* Bronchitis (acute or nonspecified) PCORnet Weak positive
J21* Acute bronchiolitis PCORnet Weak positive
J96* Respiratory failure PCORnet Weak positive
J22* 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* Acute respiratory distress syndrome PCORnet Weak positive
R43.0 Anosmia Weak positive
R43.2 Parageusia Weak positive

HCPCS/CPT Codes

HCPCS/CPT Code CPT Name Provenance Notes
U0001 Coronavirus testing using the Centers for Disease Control and Prevention (CDC) 2019 Novel Coronavirus Real Time RT-PCR Diagnostic Test Panel PCORnet Effective date 2/4/2020
U0002 Validated non-CDC laboratory tests for SARS-CoV-2/2019-nCoV (COVID-19) PCORnet Effective date 2/4/2020
87635 Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique. PCORnet Effective date 3/13/2020
86318 Infectious agent antibody American Medical Association Effective date 4/10/2020
86328 IA NFCT AB SARSCOV2 COVID19 American Medical Association Effective date 4/10/2020
86769 SARS-COV-2 COVID-19 ANTIBODY American Medical Association Effective date 4/10/2020

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

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

OMOP Concept Code Name Provenance Confidence Level
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

Changelog (from previous version):

  • Reformated, to separate inclusion criteria from clinical categories. No logic change for coders.
  • Added new SNOMED codes. Coders, please add to phenotype code.
  • Added new logic to make B97.21 weak ON OR AFTER 4/1/2020. Coders, please add to phenotype code.
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