A comprehensive, open-access resource providing the research community with information, tools and phenotyping algorithms for defining COVID-19 related phenotypes in UK electronic health records data.
- Excess risk of mortality calculator
- Controlled clinical terminology terms
- Reporting templates and proformas
- Public Health England high risk definition
- How to contribute
Excess risk of mortality
We recently used large-scale samples of NHS patient data to estimate the excess risk of mortality which may be associated with coronavirus (COVID-19).
EHR case definitions and related codes
Codes used to record COVID-19 related events in electronic health records.
Contributors: Aziz Sheikh, Jenni Quint, the Health Data Research Hub for Respiratory Health (BREATHE), Neil Sebire (GOSH), Susheel Varma (HDR UK), David Seymour (HDR UK).
International Classification of Diseases 10th revision (ICD-10)
New International Classification of Diseases emergency codes have been established by the WHO.
In the UK, the National Clinical Coding Standards have been updated to include confirmed/probably cases of COVID-19 and related manifestations (e.g. pneumonia) which should be followed by the addition of B97.2 Coronavirus as the cause of diseases classified to other chapters. - more information available from the NHS Digital guidance.
| ICD-10 code | Term |
|---|---|
| U07.1 | Diagnosis of COVID-19 confirmed by laboratory testing |
| U07.2 | Diagnosis of COVID-19 suspected or probable |
International Classification of Diseases 11th revision (ICD-11)
| ICD-11 code | Term |
|---|---|
| RA01.0 | Diagnosis of COVID-19 confirmed by laboratory testing |
| RA01.2 | Diagnosis of COVID-19 suspected or probable |
Clinical Terms Version 3 (CTV3)
| CTv3 Code | Code description |
|---|---|
| Y20d2 | Excluded 2019-nCoV (Wuhan) infection |
| Y20d1 | Confirmed 2019-nCoV (Wuhan) infection |
| Y20d0 | Tested for 2019-nCoV (Wuhan) infection |
| Y20cf | Suspected 2019-nCoV (Wuhan) infection |
| Y20ce | Exposure to 2019-nCoV (Wuhan) infection |
EMIS
| Code | Term |
|---|---|
| EMISNQEX58 | Exposure to 2019-nCoV (Wuhan) infection |
| EMISNQSU106 | Suspected 2019-nCoV (Wuhan) infection |
| EMISNQTE31 | Tested for 2019-nCoV (Wuhan) infection |
| EMISNQCO303 | 2019-nCoV (Wuhan) infection |
| EMISNQEX59 | Excluded 2019-nCoV (Wuhan) infection |
Vision
| Type | Code | Term |
|---|---|---|
| Clinical finding | 4J3R100 | 2019-nCoV (novel coronavirus) detected |
| Clinical finding | 4J3R200 | 2019-nCoV (novel coronavirus) not detected |
| Clinical finding | 9Niq. | Did not attend 2019-nCoV (novel coronavirus) vaccination |
| Clinical finding | A7951 | Disease caused by 2019-nCoV (novel coronavirus) |
| Event | 65PW100 | Exposure to 2019-nCoV (novel coronavirus) infection |
| Observable entity | 4J3R. | 2019-nCoV (novel coronavirus) serology |
| Procedure | 9N312 | Telephone consultation for suspected 2019-nCoV (novel coronavirus) |
| Situation with explicit context | 8CAO1 | Advice given about 2019-nCoV (novel coronavirus) by telephone |
| Situation with explicit context | 8CAO. | Advice given about 2019-nCoV (novel coronavirus) infection |
| Situation with explicit context | 1JX1. | Suspected disease caused by 2019-nCoV (novel coronavirus) |
UK SNOMED-CT
SNOMED-CT terms used in UK primary care extracted from de Lusignan S, et al. (2020) Emergence of a Novel Coronavirus (COVID-19): A Protocol for Extending Surveillance Used by the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE). JMIR Public Health and Surveillance. DOI: 10.2196/18606.
| Type | ConceptID | DescriptionID |
|---|---|---|
| Clinical finding | 1240581000000104 | 2019-nCoV (novel coronavirus) detected |
| Clinical finding | 1240591000000102 | 2019-nCoV (novel coronavirus) not detected |
| Clinical finding | 1240631000000102 | Did not attend 2019-nCoV (novel coronavirus) vaccination |
| Clinical finding | 1240751000000100 | Disease caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240561000000108 | Encephalopathy caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240571000000101 | Gastroenteritis caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240601000000108 | High priority for 2019-nCoV (novel coronavirus) vaccination |
| Clinical finding | 1240531000000103 | Myocarditis caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240521000000100 | Otitis media caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240551000000105 | Pneumonia caused by 2019-nCoV (novel coronavirus) |
| Clinical finding | 1240541000000107 | Upper respiratory tract infection caused by 2019-nCoV (novel coronavirus) |
| Event | 1240431000000104 | Exposure to 2019-nCoV (novel coronavirus) infection |
| Observable entity | 1240741000000103 2019-nCoV | (novel coronavirus) serology |
| Procedure | 1240491000000103 | 2019-nCoV (novel coronavirus) vaccination |
| Procedure | 1240511000000106 | Detection of 2019-nCoV (novel coronavirus) using polymerase chain reaction technique |
| Procedure | 1240461000000109 | Measurement of 2019-nCoV (novel coronavirus) antibody |
| Procedure | 1240471000000102 | Measurement of 2019-nCoV (novel coronavirus) antigen |
| Procedure | 1240451000000106 | Telephone consultation for suspected 2019-nCoV (novel coronavirus) |
| Qualifier value | 1240421000000101 | Serotype 2019-nCoV (novel coronavirus) |
| Situation with explicit context | 1240661000000107 | 2019-nCoV (novel coronavirus) vaccination contraindicated |
| Situation with explicit context | 1240651000000109 | 2019-nCoV (novel coronavirus) vaccination declined |
| Situation with explicit context | 1240781000000106 | 2019-nCoV (novel coronavirus) vaccination invitation short message service text nessage |
| Situation with explicit context | 1240681000000103 | 2019-nCoV (novel coronavirus) vaccination not done |
| Situation with explicit context | 1240671000000100 | 2019-nCoV (novel coronavirus) vaccination not indicated |
| Situation with explicit context | 1240701000000101 | 2019-nCoV (novel coronavirus) vaccine not available |
| Situation with explicit context | 1240731000000107 | Advice given about 2019-nCoV (novel coronavirus) by telephone |
| Situation with explicit context | 1240721000000105 | Advice given about 2019-nCoV (novel coronavirus) infection |
| Situation with explicit context | 1240711000000104 | Educated about 2019-nCoV (novel coronavirus) infection |
| Situation with explicit context | 1240761000000102 | Suspected disease caused by 2019-nCoV (novel coronavirus) |
| Substance | 1240401000000105 | Antibody to 2019-nCoV (novel coronavirus) |
| Substance | 1240391000000107 | Antigen of 2019-nCoV (novel coronavirus) |
| Substance | 1240411000000107 | Ribonucleic acid of 2019-nCoV (novel coronavirus) |
On April 1st 2020, the SNOMED CT UK Clinical Edition, RF2 edition added a further 30 terms related to COVID-19 (SNOMEDCT2_29.0.0_20200401000001):
| ConceptID | Description | Type |
|---|---|---|
| 1300671000000104 | COVID-19 severity scale | (assessment scale) |
| 1321071000000107 | Has NHS digital isolation note | (finding) |
| 1321081000000109 | Self-isolation note issued to patient | (finding) |
| 1321091000000106 | Household isolation note issued to patient | (finding) |
| 1300591000000101 | Low risk category for developing complication from COVID-19 infection | (finding) |
| 1300571000000100 | Moderate risk category for developing complication from COVID-19 infection | (finding) |
| 1300561000000107 | High risk category for developing complication from COVID-19 infection | (finding) |
| 1300631000000101 | COVID-19 severity score | (observable entity) |
| 1300681000000102 | Assessment using COVID-19 severity scale | (procedure) |
| 1321161000000104 | Household isolation to prevent exposure of community to contagion | (procedure) |
| 1321131000000109 | Self-isolation to prevent exposure of community to contagion | (procedure) |
| 1321141000000100 | Shielding of household to prevent exposure of uninfected subject to contagion | (procedure) |
| 1321151000000102 | Shielding of uninfected subject to prevent exposure to contagion | (procedure) |
| 1321231000000101 | Signposting to CHMS (COVID-19 Home Management Service) | (procedure) |
| 1321061000000100 | Signposting to NHS online isolation note service | (procedure) |
| 1320971000000102 | Taking of swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) | (procedure) |
| 1300721000000109 | COVID-19 confirmed by laboratory test | (situation) |
| 1300731000000106 | COVID-19 confirmed using clinical diagnostic criteria | (situation) |
| 1321101000000103 | COVID-19 excluded | (situation) |
| 1321111000000101 | COVID-19 excluded by laboratory test | (situation) |
| 1321121000000107 | COVID-19 excluded using clinical diagnostic criteria | (situation) |
| 1321221000000103 | Consultation via video conference not available | (situation) |
| 1321171000000106 | Provision of advice, assessment or treatment limited due to COVID-19 pandemic | (situation) |
| 1321031000000105 | Self-taken swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) completed | (situation) |
| 1321041000000101 | Self-taken swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) offered | (situation) |
| 1321051000000103 | Swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) taken by healthcare professional | (situation) |
| 1321201000000107 | COVID-19 health issues simple reference set | (foundation metadata concept) |
| 1321211000000109 | COVID-19 presenting complaints simple reference set | (foundation metadata concept) |
| 1321191000000105 | COVID-19 procedures simple reference set | (foundation metadata concept) |
| 1321181000000108 | COVID-19 record extraction simple reference set | (foundation metadata concept) |
National Pathology Exchange (NPEx)
Two SNOMED-CT terms are used to record PCR-driven COVID-19 RNA detection:
| Description | ConceptID |
|---|---|
| Detection of 2019-nCoV (novel coronavirus) using polymerase chain reaction technique | 1240511000000100 |
| Coronavirus RNA (ribonucleic acid) detection assay | 1008541000000100 |
SNOMED-CT
The March 2020 release contains relevant COVID-19 concepts including any applicable changes to descriptions (source). These terms are not compatible with current UK clinical codes)
| ConceptID | Type | DescriptionID | Term |
|---|---|---|---|
| 138875005 | FSN | 3947198019 | SNOMED Clinical Terms version: 20200309 [R] (March 2020 Interim Release) |
| 840539006 | FSN | 3947183016 | Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder) |
| 840539006 | Synonym | 3947184010 | Disease caused by severe acute respiratory syndrome coronavirus 2 |
| 840539006 | Synonym | 3947185011 | COVID-19 |
| 840544004 | FSN | 3947197012 | Suspected disease caused by severe acute respiratory coronavirus 2 (situation) |
| 840544004 | Synonym | 3947196015 | Suspected disease caused by severe acute respiratory coronavirus 2 |
| 840544004 | Synonym | 3947195016 | Suspected disease caused by SARS-CoV-2 |
| 840544004 | Synonym | 3950926016 | Suspected COVID-19 |
| 840546002 | FSN | 3947186012 | Exposure to severe acute respiratory syndrome coronavirus 2 (event) |
| 840546002 | Synonym | 3947187015 | Exposure to SARS-CoV-2 |
| 840546002 | Synonym | 3947188013 | Exposure to severe acute respiratory syndrome coronavirus 2 |
| 840533007 | FSN | 3947189017 | Severe acute respiratory syndrome coronavirus 2 (organism) |
| 840533007 | Synonym | 3947191013 | Severe acute respiratory syndrome coronavirus 2 |
| 840533007 | Synonym | 3947190014 | SARS-CoV-2 |
| 840536004 | FSN | 3947180018 | Antigen of severe acute respiratory syndrome coronavirus 2 (substance) |
| 840536004 | Synonym | 3947181019 | Antigen of severe acute respiratory syndrome coronavirus 2 |
| 840536004 | Synonym | 3947182014 | Antigen of SARS-CoV-2 |
| 840535000 | FSN | 3947177019 | Antibody to severe acute respiratory syndrome coronavirus 2 (substance) |
| 840535000 | Synonym | 3947178012 | Antibody to severe acute respiratory syndrome coronavirus 2 |
| 840535000 | Synonym | 3947179016 | Antibody to SARS-CoV-2 |
| 840534001 | FSN | 3947192018 | Severe acute respiratory syndrome coronavirus 2 vaccination (procedure) |
| 840534001 | Synonym | 3947194017 | Severe acute respiratory syndrome coronavirus 2 vaccination |
| 840534001 | Synonym | 3947193011 | SARS-CoV-2 vaccination |
| 840534001 | Synonym | 3950925017 | COVID-19 vaccination |
Logical Observation Identifiers Names and Codes (LOINC)
- LOINC terms for commercial in vitro diagnostics (IVD) test kits/
openEHR
- Archetypes and templates related to data sets representing all aspects of COVID-19 data recording and capture, including but not limited to risk assessment, contact tracing and reporting.
Implementation
Collation of codes available as an executable phenotype implementation via the Phenoflow portal.
Reporting templates and proformas
- Professional Record Standards Body clinical guidelines on COVID-19 SNOMED codes
- British Society of Thoracic Imaging COVID-19 guidance for radiologists
- OHDSI OMOP
Public Health England definition for populations at increased risk of severe illness from coronavirus (COVID-19):
PHE guidance on clinically vulnerable and extremely vulnerable populations (source).
-
Aged 70 or older (regardless of medical conditions).
-
Under 70 with an underlying health condition listed below (ie anyone instructed to get a flu jab as an adult each year on medical grounds):
- chronic (long-term) respiratory diseases, such as asthma, chronic obstructive pulmonary disease (COPD), emphysema or bronchitis
- chronic heart disease, such as heart failure
- chronic kidney disease
- chronic liver disease, such as hepatitis
- chronic neurological conditions, such as Parkinson’s disease, motor neurone disease, multiple sclerosis (MS), a learning disability or cerebral palsy
- diabetes
- problems with your spleen – for example, sickle cell disease or if you have had your spleen removed
- a weakened immune system as the result of conditions such as HIV and AIDS, or medicines such as steroid tablets or chemotherapy
- being seriously overweight (a body mass index (BMI) of 40 or above)
- those who are pregnant
There are some clinical conditions which put people at even higher risk of severe illness from COVID-19:
- people who have received an organ transplant and remain on ongoing immunosuppression medication
- people with cancer who are undergoing active chemotherapy or radiotherapy
- people with cancers of the blood or bone marrow such as leukaemia who are at any stage of treatment
- people with severe chest conditions such as cystic fibrosis or severe asthma (requiring hospital admissions or courses of steroid tablets)
- people with severe diseases of body systems, such as severe kidney disease (dialysis)
NHS Digital has provided the rules and controlled clinical terminology terms (ICD-10 and OPCS-4) used to compile the high risk shielded patient list which should practice complete social “shielding”:
- Solid organ transplant recipients who remain on long term immune suppression therapy.
- People with specific cancers
- people with cancer who are undergoing active chemotherapy or radical radiotherapy for lung cancer
- people with cancers of the blood or bone marrow such as leukaemia, lymphoma or myeloma who are at any stage of treatment
- people having immunotherapy or other continuing antibody treatments for cancer *
- people having other targeted cancer treatments which can affect the immune system, such as protein kinase inhibitors or PARP inhibitors.
- People who have had bone marrow or stem cell transplants in the last 6 months, or who are still taking immunosuppression drugs.
- People with severe respiratory conditions including all cystic fibrosis, severe asthma and severe COPD.
- People with rare diseases and inborn errors of metabolism that significantly increase the risk of infections (such as SCID, homozygous sickle cell).
- People on immunosuppression therapies sufficient to significantly increase risk of infection.*
- People who are pregnant with significant congenital heart disease.
Contributing
Contributions are encouraged!
You can contribute by:
- a pull request to this repository
- or emailing s.denaxas[@]ucl.ac.uk