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.



Modelled Prevalence Estimates

Phenotype Data Sources Country Authors Ref
CVD, diabetes, CKD, COPD, HIV, others CALIBER primary care, hospitalization, mortality EHR UK Banerjee A. * Preprint on ResearchGate
* Algorithms
COPD, CHD, stroke, PAD, HF, HT, depression Clinical Practice Research Datalink UK Public Health England, Imperial College PHE fingertips
CVD, Respiratory, high-dependency conditions Primary care - QoF UK NHS Digital Quality and Outcomes Framework, Achievement, prevalence and exceptions data 2018-19
Comorbidities for severe COVID-19 infections meta analyses China Jain V Systematic review and meta-analysis of predictive symptoms and comorbidities for severe COVID-19 infection

Public Health England definition for populations at increased risk of severe illness from coronavirus (COVID-19):

  1. Aged 70 or older (regardless of medical conditions).

  2. 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.

Phenotyping algorithms

Respiratory

Phenotype Data Sources Country Authors PMID/URL
Asthma UK Biobank
primary care
hospital admissions data
mortality data
UK Quint J. K. 30662273
Chronic Obstructive Pulmonary Disease Clinical Practice Research Datallink
Hospital Episode Statistics
Office of National Statistics mortality
UK Kuan V. 31650125
Chronic obstructive pulmonary disease UK Biobank
primary care
hospital admissions data
mortality data
UK Quint J. K. 25056980

Endocrine

Phenotype Data Sources Country Authors PMID/URL
Diabetes Clinical Practice Research Datallink
Hospital Episode Statistics
Office of National Statistics mortality
UK Kuan V. 31650125

Renal disease

Phenotype Data Sources Country Authors PMID/URL
End Stage Renal Disease UK Biobank UK Kathryn Bush, John Nolan, Qiuli Zhang, Will Herrington and Cathie Sudlow URL

Coronary Heart Disease

Phenotype Data Sources Country Authors PMID/URL
HF Clinical Practice Research Datalink, Hospital Episode Statistics, Office of National Statistics UK CALIBER team URL
CHD Clinical Practice Research Datalink, Hospital Episode Statistics, Office of National Statistics UK CALIBER team URL

Pregnancy

Phenotype Data Sources Country Authors PMID/URL
Pregnancy Clinical Practice Research Datalink, Hospital Episode Statistics UK CALIBER team URL

Reporting templates and proformas

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.

Contributing

Contributions are encouraged!

You can contribute by:

  • a pull request to this repository
  • or emailing s.denaxas[@]ucl.ac.uk