Metadata

Name CCU002_01 COVID19 infection
Type Disease or Syndrome
Group Disease or Syndrome
Data Sources






Clinical Terminologies SNOMED-CT
ICD-10
Codelists covid_impact_ccu01301_01_GP_covid_diagnosis_England_SNOMEDCT.csv covid_impact_ccu01301_02_Covid_admission_England_ICD10.csv covid_impact_ccu01301_03_ECMO_treatment_England_OPCS.csv covid_impact_ccu01301_03_IMV_treatment_England_OPCS.csv covid_impact_ccu01301_03_NIV_treatment_England_OPCS.csv covid_impact_ccu01301_04_Fatal_with_covid_diagnosis_England_ICD10.csv
Valid Event Data Range 23/01/2020 - 31/05/2021
Sex Female
Male
Authors Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas
Agreement Date 9 Nov 2021
Version (UUID) Revision 1 (COVID-IMPACT)

Publication

Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination

Johan H Thygesen, Christopher Tomlinson, Sam Hollings, Mehrdad Mizani, Alex Handy, Ashley Akbari, Amitava Banerjee, Jennifer Cooper, Alvina Lai, Ken Li, Bilal Mateen, Naveed Sattar, Reecha Sofat, Ana Torralbo, Honghan Wu, Angela Wood, Jonathan A C Sterne, Christina Pagel, William Whiteley, Cathie Sudlow, Harry Hemingway, Spiros Denaxas

medRxiv 2021.11.08.21265312; doi: https://doi.org/10.1101/2021.11.08.21265312

Primary care EHR England

covid_phenotype clinical_code terminology description covid_status source
01_GP_covid_diagnosis 1008541000000105 SNOMEDCT Coronavirus ribonucleic acid detection assay (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1029481000000103 SNOMEDCT Coronavirus nucleic acid detection assay (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 120814005 SNOMEDCT Coronavirus antibody (substance) confirmed GDPPR
01_GP_covid_diagnosis 1240381000000105 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 (organism) confirmed GDPPR
01_GP_covid_diagnosis 1240391000000107 SNOMEDCT Antigen of severe acute respiratory syndrome coronavirus 2 (substance) confirmed GDPPR
01_GP_covid_diagnosis 1240401000000105 SNOMEDCT Antibody to severe acute respiratory syndrome coronavirus 2 (substance) confirmed GDPPR
01_GP_covid_diagnosis 1240411000000107 SNOMEDCT Ribonucleic acid of severe acute respiratory syndrome coronavirus 2 (substance) confirmed GDPPR
01_GP_covid_diagnosis 1240421000000101 SNOMEDCT Serotype severe acute respiratory syndrome coronavirus 2 (qualifier value) confirmed GDPPR
01_GP_covid_diagnosis 1240511000000106 SNOMEDCT Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure) confirmed GDPPR
01_GP_covid_diagnosis 1240521000000100 SNOMEDCT Otitis media caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240531000000103 SNOMEDCT Myocarditis caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240541000000107 SNOMEDCT Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240551000000105 SNOMEDCT Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240561000000108 SNOMEDCT Encephalopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240571000000101 SNOMEDCT Gastroenteritis caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1240581000000104 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 ribonucleic acid detected (finding) confirmed GDPPR
01_GP_covid_diagnosis 1240741000000103 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 serology (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1240751000000100 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1300631000000101 SNOMEDCT Coronavirus disease 19 severity score (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1300671000000104 SNOMEDCT Coronavirus disease 19 severity scale (assessment scale) confirmed GDPPR
01_GP_covid_diagnosis 1300681000000102 SNOMEDCT Assessment using coronavirus disease 19 severity scale (procedure) confirmed GDPPR
01_GP_covid_diagnosis 1300721000000109 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation) confirmed GDPPR
01_GP_covid_diagnosis 1300731000000106 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation) confirmed GDPPR
01_GP_covid_diagnosis 1321181000000108 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 record extraction simple reference set (foundation metadata concept) confirmed GDPPR
01_GP_covid_diagnosis 1321191000000105 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 procedures simple reference set (foundation metadata concept) confirmed GDPPR
01_GP_covid_diagnosis 1321201000000107 SNOMEDCT Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 health issues simple reference set (foundation metadata concept) confirmed GDPPR
01_GP_covid_diagnosis 1321241000000105 SNOMEDCT Cardiomyopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder) confirmed GDPPR
01_GP_covid_diagnosis 1321301000000101 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 ribonucleic acid qualitative existence in specimen (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321311000000104 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin M qualitative existence in specimen (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321321000000105 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin G qualitative existence in specimen (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321331000000107 SNOMEDCT Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 total immunoglobulin in serum (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321341000000103 SNOMEDCT Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin G in serum (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321351000000100 SNOMEDCT Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin M in serum (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321541000000108 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin G detected (finding) confirmed GDPPR
01_GP_covid_diagnosis 1321551000000106 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin M detected (finding) confirmed GDPPR
01_GP_covid_diagnosis 1321761000000103 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin A detected (finding) confirmed GDPPR
01_GP_covid_diagnosis 1321801000000108 SNOMEDCT Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin A in serum (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1321811000000105 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 immunoglobulin A qualitative existence in specimen (observable entity) confirmed GDPPR
01_GP_covid_diagnosis 1322781000000102 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 antigen detection result positive (finding) confirmed GDPPR
01_GP_covid_diagnosis 1322871000000109 SNOMEDCT Severe acute respiratory syndrome coronavirus 2 antibody detection result positive (finding) confirmed GDPPR
01_GP_covid_diagnosis 186747009 SNOMEDCT Coronavirus infection (disorder) confirmed GDPPR

Hospitalization EHR England

covid_phenotype clinical_code terminology description covid_status source
02_Covid_admission U07.1 ICD10 Confirmed_COVID19 confirmed HES APC
02_Covid_admission U07.2 ICD10 Suspected_COVID19 suspected HES APC
02_Covid_admission U07.1 ICD10 Confirmed_COVID19 confirmed SUS
02_Covid_admission U07.2 ICD10 Suspected_COVID19 suspected SUS

Primary care EHR England

covid_phenotype clinical_code terminology description covid_status source
03_ECMO_treatment X58.1 OPCS Extracorporeal membrane oxygenation confirmed HES APC
03_ECMO_treatment X58.1 OPCS Extracorporeal membrane oxygenation confirmed SUS

Primary care EHR England

covid_phenotype clinical_code terminology description covid_status source
03_IMV_treatment E85.1 OPCS Invasive ventilation confirmed HES APC
03_IMV_treatment X56 OPCS Intubation of trachea confirmed HES APC
03_IMV_treatment E85.1 OPCS Invasive ventilation confirmed SUS
03_IMV_treatment X56 OPCS Intubation of trachea confirmed SUS

Primary care EHR England

covid_phenotype clinical_code terminology description covid_status source
03_NIV_treatment E85.2 OPCS Non-invasive ventilation NEC confirmed HES APC
03_NIV_treatment E85.6 OPCS Continuous positive airway pressure confirmed HES APC
03_NIV_treatment E85.2 OPCS Non-invasive ventilation NEC confirmed SUS
03_NIV_treatment E85.6 OPCS Continuous positive airway pressure confirmed SUS

Hospitalization EHR England

covid_phenotype clinical_code terminology description covid_status source
04_Fatal_with_covid_diagnosis U071 ICD10 confirmed deaths
04_Fatal_with_covid_diagnosis U072 ICD10 suspected deaths