Phenotype Library | phenotype: COVID-19 infection

COVID-19 infection

BHF CVD COVID UK Consortium

PH1

Version ID

Type

Disease or Syndrome

Data Sources

GPES Data for Pandemic Planning and Research (COVID-19) , Hospital Episode Statistics Admitted Patient Care , Covid-19 Second Generation Surveillance System , Civil Registration - Deaths

Valid event data range

01/01/2020 - 31/10/2020

Sex

♀ Female ♂ Male

Agreement Date

2021-01-01

Coding system

ICD10 codes SNOMED CT codes

Collections

BHF Data Science Centre Phenotype Library

Definition

We ascertained people with a confirmed or suspected Covid-19 diagnosis as follows:

1) a positive PCR or antigen test from the Covid-19 laboratory test data, with specimen date on or before 31 October 2020; or

2) a Covid-19 diagnosis SNOMED-CT concept code appearing in the primary care data, with event date on or before 31 October; or

3) a diagnosis ICD-10 code appearing in the hospital episodes (main or secondary diagnostic code position in the admitted patient care component of the hospital episode statistics), with admission date on or before 31 October or

4) death registration with a mention (as underlying on contributing cause) of a diagnosis ICD-10 code , with death registration date on or before 31 October 2020.

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/1

Publications

No data available

Clinical Code List

CSV

JSON

XML

Expand All / Collapse All

C714/2567 COVID-19 infection - Primary Care - SNOMED CT codes

Rows: 37

Code	Description	type
1008541000000105	Coronavirus ribonucleic acid detection assay (observable entity)	1
1029481000000103	Coronavirus nucleic acid detection assay (observable entity)	1
120814005	Coronavirus antibody (substance)	1
1240391000000107	Antigen of severe acute respiratory syndrome coronavirus 2 (substance)	1
1240401000000105	Antibody to severe acute respiratory syndrome coronavirus 2 (substance)	1
1240421000000101	Serotype severe acute respiratory syndrome coronavirus 2 (qualifier value)	1
1240511000000106	Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure)	1
1240521000000100	Otitis media caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240531000000103	Myocarditis caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240541000000107	Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240551000000105	Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240561000000108	Encephalopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240571000000101	Gastroenteritis caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1240581000000104	Severe acute respiratory syndrome coronavirus 2 ribonucleic acid detected (finding)	1
1240741000000103	Severe acute respiratory syndrome coronavirus 2 serology (observable entity)	1
1240751000000100	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1300631000000101	Coronavirus disease 19 severity score (observable entity)	1
1300671000000104	Coronavirus disease 19 severity scale (assessment scale)	1
1300681000000102	Assessment using coronavirus disease 19 severity scale (procedure)	1
1300721000000109	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)	1
1300731000000106	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation)	1
1321181000000108	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 record extraction simple reference set (foundation metadata concept)	1
1321191000000105	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 procedures simple reference set (foundation metadata concept)	1
1321201000000107	Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 health issues simple reference set (foundation metadata concept)	1
1321241000000105	Cardiomyopathy caused by severe acute respiratory syndrome coronavirus 2 (disorder)	1
1321301000000101	Severe acute respiratory syndrome coronavirus 2 ribonucleic acid qualitative existence in specimen (observable entity)	1
1321311000000104	Severe acute respiratory syndrome coronavirus 2 immunoglobulin M qualitative existence in specimen (observable entity)	1
1321321000000105	Severe acute respiratory syndrome coronavirus 2 immunoglobulin G qualitative existence in specimen (observable entity)	1
1321331000000107	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 total immunoglobulin in serum (observable entity)	1
1321341000000103	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin G in serum (observable entity)	1
1321351000000100	Arbitrary concentration of severe acute respiratory syndrome coronavirus 2 immunoglobulin M in serum (observable entity)	1
1321541000000108	Severe acute respiratory syndrome coronavirus 2 immunoglobulin G detected (finding)	1
1321551000000106	Severe acute respiratory syndrome coronavirus 2 immunoglobulin M detected (finding)	1
1321761000000103	Severe acute respiratory syndrome coronavirus 2 immunoglobulin A detected (finding)	1
1322781000000102	Severe acute respiratory syndrome coronavirus 2 antigen detection result positive (finding)	1
1322871000000109	Severe acute respiratory syndrome coronavirus 2 antibody detection result positive (finding)	1
186747009	Coronavirus infection (disorder)	1

C715/2569 COVID-19 infection - Hospitalizations - ICD10 codes

Rows: 2

Code	Description	type
U071	COVID-19, virus identified	1
U072	COVID-19, virus not identified	1

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH1/version/2/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH1/version/2/detail/?format=json
R Package	`# Download here library(ConceptLibraryClient) # Connect to API client = connect_to_API(public=TRUE) # Get details of phenotype details = get_phenotype_detail_by_version('PH1', '2', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH1/version/2/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH1/version/2/export/codes/?format=json
CSV	site_root/phenotypes/PH1/version/2/export/codes/
R Package	`# Download here library(ConceptLibraryClient) # Connect to API client = connect_to_API(public=TRUE) # Get codelists of phenotype codelists = get_phenotype_code_list('PH1', '2', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
2	COVID-19 infection	ieuan.scanlon	2021-10-06	currently shown