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SNOMED CT Guide for COVID-19

SNOMED CT COVID-19 Coding Guide

As the global terminology for health, SNOMED CT can serve as a common language for recording, sharing, integrating and analyzing COVID-19 related data. This guide provides practical examples of SNOMED CT subsets that can be used to code a variety of COVID-19 related data elements, such as symptoms, risk factors and test results. These SNOMED CT subsets can be adapted to meet local requirements for healthcare service delivery, pandemic surveillance, international collaboration and retrospective data analysis. A set of computable also accompanies this guide.

How to Use this Guide

Any SNOMED CT subset used to code COVID-19 data should be designed based on its purpose and the context in which it will be used.

To make the process of planning and designing your SNOMED CT subsets more efficient and internationally consistent, we recommend the following three steps.

These three steps are explained in more detail below.

The first step is to identify the data elements that may require SNOMED CT coding. These data elements may already be defined in national reporting requirements 123, as part of a healthcare data standard you are using (e.g. a HL7 FHIR profile4 or openEHR archetypes5), or you may be developing a new information model (or data set) for this purpose. Your requirements for coded content will depend on your specific use case and the data items in your information model. In addition, different countries, regions, and hospitals may apply different clinical techniques or practices, which can also result in differing coding requirements. Therefore, deciding which subsets to implement requires clarification of the scope of content needed, by answering questions such as:

Coding COVID-19 Related Data

The collection of coded COVID-19 related data can be critical for frontline service delivery, pandemic surveillance, and retrospective data analysis.

The following table lists a collection of data elements for which SNOMED CT can be used to capture COVID-19 related data.

|--- Provider and facility details([section 2.1](https://confluence.ihtsdotools.org/display/WIPCV19/2.1+Provider+and+Facility+Details?src=sidebar))|

Healthcare profession
Site of care
Health management finding
Personal protective equipment

Patient demographics

Biological sex
Gender identity
Marital or partnership status
Nationality

Clinical assessment

Symptoms
Severity
Clinical measurements
Clinical examination findings

Tests and Investigations

Specimen
Laboratory tests
Radiology procedures
Substances and virus

Prevention, treatment and education

Prevention
Prevention findings
Education
Medication

Note

The SNOMED CT subsets are provided as a guide only, and may need to be constrained or extended to meet local requirements.

Provider and Facility Details

Information about the healthcare providers and facilities involved with the investigation, treatment, and care of patients with suspected or confirmed COVID-19 are usually recorded in electronic health records. The monitoring of medical equipment availability at healthcare facilities, such as Personal Protective Equipment (PPE) and respiratory devices, is also of utmost importance during the COVID-19 pandemic. Relevant details, which can be recorded using SNOMED CT include:

Healthcare profession
Site of care
Health management finding
Personal protective equipment

These data elements are described below, with example SNOMED CT subsets for each.

The healthcare profession is the occupation or qualification of the healthcare provider who is involved in the investigation, treatment, care or education of the patient - for example or .

CV19-PFD-HealthcareProfession Intensional Definition : <

The site of care refers to the location of the specific investigation, treatment or care setting - for example , , or .

CV19-PFD- SiteOfCare Intensional Definition : < OR << OR << OR << OR << OR <<

2.1.3 Health Management Finding

Health management finding includes concepts that describe the circumstances which affect whether the planned patient outcomes are attained, that different areas within a health organization are running appropriately, that tasks are correctly defined and assessed and that resources are used efficiently. -for example , or .

CV19-PFD- HealthManagementFinding Intensional Definition : <

Personal protective equipment is protective clothing, or other garments or equipment designed to protect the wearer's body from injury or infection - for example and

CV19-PFD- PersonalProtectiveEquipment Intensional Definition : << OR << OR << OR << OR << OR << OR << OR <<

Mapping to ICD-10

The following map members from SNOMED CT to the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (© World Health organisation 1994) 2016 Version are published (or will be published) in the SNOMED CT International Edition. These maps use ICD-10 codes identified in the WHO's Emergency use ICD codes for COVID-19 disease outbreak update 1.

1119302008

Acute disease caused by Severe acute respiratory syndrome coronavirus 2 (disorder)

U07.1

COVID-19, virus identified

MAPPED FOLLOWING WHO GUIDANCE | POSSIBLE REQUIREMENT FOR ADDITIONAL CODE TO FULLY DESCRIBE DISEASE OR CONDITION

Footnotes

Provider and Facility Details

Healthcare profession
Site of care
Health management finding
Personal protective equipment

These data elements are described below, with example SNOMED CT subsets for each.

The healthcare profession is the occupation or qualification of the healthcare provider who is involved in the investigation, treatment, care or education of the patient - for example or .

CV19-PFD-HealthcareProfession Intensional Definition : <

The site of care refers to the location of the specific investigation, treatment or care setting - for example , , or .

CV19-PFD- SiteOfCare Intensional Definition : < OR << OR << OR << OR << OR <<

2.1.3 Health Management Finding

CV19-PFD- HealthManagementFinding Intensional Definition : <

Personal protective equipment is protective clothing, or other garments or equipment designed to protect the wearer's body from injury or infection - for example and

CV19-PFD- PersonalProtectiveEquipment Intensional Definition : << OR << OR << OR << OR << OR << OR << OR <<

Coding COVID-19 Related Data

The collection of coded COVID-19 related data can be critical for frontline service delivery, pandemic surveillance, and retrospective data analysis.

The following table lists a collection of data elements for which SNOMED CT can be used to capture COVID-19 related data.

|--- Provider and facility details([section 2.1](https://confluence.ihtsdotools.org/display/WIPCV19/2.1+Provider+and+Facility+Details?src=sidebar))|

Healthcare profession
Site of care
Health management finding
Personal protective equipment

Patient demographics

Biological sex
Gender identity
Marital or partnership status
Nationality

Clinical assessment

Symptoms
Severity
Clinical measurements
Clinical examination findings

Tests and Investigations

Specimen
Laboratory tests
Radiology procedures
Substances and virus

Prevention, treatment and education

Prevention
Prevention findings
Education
Medication

Note

The SNOMED CT subsets are provided as a guide only, and may need to be constrained or extended to meet local requirements.

Introduction

IMPORTANT NOTE: This guide is no longer updated, and it is maintained only as a historical reference.

Background

On March 11, 2020, the World Health Organization formally characterized coronavirus, COVID-19, as a global pandemic and health systems globally are continuing their efforts to manage the outbreak. Coronavirus disease COVID-19 is an infectious disease caused by a newly discovered coronavirus.

As part of the global effort to manage and contain this global public health emergency, SNOMED International is doing their part to support care teams and researchers in their efforts to address its containment. SNOMED International took swift action by publishing a set of coronavirus related concepts in the January 31st 2020 International Edition of SNOMED CT, with updated descriptions and SNOMED CT to ICD-10 maps in the interim March 2020 International Edition release. Since then, SNOMED International has published additional COVID-19 related content requested by the international community. This SNOMED CT Coronavirus Content will be made available as part of the Global Patient Set (GPS) in the September 2020 GPS release. In the meantime, this content is available and can be used under the same open license as the GPS, the Creative Commons Attribution 4.0 International License.

Purpose

For more information on performing data analytics using SNOMED CT please refer to Data Analytics with SNOMED CT. Additional guidance can be found in the SNOMED CT Document Library.

The scope of this document has been guided by the collective needs and experiences of our SNOMED International Members.

The primary focus of the guide is to provide example SNOMED CT subsets for data elements covering the following key areas:

Provider and facility details - e.g. healthcare profession, site of care, personal protective equipment
Patient demographics - e.g. biological sex, foreign travel history, living arrangements
Clinical assessment - e.g. symptoms, diagnosis, complications

These subsets provide examples of SNOMED CT concepts that may be used to code data elements in national reporting requirements, as part of a healthcare data standard (e.g. a HL7 FHIR profile or openEHR archetype), or a newly developed information model (data set). Before they can be used in a production system, these subsets should be carefully reviewed and updated to ensure that they fully meet the requirements of the intended use case.

The example subsets included in this guide use concepts that are in (or are planned to be added to) the SNOMED CT International Edition. This provides a foundation for international collaboration and research on COVID-19. Some examples of SNOMED CT extension concepts, added in National Editions of SNOMED CT, are also provided for a number of data elements. Please note that all concepts referenced in this guide should be used only in implementations where the relevant Edition is deployed.

The primary audience of this guide is the SNOMED National Release Centers (NRCs), who themselves may be required to provide national or regional guidance to their local implementations during or after the COVID-19 pandemic.

This guide has been developed in collaboration with our SNOMED National Release Centers (NRCs) and other Member representatives. We would like to thank you all for sharing your knowledge and experience to collectively help in the development of this COVID-19 guide.

The following references were used in the development of this guide.

, IFIC Basic Concepts of Infection Control (Chapter 6), 3rd edition, 2016, International Federation of Infection Control
, Centers for Disease Control and Prevention, U.S.

Tests and Investigations

Laboratory testing for COVID-19 and the associated SARS-CoV-2 virus includes methods that detect the presence of the virus and antibodies produced in response to infection, in specimen samples taken from potentially infected individuals. Test and investigation data which can be recorded using SNOMED CT includes:

Specimen
Laboratory Tests
Radiology Procedures
Substances and Virus
Laboratory Test Results
Other Investigations

These data elements are described below, with example SNOMED CT subsets for each.

Specimens are samples of substances taken from an individual for testing - for example or . The following specimens may be relevant to COVID-19 testing in one or more countries affected by the virus.

CV19-INV-Specimen

The specimens prefixed with a star '*' are a subtype of another member of this subset.

Laboratory tests can be performed to detect the presence of the COVID-19 virus and antibodies produced in response to this virus. The following SNOMED CT concepts can be used to record laboratory tests that may be performed during the investigation process.

CV19-INV-LaboratoryTests

Radiology procedures are procedures that obtain images of the inside of the body. The following SNOMED CT concepts may be used to record radiology procedures that may be performed during the investigation and treatment of suspected or confirmed Covid-19 patients.

CV19-INV-RadiologyProcedures

An antibody is a protective protein produced by the immune system in response to the presence of a foreign substance, called an antigen. The following antibody/antigen and virus organism concepts can be used to record the focus of a COVID-19 investigation.

CV19-INV-SubstancesAndVirus

Laboratory test results are used to specify whether the Laboratory test focus was detected or not detected following the conducted laboratory test. The following qualifier values may be used for this purpose.

CV19-INV-LabTestResults

Other investigative procedures - e.g. and and and - may be performed to assess a COVID-19 patient. The following subset represents procedures that can be performed during the clinical assessment process.

The following subset represents a collection of findings with context that may be related to these investigations and captured using SNOMED CT - for example or .

Footnotes

1 , Division of Laboratory Systems, CDC, US

2 , The Native Antigen Company, UK

Prevention, Treatment and Education

Preventing the potential spread of COVID-19 can involve a range of precautions, such as isolation and the wearing of personal protective equipment, and education to patients, healthcare workers and the broader community. Once COVID-19 is diagnosed, various treatments may be considered, together with education for the patient and their families/caregivers

Prevention
Prevention Findings
Education
Medication
Administrative Procedures
Therapeutic Procedures
Treatment Findings
Treatment Equipment

These data elements are described below, with example SNOMED CT subsets where applicable.

Precautionary measures, such as , , and are extremely important in the fight against infectious diseases such as COVID-19. The following preventative measures can be recorded using SNOMED CT.

CV19-PTE-PreventionProcedures

Clinical findings (or situations) relating to the COVID-19 preventative measures performed may be captured in a health record. The following prevention findings (or situations) may be recorded using SNOMED CT.

CV19-PTE-PreventionFindings

Education is an important aspect of preventing and managing COVID-19 infection. The following SNOMED CT concepts may be used to record this data.

CV19-PTE-Education

A number of countries are trialling the use of medication to treat COVID-19. Many of these medications can be found in the hierarchy of SNOMED CT. However until there is sufficient evidence, the WHO is cautioning against associations recommending or administering these unproven treatments to patients with COVID-19 or people self-medicating with them. For this reason, we have not included a medication treatment subset at this time.

COVID-19 vaccines, however, have been proven to be effective in clinical trials. The following generic vaccine concepts may be recorded using SNOMED CT.

CV19-PTE-Vaccines

Patients with severe symptoms or complications may require admission to hospital, or other administrative procedures. The following administrative procedures may be recorded using SNOMED CT.

CV19-PTE-AdministrativeProcedures

Patients suffering from severe COVID-19 symptoms or complications may require a range of therapeutic procedures, many of them involving supportive care to help them breathe. The following therapeutic procedures may be recorded using SNOMED CT.

CV19-PTE-TherapeuticProcedures

Clinical findings relating to the treatment performed on a patient may be captured in a health record. The following treatment findings may be recorded using SNOMED CT.

CV19-PTE-TreatmentPreventionFindings

Respiratory equipment includes those medical devices used to support breathing and respiratory function - for example , and .

Footnotes

1 , IFIC Basic Concepts of Infection Control (Chapter 6), 3rd edition, 2016, International Federation of Infection Control

Clinical Assessment

The first step in delivering comprehensive care is to undertake a clinical assessment. Clinical assessment data which can be recorded using SNOMED CT includes:

Symptoms
Severity
Clinical Measurements
Clinical Examination Findings
Diagnosis and Certainty
Clinical History
Secondary Conditions and Complications
Potential Risk Factors
Comorbidities
Exposure Event
Covid-19 and Viral Co-Infections

These data elements are described below, with example SNOMED CT subsets for each.

Please note that all published concepts referred to on this page are included in SNOMED International's , which is available to be used internationally under the . Please refer to for more information.

Symptoms represent physical or mental features which are regarded as an indication of a condition or disease, particularly those features that are apparent to the patient. This SNOMED CT subset of COVID-19 symptoms has been developed based on a range of literature, including relevant articles found in Pubmed, research performed by Kings College London, and a review of COVID-19 data collection forms. Please note that this subset includes the concept , which can be used to represent the absence of symptoms.

CV19-ASS-Symptoms

Severity represents the quality of the condition - for example, . Severity may be recorded for each symptom, or as a general statement of their disease state 4.

CV19-ASS-Severity

Clinical measurements involve the performance of physiological tests to diagnose and refine therapeutic management of an already established disease. The following clinical measurements (and related observables) can be used in the assessment of a COVID-19 patient.

CV19-ASS- ClinicalMeasurements

Clinical examination findings are the result of measuring, questioning, evaluating, or otherwise examining a patient in healthcare. The following clinical findings are positive or negative indications that signs are present in a COVID-19 patient.

CV19-ASS-ClinicalExaminationFindings

A diagnosis is the identification of the nature of the illness, based on an examination of the symptoms, observations, measurements, test results and other investigation results. The following subset includes a range of diagnoses directly related to COVID-19.

CV19-ASS-Diagnosis

To represent the certainty of a positive COVID-19 diagnosis, the following subset may be used in conjunction with a diagnosis of .

CV19-ASS-DiagnosisPresentCertainty

To represent the certainty of the absence of COVID-19, the following subset may be used in conjunction with a diagnosis of .

CV19-ASS-DiagnosisAbsentCertainty

The clinical history concepts are used to record information gained by a physician by asking specific questions, either of the patient or of other people who know the person and can give suitable information, with the aim of obtaining information useful in formulating a diagnosis and providing medical care to the patient.

CV19-ASS-ClinicalHistory

A secondary condition is any additional health condition that occurs as a result of the natural progression or expected outcome of the primary condition. A complication is "a disorder caused by another disorder, procedure or event, which is not a natural progression or expected outcome of its cause .

The following subset includes SNOMED CT clinical findings that may be recorded as either secondary conditions or complications . Clinical judgement is required to determine whether these conditions are expected outcomes or unexpected complications of COVID-19.

CV19-ASS-SecondaryConditionsAndComplications

Potential risk factors are the patient conditions which may influence the course or outcomes of the COVID-19 disease. The following clinical findings may be recorded as potential risk factors.

CV19-ASS-RiskFactors

Similarly, procedures performed on the patient within a clinically relevant timeframe may also influence the course or outcomes of the COVID-19 disease. The following procedures may be recorded as potential risk factors.

CV19-ASS-ProcedureRiskFactors

Comorbidities are additional medical conditions of concern. The following SNOMED CT subset can be used to record comorbidities.

An exposure event is when an individual comes into close contact with an infected person's contaminated droplets, carried in the air or on contaminated hands, surfaces or other objects. The subset below includes SNOMED CT events for recording exposure to COVID-19.

CV19-ASS-ExposureEvent

An exposure finding is the result of an observation or evaluation that relates to the patient's exposure to an infection. The subset below includes SNOMED CT findings relating to COVID-19 exposure.

CV19-ASS-ExposureFinding

The following organism should be used when recording the organism causing COVID-19 infections.

CV19-ASS-Organism

The following organisms can be used to record the cause of related viral co-infections.

Footnotes

1 Articles found using the Pubmed query ""

3 COVID-19 Case Reporting Forms, including: , CDC, US , Global COVID-19 Clinical Platform, World Health Organization , NHS, UK

4 , Patient.info , Patient.info

5 , SNOMED International

6 Clinical papers, including:

8 , NHS, UK

9 , NHS, UK

SNOMED CT Guide for COVID-19

SNOMED CT COVID-19 Coding Guide

How to Use this Guide

Coding COVID-19 Related Data

Provider and Facility Details

Mapping to ICD-10

Mapping to ICD-10

Provider and Facility Details

Coding COVID-19 Related Data

How to Use this Guide

SNOMED CT COVID-19 Coding Guide

Healthcare Profession

Site of Care

Personal Protective Equipment

Overview

Step 1 - Identify Data Elements

Step 2 - Download Subsets

Subset Naming Convention

Subset Categories

Subset Types

Step 3 - Review and Adapt

Unpublished Content

Extension Content

Feedback

Introduction

Background

Purpose

Patient Demographics

Scope

Audience

Acknowledgments

References

Sex and Gender

Marital or Partnership Status

Nationality

Ethnic Group

Racial Group

Occupation

Travel History

Residential Location Type

Next of Kin Relationship

Living Arrangements

Care and Support Circumstances

Tests and Investigations

Specimen

Laboratory Tests

Radiology Procedures

Substances and Virus

Laboratory Test Results

Other Investigations

Prevention, Treatment and Education

Prevention

Prevention Findings

Education

Medication

Administrative Procedures

Therapeutic Procedures

Treatment Findings

Treatment Equipment

Clinical Assessment

Symptoms

Severity

Clinical Measurements

Clinical Examination Findings

Diagnosis and Certainty

Clinical History

Secondary Conditions and Complications

Potential Risk Factors

Comorbidities

Exposure

Covid-19 and Viral Co-Infections