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

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 SNOMED CT subset artefacts also accompanies this guide.

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

• Tests and procedures - e.g. specimen, laboratory test results

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.

• , World Health Organization

Overview

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.

Step 1 - Identify Data Elements

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:

• What will your SNOMED CT subsets be used for?

  • Will they be used to capture new data in a clinical information system to support frontline service delivery?

  • Will they be used for disease surveillance?

  • Will they be used to integrate data from various sources?

  • Will they be used for international collaboration?

  • Will they be used for retrospective analysis of data?

• Which data elements are required for your use case?

  • What coded data needs to be collected to support clinical care?

  • What coded data needs to be collected to provide disease surveillance?

  • What coded data needs to be shared between or integrated from different sources?
• What existing subsets are available for the data elements of interest?

  • Where these subsets designed based on the same or compatible requirements?

Answering these questions will help in understanding which of the existing subsets are relevant for your context. It may also help to identify potential content gaps in the subsets, or extraneous concepts which are not required for your specific scenario. Please note that the questions above are provided for inspiration only. Additional questions specific to your use case are likely to be needed.

The second step is to download any available existing subsets that are associated with your required data elements.

The example COVID-19 subsets in this guide can be downloaded from Appendix A - Example Subsets.

The example COVID-19 subsets provided by SNOMED International have been named using the following convention.

• SNOMED CT COVID-19 subsets:CV19- -

• SNOMED CT COVID-19 subsets including subtypes of members:CV19- --withSubtypes

The table below shows some examples of subsets named using this convention.

Examples of Named Subset Category| Subset| Name Provider and Facility Details (PFD)| Site of care subset| CV19-PFD-SiteOfCare Patient Demographics (PAT)| Marital status subset| CV19-PAT-MaritalStatus Marital status subset including subtypes| CV19-PAT-MaritalStatus-withSubtypes Clinical Assessment (ASS)| Symptoms subset| CV19-ASS-Symptoms Symptoms subset including subtypes| CV19-ASS-Symptoms-withSubtypes

The international SNOMED CT subsets have been organized into a number of categories, based on groupings of data elements that are likely to be recorded together. The five categories identified are:

• Provider and Facility Details (PFD)

• Patient Demographics (PAT)

• Clinical Assessment (ASS)

• Tests and Investigations (INV)

Please follow the links above for information on the specific subsets within each category.

Some of the international subsets have been developed intensionally, while others have been developed extensionally. Please refer to the Practical Guide to Reference Sets, section 2.1.1. Subset Definitions for information on the difference between intensionally and extensionally defined subsets.

For each extensionally-defined subset, where the members have subtypes, we provide two versions:

1. One subset which includes only the listed members. This version supports use cases (e.g. reporting, data integration) that require more abstract concepts.

2. One subset which includes the members listed and all the subtypes of each of these members. This version supports use cases that may require more specific values (e.g. data collection where more clinical detail is required).

   • Please note that this second type of subset is automatically generated from the corresponding subset with listed members. No manual curation has been performed, and therefore these subsets may contain concepts that are not relevant for the context of use.

The third step is to carefully review each international subset, and adapt it to meet your specific requirements. The subsets provided represent a collection of concepts that have been contributed from a range of SNOMED International Members. It is therefore important to review each subset member to:

1. Remove any concepts that are not required for your use case

2. Add any concepts missing from the subset that may be required for your specific use case

   • Please note, if the concept you require is not included in the SNOMED CT Edition you are using, please follow the content request processes in each country. For more information, refer to the relevant .

   • SNOMED International National Release Centers and other authorized users may request additions or changes to the SNOMED CT International Edition via the SNOMED CT Content Request Service. For more information, refer to the CRS User Guide or contact

Please note that the subsets in this guide may include some unpublished content that is planned for a future SNOMED CT edition. This content should not be used until it has been officially published, as we cannot guarantee that the identifiers or terms will not change. For this reason, these unpublished concepts are not included in the downloadable versions of the subsets. Unpublished concepts are included in this guide to assist with planning (e.g. planning of national extensions).

Unpublished content is shown in this guide using grey, italic font on a pink background, as shown in the example below.

In response to an immediate need for COVID-19-specific concepts, various Member countries have developed concepts within their national SNOMED CT Extensions. Please note, however, that extension concepts should only be used when the module in which they are published is included in the implemented SNOMED CT Edition. SNOMED CT extension concepts are not included in the subsets downloadable from the Reference Set tool.

SNOMED International welcomes comments on this guide and suggestions for new or updated content. Please use the Feedback button at the bottom of each page to send us your feedback.

Footnotes

1 "Coronavirus Disease 2019 (COVID-19)" , Centers for Disease Control and Prevention,

2 "COVID-19 Hospitalisation in England Surveillance System (CHESS) Daily Reporting,NHS -

3 , Wellington: Ministry of Health 2020, New Zealand

4 , U.S.

5 (COVID-19 incubator)