JIRA Link: https://projects.jira.snomed.org/browse/IHTSDO-1233

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Approvals 

1. Content Issue Summary 

An inquiry by the National Library of Medicine (NLM) regarding the proper location of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the organism hierarchy resulted in the review of the parent concept, 415360003 |Severe acute respiratory syndrome-related coronavirus (organism)|. It was determined that the terming and placement of this concept is confusing in that it can be used to represent two separate concepts: 1) “Severe acute respiratory syndrome (SARS) coronavirus, the strain that caused the 2002–2004 outbreak of severe acute respiratory syndrome (SARS), as well as 2) “Severe acute respiratory syndrome-related coronavirus”, the parent species.

2. Analysis of Issue 

• Terming analysis:

  • FSN: “Severe acute respiratory syndrome-related coronavirus” - Represents the species: https://ictv.global/taxonomy/taxondetails?taxnode_id=202101868

  • PT: SARS coronavirus - Represents the strain

  • Synonyms:

    • Severe acute respiratory syndrome-related coronavirus - Same as FSN - Represents the species

    • SARS - Represents the viral respiratory disease caused by the strain - Need to be inactivated

    • SARS virus - Represents the strain

    • Severe acute respiratory syndrome (SARS) coronavirus - Represents the strain

    • Severe acute respiratory syndrome coronavirus - Represents the strain

    • SARS-CoV - This acronym is a source of ambiguity, as, depending on the reference and context, it can represent either the species or the strain:

      • This acronym is generally used to represent the strain in official resources:

        • ICTV: https://ictv.global/news/news-2020

        • CDC: https://www.cdc.gov/sars/index.html

        • WHO: https://www.who.int/publications/i/item/who-r-d-blueprint-novel-coronavirus-prospects-for-evaluating-cross-reactivity-of-ncov-with-sars-cov

      • There are references indicating that once SARS-CoV-2 emerged, “SARS-CoV" became known as "SARS-CoV-1”: 

        • https://www.uptodate.com/contents/severe-acute-respiratory-syndrome-sars?search=SARS&source=search_result&selectedTitle=1~150&usage_type=default&display_rank=1

        • https://www.who.int/news/item/03-02-2022-2022-celebrating-70-years-of-gisrs-(the-global-influenza-surveillance-and-response-system)

        • https://sciencemediahub.eu/2020/04/23/the-differences-between-sars-cov-1-and-sars-cov-2/

• Modeling and placement analysis:

  • SARS-CoV-2 placement may need to be updated. Depending on which organism 415360003 |Severe acute respiratory syndrome-related coronavirus (organism)| represents, the placement might be incorrect.

3. Additional issues identified  

• The value of the child concepts representing SARS coronavirus subtypes (140 in total) should be evaluated.

• There are a total of 6 concepts (1 event, 4 disorders, and 1 procedure) that are defined by 415360003 |Severe acute respiratory syndrome-related coronavirus (organism). The modeling and terming of these concepts should be reviewed to determine the applicability of the attribute/value: 

  • Associated with (attribute): 

    • 444482005 |Exposure to Severe acute respiratory syndrome coronavirus (event)|

  • Causative agent (attribute):

    • 398447004 |Severe acute respiratory syndrome (disorder)|

    • 715882005 |Severe acute respiratory syndrome of upper respiratory tract (disorder)|

    • 441590008 |Pneumonia caused by Severe acute respiratory syndrome coronavirus (disorder)| 

    • 408688009 |Healthcare associated severe acute respiratory syndrome (disorder)| – See synonym: Healthcare associated SARS

  • Component (attribute):

    • 399150003 |Polymerase chain reaction test for severe acute respiratory syndrome (procedure)|

4. Solution 

• Resolving ambiguity for 415360003 |Severe acute respiratory syndrome-related coronavirus (organism)|- options to consider:

  1. Option 1: Use FSN as the source of truth: keep 415360003 |Severe acute respiratory syndrome-related coronavirus (organism)| active, with the understanding that this concept would represent the parent (species) concept. Remove all descriptions referencing “Severe acute respiratory syndrome (SARS) coronavirus” (the child strain) and create a new concept for the latter strain.

     1. Pros: 

        1. Concept meaning will mirror FSN i.e. no name change is required.

        2. The association between this concept and the child concept, 840533007 |Severe acute respiratory syndrome coronavirus 2 (organism)|, remains intact.

     2. Cons:

        1. Very likely to have an impact on the implementers as this concept is the only one available to represent the strain that caused SARS (2002-2004).

  2. Option 2: Use Preferred Term (PT) as the source of truth: update the FSN with the understanding that this concept would represent the strain that caused SARS (2002-2004) and create a new parent concept representing the species.

     1. Pros: 

        1. The general understanding is that this concept was created to represent the strain that caused the 2003 outbreak of “Severe acute respiratory syndrome (SARS) coronavirus”.

        2. Minimal impact on the implementers who have used this concept to represent the strain caused by SARS (2002-2004).

     2. Cons: 

        1. Changes the meaning of the concept (by changing the FSN), which is contradictory to SNOMED CT guidelines.

        2. Results in creation of a new concept with an existing inactive FSN. This would generate a validation error that needs to be added to the exception list.

        3. Results in potential impact on the implementers as the concept might have been used to represent the parent species (very unlikely).

  3. Option 3 (preferred): Consider this concept an ambiguous one, inactivate it, and create net new concepts representing the associated strain and species:

     1. Pros:

        1. Follows editorial guidelines.

        2. Is in line with decisions made in similar previous cases.

        3. Minimizes impact on users by giving them clear choices for replacing historical data.

     2. Cons:

        1. Results in creation of a new concept with an existing inactive FSN. This would generate a validation error that needs to be added to the exception list. 

• Assignment of “SARS-CoV” as acronym - options to consider:

  1. Option 1 (preferred):

     1. “SARS-CoV” is still used officially by ICTV for the strain that caused the SARS outbreak in 2002-2004. The parent species would have “SARSr-CoV” as the acronym (which is more accurate). The strain can have an additional acronym of "SARS-CoV-1" for further clarity and in accordance with resources that refer to the name change.

  2. Option 2:

     1. Apply “SARS-CoV” for both concepts but add expanded terms to the acronym, e.g. "SARS-CoV - Severe acute respiratory syndrome coronavirus" and SARS-CoV - Severe acute respiratory syndrome-related coronavirus".

• Modeling 840533007 |Severe acute respiratory syndrome coronavirus 2 (organism)|:

  • 840533007 |Severe acute respiratory syndrome coronavirus 2 (organism)| will be a sibling of the “Severe acute respiratory syndrome (SARS) coronavirus” strain and a subtype of “Severe acute respiratory syndrome-related coronavirus” species.

• Inactivate current child concepts of 415360003 |Severe acute respiratory syndrome-related coronavirus (organism)| that represent SARS strain subtypes (140 in total):

  1. Use "Outdated component" as inactivation reason and provide a "Replaced by" association to the concept representing “Severe acute respiratory syndrome (SARS) coronavirus".

  2. The potential impact is expected to be minimal:

     1. They are related to a disease that has not been seen in many years.

     2. These variants have disappeared and they are not clinically significant.

     3. This approach will be consistent with that of SARS-CoV-2, where the subtypes have not been added due to clinical insignificance.

5. Construction 

• Due to substantial nomenclature changes and inactivation of a large number of concepts, once the preferred options are selected and a solution is finalized, a briefing note will be submitted to the MF and the CMAG as well as the MF Microbiology working group for review and feedback regarding potential impact to implementers’ systems. (Estimated timeline: November - December 2022). 

• Modeling can begin after this step is complete. All changes should be completed within one authoring cycle/monthly release to minimize disruption and inconsistencies (Estimated timeline January-February 2023) 

6. Glossary of Terms