SARS-CoV-2 variant of concern explained

The term variant of concern (VOC) for SARS-CoV-2, which causes COVID-19, is a category used for variants of the virus where mutations in their spike protein receptor binding domain (RBD) substantially increase binding affinity (e.g., N501Y) in RBD-hACE2 complex (genetic data), while also being linked to rapid spread in human populations (epidemiological data).[1]

Before being allocated to this category, an emerging variant may have been labeled a variant of interest (VOI), or in some countries a variant under investigation (VUI). During or after fuller assessment as a variant of concern the variant is typically assigned to a lineage in the Pango nomenclature system[2] and to clades in the Nextstrain[3] and GISAID[4] systems.

During the COVID-19 pandemic, the SARS-CoV-2 virus has been observed to mutate, with certain combinations of specific point mutations proving to be more concerning than others. This was principally for reasons of transmissibility and virulence, and also with regard to the possible emergence of escape mutations.

Criteria

See also: Strain (biology). Several national and international health organisations (e.g. Centers for Disease Control and Prevention (CDC) (US), Public Health England (PHE) and the COVID-19 Genomics UK Consortium for the UK, and the Canadian COVID Genomics Network (CanCOGeN)) use some or all of the following criteria to assess variants:[5] [6]

Variants that appear to meet one or more of these criteria may be labeled "variants of interest" or "variants under investigation" ('VUI') pending verification and validation of these properties. Once validated, variants of interest /VUI may be renamed "variants of concern" by monitoring organizations, such as the CDC.[7] [8] [9] A related category is "variant of high consequence", used by the CDC if there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced.[10]

Classifications by country

World Health Organization

The WHO maintains a list of variants of global concern.[11] On 26 November 2021, the WHO added a fifth variant of concern, the Omicron variant, previously known as B.1.1.529.[12] Omicron joins the Alpha, Beta, Gamma, and Delta variants. As of March 2023, these are all considered to be 'previously circulating' variants of concern, and classified Omicron sublineages independently as variants under monitoring (VUMs), VOIs, or VOCs.[13]

Africa

The NICD in South Africa maintains a list of variants and testing facilities locally in collaboration with KRISP.[14] [15]

Europe

As of November 2021, the European Centre for Disease Prevention and Control declared four variants to be 'variants of concern': Beta, Gamma, Delta, and B.1.1.529 (named 'Omicron' after the reference was updated); Mu, Lambda and AY.4.2 were named as Variants of Interest (VOI), while there were 9 'Variants under monitoring'. 25 variants were described as 'de-escalated'.[16]

United Kingdom

As of November 2021, the United Kingdom has fifteen variants on its 'watch list', 4 with 'VOC' status and 11 rated as 'VUI'. Those designated 'VOC' were Alpha, Beta, Gamma, and Delta. In early December 2021, Omicron was added to the VOCs. Among the Variants under investigation is 'VUI-21OCT-01/ A.Y 4.2'.[17]

North America

Canada (via health-infobase.canada.ca)[18] and the United States (via the CDC)[19] also maintain lists of variants of concern. As of early December, Canada was monitoring five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron, while the US was monitoring two: Delta and Omicron.[20]

Notes and References

  1. Shahhosseini. Nariman. Babuadze. George (Giorgi). Wong. Gary. Gary Kobinger. Kobinger. Gary P.. May 2021. Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Microorganisms. en. 9. 5. 926. 10.3390/microorganisms9050926. 33925854. 8146828. free.
  2. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology . etal. Rambaut, A. . Holmes, E.C.. O'Toole, Á. . Nature Microbiology . 2020 . 5 . 11 . 1403–1407. 10.1038/s41564-020-0770-5 . 32669681 . 7610519 . 220544096 . free .
  3. Web site: Trevor . Bedford . Emma B . Hodcroft . Richard A . Neher . Updated Nextstrain SARS-CoV-2 clade naming strategy . 6 January 2021 . nextstrain.org/blog . 19 January 2021.
  4. Web site: clade tree (from 'Clade and lineage nomenclature') . 4 July 2020 . www.gisaid.org . 7 January 2021.
  5. Web site: Daniel R. . Lucey. 2021-02-02. COVID "Mega-variant" and eight criteria for a template to assess all variants. 2022-06-05 . Science Speaks: Global ID News . en-US.
  6. Web site: CDC. Emerging SARS-CoV-2 Variants. 11 February 2020. 2021-01-04. Centers for Disease Control and Prevention. en-us.
  7. Web site: Variants: distribution of cases data . GOV.UK . 28 January 2021 . At "Differences between a Variant of Concern and Variant Under Investigation" . 19 February 2021 . SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological, or pathogenic properties, are raised for formal investigation. At this point they are designated Variant Under Investigation (VUI) with a year, month, and number. Following a risk assessment with the relevant expert committee, they may be designated Variant of Concern (VOC).
  8. Web site: CanCOGeN Interim Recommendations for Naming, Identifying, and Reporting SARS-CoV-2 Variants of Concern . 2021-01-15 . 25 February 2021 . CanCOGeN (nccid.ca) . Emma . Griffiths . Jennifer . Tanner . Natalie . Knox . Will . Hsiao . Gary . Van Domselaar.
  9. Web site: Investigation of SARS-CoV-2 variants of concern in England; Technical briefing 6 (See section: Nomenclature of variants in the UK, P.3) . 13 February 2021 . assets.publishing.service.gov.uk . 27 February 2021.
  10. Web site: CDC. 2020-02-11. Cases, Data, and Surveillance. 2021-03-16. Centers for Disease Control and Prevention. en-us.
  11. Web site: Tracking SARS-CoV-2 variants. 2021-11-28. www.who.int. en.
  12. Web site: Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. 28 November 2021. World Health Organization.
  13. Web site: Statement on the update of WHO's working definitions and tracking system for SARS-CoV-2 variants of concern and variants of interest . www.who.int . 19 April 2024 . en.
  14. Web site: 2021-11-25 . New COVID-19 variant detected in South Africa . 2021-11-29 . NICD . en-US.
  15. Web site: Kwazulu-Natal Research Innovation and Sequencing Platform . 2021-11-29 . www.krisp.org.za.
  16. Web site: SARS-CoV-2 variants of concern . 26 November 2021 . www.ecdc.europa.eu . 27 November 2021.
  17. Web site: Variants of concern or under investigation: data up to 24 November 2021 . 26 November 2021 . www.gov.uk . 27 November 2021.
  18. Web site: Canada . Public Health Agency of . COVID-19 daily epidemiology update: Summary . aem . 2021-05-13 . 19 April 2020.
  19. Web site: 11 February 2020. SARS-CoV-2 Variant Classifications and Definitions. 30 April 2021. Centers for Disease Control and Prevention. en-us.
  20. Web site: Coronavirus Disease 2019 (COVID-19) . Centers for Disease Control and Prevention . 2021-12-07 . en-us . 11 February 2020.

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