Variant of concern

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SARS-CoV-2, the virus that causes COVID-19

The term variant of concern (VOC) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, which causes COVID-19) is a category used when mutations in 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 this, an emerging variant may have been labeled a "variant of interest".[2] During or after fuller assessment as a "variant of concern" the variant is typically assigned to a lineage in the PANGOLIN nomenclature system[3] and to clades in the Nextstrain[4] and GISAID[5] 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.[6] This was principally for reasons of transmissibility and virulence, and also with regard to the possible emergence of escape mutations.

Criteria considered during the COVID-19 pandemic

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:[7][8]

  • Increased transmissibility
  • Increased morbidity
  • Increased mortality
  • Increased risk of "long COVID"
  • Ability to evade detection by diagnostic tests
  • Decreased susceptibility to antiviral drugs (if and when such drugs are available)
  • Decreased susceptibility to neutralizing antibodies, either therapeutic (e.g., convalescent plasma or monoclonal antibodies) or in laboratory experiments
  • Ability to evade natural immunity (e.g., causing reinfections)
  • Ability to infect vaccinated individuals
  • Increased risk of particular conditions such as multisystem inflammatory syndrome or long-haul COVID.
  • Increased affinity for particular demographic or clinical groups, such as children or immunocompromised individuals.

Terminology

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.[2][6][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]

Examples

Canada

As of 12 May 2021, Canada was specifically tracking three variants of concern – B.1.1.7, B.1.351, and P.1.[11]

Europe

As of 11 May 2021, the European Centre for Disease Prevention and Control had declared interest in four variants of concern, B.1.1.7, B.1.1.7+E484K, B.1.351, and P.1. They named a further nine variants of interest (VOI): B.1.525, B.1.427/B.1.429, P.3, B.1.616, B.1.617.1, B.1.617.2, B.1.617.3, B.1.620, and B.1.621, while 17 more were described as variants under monitoring.[12]

United Kingdom

As of 5 March 2021, the United Kingdom has eight variants on its 'watch list', 4 with 'VOC' status and 4 rated as 'VUI', with PHE adding the fourth VUI after 16 people had tested positive for it at dates beginning with 15 February.[13] The latest variant is VUI-21FEB-04 (Lineage B.1.1.318), and was designated a VUI on 24 February. Other VUIs are P.2, VUI-21FEB-01 (A.23.1 with E484K), and B.1.525, while VOCs are Lineage B.1.1.7, Lineage B.1.351 and Lineage P.1.[14][15]

Note that in March 2021, PHE changed their naming convention to use the format [YY][MMM]-[NN], where the month is written out using a three-letter code.[16]

United States

The CDC maintains a list of variants of concern. As of May 2021, they are tracking B.1.1.7, B.1.351, the related variants B.1.427 and B.1.429, and P.1.[17]

World Health Organization

The WHO maintains a list of variants of global concern.[18][19]

References

  1. ^ Shahhosseini, Nariman; Babuadze, George (Giorgi); Wong, Gary; Kobinger, Gary P. (May 2021). "Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern". Microorganisms. 9 (5): 926. doi:10.3390/microorganisms9050926. PMC 8146828. PMID 33925854.
  2. ^ a b "Variants: distribution of cases data". GOV.UK. 28 January 2021. At "Differences between a Variant of Concern and Variant Under Investigation". Retrieved 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)
  3. ^ Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.
  4. ^ Bedford, Trevor; Hodcroft, Emma B; Neher, Richard A (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". nextstrain.org/blog. Retrieved 19 January 2021.
  5. ^ "clade tree (from 'Clade and lineage nomenclature')". www.gisaid.org. 4 July 2020. Retrieved 7 January 2021.
  6. ^ a b Griffiths, Emma; Tanner, Jennifer; Knox, Natalie; Hsiao, Will; Van Domselaar, Gary (15 January 2021). "CanCOGeN Interim Recommendations for Naming, Identifying, and Reporting SARS-CoV-2 Variants of Concern" (PDF). CanCOGeN (nccid.ca). Retrieved 25 February 2021.
  7. ^ Contributor, IDSA (2 February 2021). "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. Retrieved 20 February 2021.
  8. ^ CDC. "Emerging SARS-CoV-2 Variants". Centers for Disease Control and Prevention. Retrieved 4 January 2021. Public Domain This article incorporates text from this source, which is in the public domain.
  9. ^ Investigation of SARS-CoV-2 variants of concern in EnglandTechnical briefing 6 13 February 2021 (See section: Nomenclature of variants in the UK, P.3) assets.publishing.service.gov.uk, accessed 27 February 2021
  10. ^ CDC (11 February 2020). "Cases, Data, and Surveillance". Centers for Disease Control and Prevention. Retrieved 16 March 2021.
  11. ^ COVID-19 daily epidemiology update 12 May 2021 health-infobase.canada.ca accessed 13 May 2021
  12. ^ SARS-CoV-2 variants of concern as of 11 May 2021 11 May 2021 www.ecdc.europa.eu accessed 13 May 2021
  13. ^ Covid-19: Another new variant added to UK watch list Michelle Roberts, 4 March 2021 www.bbc.com, accessed 5 March 2021
  14. ^ Variants of concern or under investigation: data up to 3 March 2021 4 March 2021 www.gov.uk, accessed 5 March 2021
  15. ^ Latest update: New Variant Under Investigation designated in the UK 4 March 2021 www.gov.uk, accessed 5 March 2021
  16. ^ Public Health England (22 March 2021). "Variants: distribution of cases data". GOV.UK. Retrieved 22 March 2021.
  17. ^ "SARS-CoV-2 Variant Classifications and Definitions". Centers for Disease Control and Prevention. 11 February 2020. Retrieved 30 April 2021.
  18. ^ "WHO says India Covid variant of 'global concern'". BBC. 11 May 2021.
  19. ^ "Tracking SARS-CoV-2 variants". www.who.int. Retrieved 16 June 2021.

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