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SARS-CoV-2 variant of concern

May 04, 2024

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]

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

Before being allocated to this category, an emerging variant may have been labeled a variant of interest (VOI),[2] or in some countries a variant under investigation (VUI).[3] During or after fuller assessment as a variant of concern the variant is typically assigned to a lineage in the Pango nomenclature system[4] and to clades in the Nextstrain[5] and GISAID[6] 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.[7] This was principally for reasons of transmissibility and virulence, and also with regard to the possible emergence of escape mutations.

Criteria edit

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:[8][9]

  • 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.

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.[3][7][10] 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.[11]

Classifications by country edit

World Health Organization edit

The WHO maintains a list of variants of global concern.[2] 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.[citation needed] 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 edit

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

Europe edit

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 edit

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 edit

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]

References edit

  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 "Tracking SARS-CoV-2 variants". www.who.int. Retrieved 28 November 2021.
  3. ^ 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)
  4. ^ 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.
  5. ^ 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.
  6. ^ "clade tree (from 'Clade and lineage nomenclature')". www.gisaid.org. 4 July 2020. Retrieved 7 January 2021.
  7. ^ 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.
  8. ^ Lucey, Daniel R. (2 February 2021). "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. Retrieved 5 June 2022.
  9. ^ CDC (11 February 2020). "Emerging SARS-CoV-2 Variants". Centers for Disease Control and Prevention. Retrieved 4 January 2021.   This article incorporates text from this source, which is in the public domain.
  10. ^ "Investigation of SARS-CoV-2 variants of concern in England; Technical briefing 6 (See section: Nomenclature of variants in the UK, P.3)" (PDF). assets.publishing.service.gov.uk. 13 February 2021. Retrieved 27 February 2021.
  11. ^ CDC (11 February 2020). "Cases, Data, and Surveillance". Centers for Disease Control and Prevention. Retrieved 16 March 2021.
  12. ^ "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". World Health Organization. Retrieved 28 November 2021.
  13. ^ "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. Retrieved 19 April 2024.
  14. ^ "New COVID-19 variant detected in South Africa". NICD. 25 November 2021. Retrieved 29 November 2021.
  15. ^ "Kwazulu-Natal Research Innovation and Sequencing Platform". www.krisp.org.za. Retrieved 29 November 2021.
  16. ^ "SARS-CoV-2 variants of concern". www.ecdc.europa.eu. 26 November 2021. Retrieved 27 November 2021.
  17. ^ "Variants of concern or under investigation: data up to 24 November 2021". www.gov.uk. 26 November 2021. Retrieved 27 November 2021.
  18. ^ Canada, Public Health Agency of (19 April 2020). "COVID-19 daily epidemiology update: Summary". aem. Retrieved 13 May 2021.
  19. ^ "SARS-CoV-2 Variant Classifications and Definitions". Centers for Disease Control and Prevention. 11 February 2020. Retrieved 30 April 2021.
  20. ^ "Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. 11 February 2020. Retrieved 7 December 2021.

May 04, 2024
sars, variant, concern, term, variant, concern, sars, which, causes, covid, category, used, variants, virus, where, mutations, their, spike, protein, receptor, binding, domain, substantially, increase, binding, affinity, n501y, hace2, complex, genetic, data, w. 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 SARS CoV 2 the virus that causes COVID 19 Before being allocated to this category an emerging variant may have been labeled a variant of interest VOI 2 or in some countries a variant under investigation VUI 3 During or after fuller assessment as a variant of concern the variant is typically assigned to a lineage in the Pango nomenclature system 4 and to clades in the Nextstrain 5 and GISAID 6 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 7 This was principally for reasons of transmissibility and virulence and also with regard to the possible emergence of escape mutations Contents 1 Criteria 2 Classifications by country 2 1 World Health Organization 2 2 Africa 2 3 Europe 2 4 United Kingdom 2 5 North America 3 ReferencesCriteria editSee 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 8 9 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 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 3 7 10 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 11 Classifications by country editWorld Health Organization edit The WHO maintains a list of variants of global concern 2 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 citation needed 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 edit The NICD in South Africa maintains a list of variants and testing facilities locally in collaboration with KRISP 14 15 Europe edit 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 edit 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 edit 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 References edit 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 a b Tracking SARS CoV 2 variants www who int Retrieved 28 November 2021 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 Rambaut A Holmes E C O Toole A 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 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 clade tree from Clade and lineage nomenclature www gisaid org 4 July 2020 Retrieved 7 January 2021 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 Lucey Daniel R 2 February 2021 COVID Mega variant and eight criteria for a template to assess all variants Science Speaks Global ID News Retrieved 5 June 2022 CDC 11 February 2020 Emerging SARS CoV 2 Variants Centers for Disease Control and Prevention Retrieved 4 January 2021 nbsp This article incorporates text from this source which is in the public domain Investigation of SARS CoV 2 variants of concern in England Technical briefing 6 See section Nomenclature of variants in the UK P 3 PDF assets publishing service gov uk 13 February 2021 Retrieved 27 February 2021 CDC 11 February 2020 Cases Data and Surveillance Centers for Disease Control and Prevention Retrieved 16 March 2021 Classification of Omicron B 1 1 529 SARS CoV 2 Variant of Concern World Health Organization Retrieved 28 November 2021 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 Retrieved 19 April 2024 New COVID 19 variant detected in South Africa NICD 25 November 2021 Retrieved 29 November 2021 Kwazulu Natal Research Innovation and Sequencing Platform www krisp org za Retrieved 29 November 2021 SARS CoV 2 variants of concern www ecdc europa eu 26 November 2021 Retrieved 27 November 2021 Variants of concern or under investigation data up to 24 November 2021 www gov uk 26 November 2021 Retrieved 27 November 2021 Canada Public Health Agency of 19 April 2020 COVID 19 daily epidemiology update Summary aem Retrieved 13 May 2021 SARS CoV 2 Variant Classifications and Definitions Centers for Disease Control and Prevention 11 February 2020 Retrieved 30 April 2021 Coronavirus Disease 2019 COVID 19 Centers for Disease Control and Prevention 11 February 2020 Retrieved 7 December 2021 Retrieved from https en wikipedia org w index php title SARS CoV 2 variant of concern amp oldid 1220891753, wikipedia, wiki, book, books, library,

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