Variant of concern

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SARS-CoV-2, the virus that causes COVID-19 Novel Coronavirus SARS-CoV-2.jpg
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]

Contents

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]

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]

Related Research Articles

Severe acute respiratory syndrome coronavirus 2 Virus that causes COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is the virus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. Also colloquially known simply as the coronavirus, it was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019. First identified in the city of Wuhan, Hubei, China, the World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. As described by the US National Institutes of Health, it is the successor to SARS-CoV-1, the virus that caused the 2002–2004 SARS outbreak.

COVID-19 Contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

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The New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) is an advisory body that advises the United Kingdom Government's Chief Medical Advisor / Chief Medical Officer for England, who in turn advises the UK Department of Health and Social Care and relevant ministers regarding threats from viral respiratory tract infections. The body replaced the UK Scientific Pandemic Influenza Advisory Committee (SPI) as part of a move to expand the scope to cover the threat of other respiratory viruses, besides pandemic influenza. The inaugural meeting was held on 19 December 2014 where the terms of reference were agreed. The group has been advising the Department of Health for some years and minutes of meetings are now regularly published, backdated to 2014. As of 2020, the group has been advising specifically on the COVID-19 pandemic.

SARS-CoV-2 Alpha variant Variant of SARS-CoV-2, the virus that causes COVID-19

The Alpha variant, also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several variants of concern, the variant is estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. It was first detected in November 2020 from a sample taken in September in the United Kingdom, and began to spread quickly by mid-December, around the same time as infections surged. This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant is also notable for having more mutations than normally seen.

SARS-CoV-2 Beta variant Variant of the SARS-CoV-2 virus

Beta variant, also known as lineage B.1.351, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa in October 2020, which was reported by the country's health department on 18 December 2020. Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay area in July or August 2020.

In microbiology and virology, the term variant or "genetic variant" is used to describe a subtype of a microorganism that is genetically distinct from a main strain, but not sufficiently different to be termed a distinct strain. A similar distinction is made in botany between different cultivated varieties of a species of plant, termed cultivars.

COVID-19 Genomics UK Consortium

The COVID-19 Genomics UK Consortium (COG-UK) is a group of public health agencies and academic institutions in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the Wellcome Sanger Institute. The consortium is known for first identifying the SARS-CoV-2 Alpha variant in November 2020. As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to the GISAID sequencing database originated from COG-UK.

Variants of SARS-CoV-2 Notable variants of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them.

SARS-CoV-2 Gamma variant Variant of the SARS-Cov-2 virus

Gamma variant, also known as lineage P.1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the World Health Organization, P.1 has been labeled Gamma variant, and is currently considered a variant of concern.

The following is a timeline of the COVID-19 pandemic in the United States during 2021.

SARS-CoV-2 Iota variant Variant of the SARS-Cov-2 virus first identified in New York City

Iota variant, also known as lineage B.1.526, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in New York City in November 2020. The variant has appeared with two notable mutations: the E484K spike mutation, which may help the virus evade antibodies, and the S477N mutation, which may help the virus bind more tightly to human cells.

SARS-CoV-2 Delta variant COVID-19 virus variant

The Delta variant, also known as lineage B.1.617.2 and the Indian variant, is a variant of lineage B.1.617 of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The World Health Organization (WHO) named it the Delta variant on 31 May 2021.

SARS-CoV-2 Theta variant Variant of the SARS-CoV-2 virus

Theta variant, also known as lineage P.3, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. The variant was first identified in the Philippines on February 18, 2021, when two mutations of concern were detected in Central Visayas. It was detected in Japan on March 12, 2021, when a traveler from the Philippines arrived at Narita International Airport in Tokyo.

SARS-CoV-2 Kappa variant COVID-19 virus variant

Kappa variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It is one of the three sublineages of Pango lineage B.1.617. The SARS-CoV-2 Kappa variant is also known as lineage B.1.617.1 and was first detected in India in December 2020. By the end of March 2021, the Kappa sub-variant accounted for more than half of the sequences being submitted from India. On 1 April 2021, it was designated a Variant Under Investigation (VUI-21APR-01) by Public Health England.

Lineage B.1.617 is a lineage of SARS-CoV-2, the virus that causes COVID-19. It first came to international attention in late March 2021 after the newly established INSACOG performed genome sequencing on positive samples throughout various Indian states. Analysis of samples from Maharashtra had revealed that compared to December 2020, there was an increase in the fraction of samples with the E484Q and L452R mutations. Lineage B.1.617 later came to be dubbed a double mutant by news media.

SARS-CoV-2 Lambda variant COVID-19 virus variant

Lambda variant, also known as lineage C.37, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Peru in August 2020. On 14 June 2021, the World Health Organization (WHO) named it Lambda variant and designated it as a variant of interest. It has spread to at least 30 countries around the world and is known to be more resistant to neutralizing antibodies compared to other strains. It is also suggested that the Lambda variant could be more infectious and resistant to vaccines than the Alpha and/or Gamma variant.

SARS-CoV-2 Epsilon variant Variant of the SARS-Cov-2 virus

Epsilon variant, also known as CAL.20C and referring to two PANGO lineages B.1.427 and B.1.429, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in California, USA in July 2020.

SARS-CoV-2 Zeta variant Variant of the SARS-Cov-2 virus

Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.

SARS-CoV-2 Eta variant Variant of the SARS-Cov-2 virus

The Eta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. The Eta variant or lineage B.1.525, also called VUI-21FEB-03 by Public Health England (PHE) and formerly known as UK1188, 21D or 20A/S:484K, does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion as found in Alpha, N439K variant and Y453F variant.

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References

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  2. 1 2 "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.
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