SARS-CoV-2 Epsilon variant

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Countries with confirmed cases of Epsilon variant as of 1 July 2021 (GISAID)
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Countries with confirmed cases of Epsilon variant as of 1 July 2021 (GISAID)
Legend:
  10000+ confirmed sequences
  1000–9999 confirmed sequences
  100–999 confirmed sequences
  10–99 confirmed sequences
  2–9 confirmed sequences
  1 confirmed sequence
  None or no data available

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. [1]

Contents

As of July 2021, Epsilon is no longer considered as a variant of interest by the WHO. [2]

Mutations

The variant has five defining mutations (I4205V and D1183Y in the ORF1ab-gene, and S13I, W152C, L452R in the spike protein's S-gene), [3] of which the L452R (previously also detected in other unrelated lineages) was of particular concern. [4] B.1.429 is possibly more transmissible than previous variants circulating locally, but further study is necessary to confirm this. [4] Centers for Disease Control and Prevention (CDC) has listed B.1.429 and the related B.1.427 as "variants of concern," and cites a preprint for saying that they exhibit a ~20% increase in viral transmissibility, that they have a "Significant impact on neutralization by some, but not all" therapeutics that have been given Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA) for treatment or prevention of COVID-19, and that they moderately reduce neutralization by plasma collected by people who have previously been infected by the virus or who have received a vaccine against the virus. [5] [6] In May 2021, the World Health Organization (WHO) gave the variant the new name 'Epsilon variant'. [7]

History

Epsilon (CAL.20C) was first observed in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic. [1] It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November. [9] [10] In November 2020, the Epsilon variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the Epsilon variant accounted for 50 percent of samples. [4] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department, [11] it was announced that the variant was also detected in multiple counties in Northern California. From November to December 2020, the frequency of the variant in sequenced cases from Northern California rose from 3% to 25%. [12] In a preprint, CAL.20C is described as belonging to Nextstrain clade 20C and contributing approximately 36% of samples, while an emerging variant from the 20G clade accounts for some 24% of the samples in a study focused on Southern California. Note however that in the US as a whole, the 20G clade predominates, as of January 2021. Following the increasing numbers of Epsilon in California, the variant has been detected at varying frequencies in most US states. Small numbers have been detected in other countries in North America, and in Europe, Asia and Australia. [9] [10] As of July 2021, the Epsilon variant had been detected in 45 countries, according to GISAID. [13] After an initial increase, its frequency rapidly dropped from February 2021 as it was being outcompeted by the more transmissible Alpha variant. In April, Epsilon remained relatively frequent in parts of northern California, but it had virtually disappeared from the south of the state and had never been able to establish a foothold elsewhere; only 3.2% of all cases in the United States were Epsilon, whereas by then more than two-thirds were Alpha. [14]

Statistics

Cases by country (Updated as of 1 July 2021) GISAID [15]
CountryConfirmed casesLast Reported Case
USA50,72323 June 2021
Mexico47408 June 2021
Canada32607 May 2021
South Korea10326 April 2021
Aruba5724 April 2021
Denmark3722 March 2021
Chile3007 June 2021
Argentina2812 May 2021
United Kingdom2110 May 2021
Japan2016 April 2021
Australia2012 April 2021
Costa Rica1205 May 2021
Germany1008 June 2021
Israel1025 February 2021
Guam827 March 2021
Taiwan831 January 2021
Guatemala7
France701 March 2021
Ireland728 April 2021
Netherlands510 March 2021
Spain503 June 2021
New Zealand428 December 2020
Singapore427 March 2021
Switzerland401 March 2021
Cameroon305 February 2021
Guadeloupe330 January 2021
Norway312 April 2021
Cambodia220 January 2021
Finland206 February 2021
Italy211 February 2021
Peru224 February 2021
Sweden228 January 2021
Turkey211 February 2021
Turks and Caicos Islands222 March 2021
Colombia208 January 2021
Anguilla119 March 2021
Antigua and Barbuda124 April 2021
Barbados112 April 2021
Belgium118 January 2021
British Virgin Islands107 January 2021
Curacao119 March 2021
India102 March 2021
North Macedonia126 January 2021
Northern Mariana Islands116 January 2021
Sint Maarten116 February 2021
Dominican Republic1
World (46 countries)Total: 51,966Total as of 1 July 2021

See also

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GISAID is a global science initiative and primary source established in 2008 that provides open-access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pandemic. On January 10, 2020, the first whole-genome sequences of SARS-CoV-2 were made available on GISAID, which enabled global responses to the pandemic, including the development of the first vaccines and diagnostic tests to detect SARS-CoV-2. GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet.

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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.

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"Cluster 5", also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), is a variant of SARS-CoV-2, the virus that causes COVID-19, that is believed to be extinct. It was discovered in North Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of North Jutland to prevent the mutation from spreading, which could compromise national or international responses to 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.

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.

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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.

Variant of concern Newly emerged variant of a virus with transmissibility and virulence that causes concerns

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

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

The Delta variant, also known as lineage B.1.617.2, 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

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

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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.

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References

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