SARS-CoV-2 Epsilon variant

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Countries with confirmed cases of Epsilon variant as of 1 July 2021 (GISAID) Legend: .mw-parser-output .legend{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .legend-color{display:inline-block;min-width:1.25em;height:1.25em;line-height:1.25;margin:1px 0;text-align:center;border:1px solid black;background-color:transparent;color:black}.mw-parser-output .legend-text{} 10,000+ confirmed sequences 1,000-9,999 confirmed sequences 100-999 confirmed sequences 10-99 confirmed sequences 2-9 confirmed sequences 1 confirmed sequence None or no data available Epsilon variant countries.svg
Countries with confirmed cases of Epsilon variant as of 1 July 2021 (GISAID)
Legend:
  10,000+ confirmed sequences
  1,000–9,999 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 March 2022, Epsilon is considered as a previously circulating variant of interest by the WHO. It is considered a variant being monitored by the CDC.

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), [2] of which the L452R (previously also detected in other unrelated lineages) was of particular concern. [3] B.1.429 is possibly more transmissible than previous variants circulating locally, but further study is necessary to confirm this. [3] 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. [4] [5] In May 2021, the World Health Organization (WHO) gave the variant the name 'Epsilon variant'. [6]

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 from 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. [8] [9] 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. [3] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department, [10] 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%. [11] A preprint describes CAL.20C 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. However, in the US as a whole, the 20G clade predominated 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. [8] [9] As of July 2021, the Epsilon variant had been detected in 45 countries, according to GISAID. [12] After an initial increase, its frequency rapidly decreased 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 itself elsewhere; only 3.2% of all cases in the United States were Epsilon, whereas by then more than two-thirds were Alpha. [13]

Statistics

See also

Related Research Articles

<span class="mw-page-title-main">GISAID</span> Global initiative for sharing virus data

GISAID, the Global Initiative on Sharing All Influenza Data, previously the Global Initiative on Sharing Avian Influenza Data, is a global science initiative established in 2008 to provide access to genomic data of influenza viruses. The database was expanded to include the coronavirus responsible for the COVID-19 pandemic, as well as other pathogens. The database has been described as "the world's largest repository of COVID-19 sequences". GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet.

<span class="mw-page-title-main">SARS-CoV-2</span> Virus that causes COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. The virus previously had the 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 designated the outbreak a public health emergency of international concern from January 30, 2020, to May 5, 2023. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans.

<span class="mw-page-title-main">SARS-CoV-2 Alpha variant</span> Variant of SARS-CoV-2, the virus that causes COVID-19

The Alpha variant (B.1.1.7) was a SARS-CoV-2 variant of concern. It was estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. Scientists more widely took note of this variant in early December 2020, when a phylogenetic tree showing viral sequences from Kent, United Kingdom looked unusual.

<span class="mw-page-title-main">SARS-CoV-2 Beta variant</span> Variant of the SARS-CoV-2 virus

The Beta variant, (B.1.351), was a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants initially 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.

<span class="mw-page-title-main">Variants of SARS-CoV-2</span> Notable variants of SARS-CoV-2

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are viruses that, while similar to the original, have genetic changes that are of enough significance to lead virologists to label them separately. SARS-CoV-2 is the virus that causes coronavirus disease 2019 (COVID-19). Some have been stated, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. These variants contribute to the continuation of the COVID-19 pandemic.

<span class="mw-page-title-main">SARS-CoV-2 Gamma variant</span> Variant of the virus SARS-CoV-2

The Gamma variant (P.1) was 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 in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. It 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 was labeled Gamma variant, and was considered a variant of concern until March 2022, when it was largely displaced by the delta and omicron variants.

<span class="mw-page-title-main">SARS-CoV-2 variant of concern</span> Highly transmissible and virulent strains of SARS-CoV-2

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 in RBD-hACE2 complex, while also being linked to rapid spread in human populations.

<span class="mw-page-title-main">SARS-CoV-2 Iota variant</span> 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 helps the virus bind more tightly to human cells.

<span class="mw-page-title-main">SARS-CoV-2 Delta variant</span> Variant of SARS-CoV-2 detected late 2020

The Delta variant (B.1.617.2) was a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India on 5 October 2020. The Delta variant was named on 31 May 2021 and had spread to over 179 countries by 22 November 2021. The World Health Organization (WHO) indicated in June 2021 that the Delta variant was becoming the dominant strain globally.

<span class="mw-page-title-main">SARS-CoV-2 Theta variant</span> 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.

INSACOG is the forum set up under the Ministry of Health and Family Welfare by the Government of India on 30 December 2020, to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India. Initially it was tasked to study the virus variant Lineage B.1.1.7 earlier found in United Kingdom in December 2020.

<span class="mw-page-title-main">SARS-CoV-2 Kappa variant</span> Type of the virus detected in 2020

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.

<span class="mw-page-title-main">SARS-CoV-2 Lambda variant</span> Variant of SARS-CoV-2

The 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. On 16 March 2022, the WHO has de-escalated the Lambda variant to "previously circulating variants of concern".

<span class="mw-page-title-main">SARS-CoV-2 Zeta variant</span> 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.

<span class="mw-page-title-main">SARS-CoV-2 Eta variant</span> Variant of the SARS-Cov-2 virus

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<span class="mw-page-title-main">SARS-CoV-2 Omicron variant</span> Type of the virus first detected in November 2021

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References

  1. 1 2 "Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients". news wise (Press release). California: Cedars Sinai Medical Center. January 19, 2021. Retrieved March 3, 2021.
  2. ↑ Spike Variants: Epsilon, aka B.1.427/B.1.429, and CAL.20C/S:452R covdb.stanford.edu, accessed 3 July 2021
  3. 1 2 3 "New California Variant May Be Driving Virus Surge There, Study Suggests". The New York Times . January 19, 2021.
  4. ↑ "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. March 24, 2021. Retrieved April 4, 2021.
  5. ↑ Shen X, Tang H, Pajon R, Smith G, Glenn GM, Shi W, et al. (April 2021). "Neutralization of SARS-CoV-2 Variants B.1.429 and B.1.351". The New England Journal of Medicine. 384 (24): 2352–2354. doi: 10.1056/NEJMc2103740 . PMC   8063884 . PMID   33826819.
  6. ↑ Helen Branswell The name game for coronavirus variants just got a little easier 31 May 2021 www.statnews.com, accessed 28 June 2021
  7. ↑ "Spike Variants: Epsilon variant, aka B.1.427/B.1.429". covdb.stanford.edu. Stanford University Coronavirus Antiviral & Resistance Database. July 1, 2021. Retrieved July 5, 2021.
  8. 1 2 "B.1.429". Rambaut Group, University of Edinburgh. PANGO Lineages. February 15, 2021. Archived from the original on April 28, 2021. Retrieved February 16, 2021.
  9. 1 2 "B.1.429 Lineage Report". Scripps Research . outbreak.info. February 15, 2021. Retrieved February 16, 2021.
  10. ↑ "COVID-19 Variant First Found in Other Countries and States Now Seen More Frequently in California". California Department of Public Health. Retrieved January 30, 2021.
  11. ↑ Weise E, Weintraub K. "New strains of COVID swiftly moving through the US need careful watch, scientists say". USA Today. Retrieved January 30, 2021.
  12. ↑ "Watching the new Epsilon variant of SARS-CoV-2". Healthcare Purchasing News. July 12, 2021. Retrieved September 12, 2021. According to GISAID, 45 countries, from US to South Korea, from India to Japan have reported Epsilon variant cases.
  13. ↑ Zimmer, Carl; Mandavilli, Apoorva (May 14, 2021). "How the United States Beat the Variants, for Now". New York Times. Archived from the original on December 28, 2021. Retrieved May 17, 2021.
  14. ↑ "GISAID - hCov19 Variants". www.gisaid.org. Retrieved July 2, 2021.
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