SARS-CoV-2 Epsilon variant

Countries with confirmed cases of Epsilon variant as of 1 July 2021 (GISAID)
  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]

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


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]


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]


See also


  1. ^ a b "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. ^ "Tracking SARS-CoV-2 variants". World Health Organization.{{cite web}}: CS1 maint: url-status (link)
  3. ^ Spike Variants: Epsilon, aka B.1.427/B.1.429, and CAL.20C/S:452R, accessed 3 July 2021
  4. ^ a b c "New California Variant May Be Driving Virus Surge There, Study Suggests". The New York Times. January 19, 2021.
  5. ^ "SARS-CoV-2 Variant Classifications and Definitions". Centers for Disease Control and Prevention. March 24, 2021. Retrieved April 4, 2021.
  6. ^ 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.
  7. ^ Helen Branswell The name game for coronavirus variants just got a little easier 31 May 2021, accessed 28 June 2021
  8. ^ "Spike Variants: Epsilon variant, aka B.1.427/B.1.429". Stanford University Coronavirus Antiviral & Resistance Database. July 1, 2021. Retrieved July 5, 2021.
  9. ^ a b "B.1.429". Rambaut Group, University of Edinburgh. PANGO Lineages. February 15, 2021. Retrieved February 16, 2021.
  10. ^ a b "B.1.429 Lineage Report". Scripps Research. February 15, 2021. Retrieved February 16, 2021.
  11. ^ "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.
  12. ^ Weise E, Weintraub K. "New strains of COVID swiftly moving through the US need careful watch, scientists say". USA Today. Retrieved January 30, 2021.
  13. ^ "Watching the new Epsilon variant of SARS-CoV-2". Healthcare Purchasing News. Retrieved September 12, 2021. According to GISAID, 45 countries, from US to South Korea, from India to Japan have reported Epsilon variant cases.
  14. ^ 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.
  15. ^ "GISAID - hCov19 Variants". Retrieved July 2, 2021.

Media files used on this page

Coronavirus. SARS-CoV-2.png
Author/Creator: Alexey Solodovnikov (Idea, Producer, CG, Editor), Valeria Arkhipova (Scientific Сonsultant), Licence: CC BY-SA 4.0
Scientifically accurate atomic model of the external structure of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), a strain (genetic variant) of the coronavirus that caused Coronavirus disease (COVID-19), first identified in Wuhan, China, during December 2019

Each separate locus (amorphous blob) is an atom of:

  cobalt: membrane
  crimson: E protein
  green: M protein
  orange: glucose (glycan)
  turquoise : S (spike) glycoprotein
SARS-CoV-2 (Wikimedia colors).svg
Author/Creator: Geraki, Licence: CC BY-SA 4.0
SARS-CoV-2 logo in Wikimedia colors
Flag of the United States.svg
Author/Creator: unknown, Licence: PD
Flag of Mexico.svg
Flag of Mexico Official version of the Flag of the United Mexican States or Mexico, adopted September 16th 1968 by Decree (Published August 17th 1968), Ratio 4:7. The previous version of the flag displayed a slightly different Coat of Arms. It was redesigned to be even more resplendent due to the upcoming Mexico City 1968 Olympic Games; According to Flag of Mexico, the colors are Green Pantone 3425 C and Red Pantone 186 C. According to [1] or [2], that translates to RGB 206, 17, 38 for the red, and RGB 0, 104, 71 for the green.
Flag of Canada (Pantone).svg
Flag of Canada introduced in 1965, using Pantone colors. This design replaced the Canadian Red Ensign design.
Flag of Aruba.svg
The flag of Aruba
Flag of Maldives.svg
Flag of Maldives. The colours used are Pantone 186 C for red and Pantone 348 C for green.
Flag of Chile.svg
It is easy to put a border around this flag image
Flag of the United Kingdom.svg
Flag of the United Kingdom, Union Jack or Union Flag in a 1:2 ratio (typical on British warships and also the rank flag of an admiral of the fleet).
Flag of Japan.svg
Author/Creator: unknown, Licence: PD
Flag of Australia (converted).svg

Flag of Australia, when congruence with this colour chart is required (i.e. when a "less bright" version is needed).

See Flag of Australia.svg for main file information.
Flag of Germany.svg
Author/Creator: unknown, Licence: PD
Flag of Israel.svg
Flag of Israel. Shows a Magen David (“Shield of David”) between two stripes. The Shield of David is a traditional Jewish symbol. The stripes symbolize a Jewish prayer shawl (tallit).
Flag of Guam.svg
The flag of Guam, courtesy an e-mail from the author of xrmap. Modifications by Denelson83.
Flag of Ireland.svg
Note that the green portion of the flag was designed to represent the majority Catholic residents of the island, the orange side the minority Protestant and the white middle part peace and harmony between them.
Flag of Spain.svg
Author/Creator: unknown, Licence: PD
Flag of New Zealand.svg
Flag of New Zealand. Specification: , quoting New Zealand Gazette, 27 June 1902.
Flag of Norway.svg
Flag of Norway. The colors approximately correspond to Pantone 200 C (deep red) and 281 C (dark blue).
Flag of Italy.svg
Author/Creator: unknown, Licence: PD
Flag of Sweden.svg
Author/Creator: unknown, Licence: PD
Flag of the Turks and Caicos Islands.svg
Flag of the Turks and Caicos Islands
Flag of Anguilla.svg
Flag of Anguilla (adopted on 30 May 1990) - RGB colours, 1:2 dimensions and construction details based partly on the templates: Flag of Anguilla – A Brief History
Flag of Belgium (civil).svg
The civil ensign and flag of Belgium. It is identical to Image:Flag of Belgium.svg except that it has a 2:3 ratio, instead of 13:15.
Flag of Curaçao.svg
The flag of Curaçao is a blue field with a horizontal yellow stripe slightly below the midline and two white, five-pointed stars in the canton. The geometry and colors are according to the description at Flags of the World.
Flag of India.svg
Author/Creator: unknown, Licence:
Flag of the Northern Mariana Islands.svg
Author/Creator: unknown, Licence: CC0
Flag of the Dominican Republic.svg
The flag of the Dominican Republic has a centered white cross that extends to the edges. This emblem is similar to the flag design and shows a bible, a cross of gold and 6 Dominican flags. There are branches of olive and palm around the shield and above on the ribbon is the motto "Dios,Patria!, Libertad" ("God, Country, Freedom") and to amiable freedom. The blue is said to stand for liberty, red for the fire and blood of the independence struggle and the white cross symbolized that God has not forgotten his people. "Republica Dominicana". The Dominican flag was designed by Juan Pablo Duarte, father of the national Independence of Dominican Republic. The first dominican flag was sewn by a young lady named Concepción Bona, who lived across the street of El Baluarte, monument where the patriots gathered to fight for the independence, the night of February 27th, 1844. Concepción Bona was helped by her first cousin María de Jesús Pina.
WHO Rod.svg
The rod of Asclepius as depicted in the WHO logo.
Author/Creator: User:FoeNyx © 2004 (artistic illustration), Licence: CC-BY-SA-3.0
VIH - HIV / SIDA - AIDS viruses.
SARS-CoV-2 Epsilon variant.svg
Author/Creator: Stanford HIVDB Team, PhiLiP, Licence: CC BY-SA 4.0
Amino acid mutations of SARS-CoV-2 Epsilon variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.
Epsilon variant countries.svg
Author/Creator: TapticInfo, Licence: CC BY-SA 4.0
  10000+ confirmed cases
  1000 - 9999 confirmed cases
  100 - 999 confirmed cases
  10 - 99 confirmed cases
  2 - 9 confirmed cases
  1 confirmed case
  No confirmed cases, no population, or no data available