SARS-CoV-2 Iota variant

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Iota variant, [1] 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.[ citation needed ]

Contents

By February 2021, it had spread rapidly in the New York region and accounted for about one in four viral sequences. [2] [3] By 11 April 2021, the variant had been detected in at least 48 U.S. states and 18 countries. [4] [5]

Under the simplified naming scheme proposed by the World Health Organization, B.1.526 has been labeled Iota variant, and is considered a variant of interest (VOI), but not yet a variant of concern. [6]

Mutations

The Iota (B.1.526) genome contains the following amino-acid mutations, all of which are in the virus's spike protein code: L5F, T95I, D253G, E484K, D614G and A701V. [7]

History

The increase of the Iota variant was captured by researchers at Caltech by scanning for mutations in a database known as GISAID, a global science initiative that has documented over 700,000 genomic sequences of SARS-CoV-2. [9] [10]

The proportion of USA cases represented by the Iota variant had declined sharply by the end of July 2021 as the Delta variant became dominant. [11]

Statistics

Cases by country (Updated as of 11 August 2021) GISAID [12]
CountryConfirmed casesLast Reported Case
Flag of the United States.svg USA45,55824 June 2021
Flag of Ecuador.svg Ecuador16810 June 2021
Flag of Canada (Pantone).svg Canada158
Flag of Spain.svg Spain11917 June 2021
Flag of Colombia.svg Colombia11524 May 2021
Flag of Aruba.svg Aruba10310 June 2021
Flag of Germany.svg Germany5622 June 2021
Flag of Mexico.svg Mexico5011 June 2021
Flag of the United Kingdom.svg United Kingdom4316 May 2021
Flag of Sint Maarten.svg Sint Maarten1727 May 2021
Flag of Ireland.svg Ireland137 May 2021
Flag of Switzerland.svg  Switzerland1217 May 2021
Flag of Chile.svg Chile1112 May 2021
Flag of Denmark.svg Denmark931 May 2021
Flag of Israel.svg Israel926 April 2021
Flag of Suriname.svg Suriname910 May 2021
Flag of Argentina.svg Argentina826 April 2021
Flag of Belgium (civil).svg Belgium818 April 2021
Flag of the Dominican Republic.svg Dominican Republic810 June 2021
Flag of France.svg France825 May 2021
Flag of Lithuania.svg Lithuania828 May 2021
Flag of Singapore.svg Singapore74 April 2021
Flag of Australia (converted).svg Australia621 May 2021
Flag of Italy.svg Italy64 May 2021
Flag of Luxembourg.svg Luxembourg605 March 2021
Flag of Costa Rica.svg Costa Rica521 May 2021
Flag of the Netherlands.svg Netherlands519 April 2021
Flag of Russia.svg Russia54 June 2021
Flag of Croatia.svg Croatia49 February 2021
Flag of Japan.svg Japan47 May 2021
Flag of South Korea.svg South Korea414 April 2021
Flag of Sweden.svg Sweden414 May 2021
Flag of Turkey.svg Turkey44 May 2021
Flag of Malta.svg Malta421 December 2020
Flag of India.svg India324 March 2021
Flag of Dominica.svg Dominica315 January 2021
Flag of Slovenia.svg Slovenia318 May 2021
Flag of Austria.svg Austria222 April 2021
Flag of Ghana.svg Ghana220 March 2021
Flag of Grenada.svg Grenada217 January 2021
Flag of Indonesia.svg Indonesia28 January 2021
Flag of Jamaica.svg Jamaica22 February 2021
Flag of Liberia.svg Liberia214 May 2021
Flag of Portugal.svg Portugal24 March 2021
Flag of Romania.svg Romania217 April 2021
Flag of Anguilla.svg Anguilla121 April 2021
Flag of Antigua and Barbuda.svg Antigua and Barbuda13 May 2021
Flag of the British Virgin Islands.svg British Virgin Islands125 January 2021
Flag of the Cayman Islands.svg Cayman Islands115 April 2021
Flag of the People's Republic of China.svg China1
Flag of Curacao.svg Curacao130 April 2021
Flag of Finland.svg Finland114 March 2021
Flag of France.svg Guadeloupe19 March 2021
Flag of New Zealand.svg New Zealand116 March 2021
Flag of Poland.svg Poland131 March 2021
Flag of the Turks and Caicos Islands.svg Turks and Caicos Islands122 March 2021
Flag of Venezuela.svg Venezuela18 May 2021
World (57 countries)Total: 46,589Total as of 11 August 2021

See also

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References

  1. "Tracking SARS-CoV-2 variants". www.who.int. Retrieved June 1, 2021.
  2. Rosa-Aquino, Matt Stieb, Paola (March 21, 2021). "Everything We Know About the Coronavirus Variant Spreading in New York City". Intelligencer. Retrieved April 10, 2021.
  3. Mandavilli, Apoorva (February 24, 2021). "A New Coronavirus Variant Is Spreading in New York, Researchers Report". The New York Times. ISSN   0362-4331 . Retrieved April 10, 2021.
  4. "outbreak.info". outbreak.info. Retrieved April 10, 2021.
  5. "PANGO lineages Lineage B.1.526". cov-lineages.org. April 22, 2021. Retrieved April 22, 2021.
  6. "Tracking SARS-CoV-2 variants". www.who.int. Retrieved June 1, 2021.
  7. "SARS-CoV-2 Variant Classifications and Definitions". CDC.gov. Centers for Disease Control and Prevention. Retrieved July 5, 2021.
  8. "Spike Variants: Iota variant, aka B.1.526". covdb.stanford.edu. Stanford University Coronavirus Antiviral & Resistance Database. July 1, 2021. Retrieved July 5, 2021.
  9. Corum, Jonathan; Zimmer, Carl. "Coronavirus Variants and Mutations". The New York Times. ISSN   0362-4331 . Retrieved April 10, 2021.
  10. West, Anthony P.; Barnes, Christopher O.; Yang, Zhi; Bjorkman, Pamela J. (February 23, 2021). "SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape". bioRxiv: 2021.02.14.431043. doi:10.1101/2021.02.14.431043. PMC   8077570 . PMID   33907745. S2CID   231981267.
  11. SARS-CoV-2 sequences by variant, Jul 26, 2021, USA Our World in Data
  12. "GISAID - hCov19 Variants". www.gisaid.org. Retrieved July 2, 2021.