SARS-CoV-2 Kappa variant

Last updated

Kappa variant [1] 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. [2] By the end of March 2021, the Kappa sub-variant accounted for more than half of the sequences being submitted from India. [3] On 1 April 2021, it was designated a Variant Under Investigation (VUI-21APR-01) by Public Health England. [4]

Contents

Mutations

Defining mutations in
SARS-CoV-2 Kappa variant
Gene Nucleotide [6] Amino acid [6] [7]
ORF1ab C3457T-
C4957TT1567I
A11201GT3646A
G17523TM5753I
A20396GK6711R
P314L
G1129C
M1352I
K2310R
S2312A
Spike T21895C-
T21895CE154K
T22917GL452R
G23012CE484Q
D614G
C23604GP681R
Q1071H
N G28881TR203M
D377Y
M I82S
ORF3a C25469TS26L
ORF1a T1567I
T3646A
ORF7a T27638CV82A
Source: covariants.org [7] and PHE Technical Briefing 9 [6]

The Kappa variant has three notable alterations in the amino-acid sequences, all of which are in the virus's spike protein code. [5]

The three notable substitutions are: L452R, E484Q, P681R [8]

The European Centre for Disease Prevention and Control (ECDC) also list a fourth spike mutation of interest: [14]

The two other mutations which can be found closer to either end of the spike region are T95I and Q1071H. [5]

History

International detection

The Kappa variant was first identified in India in December 2020. [2]

By 11 May 2021, the WHO Weekly Epidemiological Update had reported 34 countries with detections of the subvariant, [18] however by 25 May 2021, the number of countries had risen to 41. [19] [20] As of 19 May 2021, the United Kingdom had detected a total of 418 confirmed cases of the SARS-CoV-2 Kappa variant. [21] On 6 June 2021, a cluster of 60 cases identified in the Australian city of Melbourne were linked to the Kappa variant. [22] According to GISAID in July 2021, India had submitted more genetic samples of the Kappa variant than any other country. [23]

Community transmission

A Public Health England technical briefing paper of 22 April 2021 reported that 119 cases of the sub-variant had been identified in England with a concentration of cases in the London area and the regions of the North West and East of England. Of the 119 cases, 94 had an established link to travel, 22 cases were still under investigation, but the remaining 3 cases were identified as not having any known link to travel. [6]

On 2 June, the Guardian reported that at least 1 in 10 of the cases in the outbreak in the Australian state of Victoria were due to contact with strangers and that community transmission was involved with clusters of the Kappa variant. However, infectious disease expert, Professor Greg Dore, said that the Kappa variant was behaving "the same as we've seen before" in relation to other variants in Australia. [24]

Vaccine efficacy

A study conducted by Oxford University in June 2021 said that the Oxford-AstraZeneca vaccine and the Pfizer-BioNTech vaccine were effective against the Kappa and Delta variants, suggesting that the current vaccines offer protection against these variants, although with slight reductions in neutralization. [25]

Covaxin was also found to be effective against the Kappa variant (B.1.617.1) as for other variants. [26]

The Moderna COVID-19 vaccine was also found to be effective against the Kappa variant, albeit with a 3.3-3.4 fold reduction in neutralization. [27]

Statistics

Cases by country (Updated as of 4 November 2023) GISAID [28]
CountryConfirmed casesCollection date
Flag of India.svg India 9,91526 May 2021
Flag of the United Kingdom.svg United Kingdom 3,31531 May 2021
Flag of the United States.svg United States 95524 June 2021
Flag of Canada (Pantone).svg Canada 52012 May 2021
Flag of Ireland.svg Ireland 2068 June 2021
Flag of Australia (converted).svg Australia 12815 June 2021
Flag of Germany.svg Germany 10222 June 2021
Flag of Singapore.svg Singapore 9513 May 2021
Flag of Denmark.svg Denmark 2831 May 2021
Flag of the Netherlands.svg Netherlands 2712 June 2021
Flag of Japan.svg Japan 277 May 2021
Flag of Angola.svg Angola 620 April 2021
Flag of France.svg France 1620 May 2021
Flag of Belgium (civil).svg Belgium 1713 May 2021
Flag of the People's Republic of China.svg China 1318 April 2021
Flag of Qatar.svg Qatar 717 May 2021
Flag of South Korea.svg South Korea 1227 April 2021
Flag of Switzerland (Pantone).svg  Switzerland 104 May 2021
Flag of Portugal (official).svg Portugal 94 May 2021
Flag of Italy.svg Italy 1924 May 2021
Flag of Bahrain.svg Bahrain 810 April 2021
Flag of Mexico.svg Mexico 72 June 2021
Flag of South Africa.svg South Africa 1518 June 2021
Flag of Finland.svg Finland 1123 May 2021
Flag of Luxembourg.svg Luxembourg 1026 April 2021
Flag of Spain.svg Spain 519 May 2021
Flag of Sweden.svg Sweden 517 April 2021
Flag of Ghana.svg Ghana 520 April 2021
Flag of Kenya.svg Kenya 729 April 2021
Flag of the Czech Republic.svg Czech Republic 44 May 2021
Flag of Jordan.svg Jordan 425 April 2021
Flag of Myanmar.svg Myanmar 42 June 2021
Flag of New Zealand.svg New Zealand 48 April 2021
Flag of Malaysia.svg Malaysia 41 June 2021
Flag of Indonesia.svg Indonesia 229 April 2021
Flag of France.svg Guadeloupe 210 March 2021
Flag of Nepal.svg   Nepal 29 May 2021
Flag of Sint Maarten.svg Sint Maarten 23 April 2021
Flag of Austria.svg Austria 21 August 2021
Flag of Curacao.svg Curaçao 123 April 2021
Flag of Greece.svg Greece 16 April 2021
Flag of Slovakia.svg Slovakia 119 April 2021
Flag of Slovenia.svg Slovenia 26 April 2021
Flag of Thailand.svg Thailand 126 April 2021
Flag of Uganda.svg Uganda 126 March 2021
Flag of Zambia.svg Zambia 12 May 2021
Flag of Romania.svg Romania 15 May 2021
Flag of Morocco.svg Morocco 122 April 2021
Flag of the Cayman Islands.svg Cayman Islands 316 April 2021
Flag of Poland.svg Poland 16 May 2021
Flag of Turkey.svg Turkey 112 March 2021
Flag of Brazil.svg Brazil 210 February 2021
Flag of Israel.svg Israel 22 January 2021
Flag of Saudi Arabia.svg Saudi Arabia 114 April 2021
Flag of Russia.svg Russia 111 April 2021
Flag of Gabon.svg Gabon 114 April 2021
Flag of Oman.svg Oman 216 May 2021
Flag of Nigeria.svg Nigeria 121 April 2021
Flag of the Philippines.svg Philippines 18 November 2021
 World (58 countries)Total: 6,476Total as of 13 September 2021

See also

References

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  2. 1 2 "Weekly epidemiological update on COVID-19 - 27 April 2021" (PDF). World Health Organization. 27 April 2021. Retrieved 6 June 2021.
  3. Le Page, Michael (4 June 2021). "Indian covid-19 variant (B.1.617)". New Scientist . Retrieved 8 June 2021.
  4. It was considered a previously circulating variant of interest by the World Health Organization on March 2022. SARS-CoV-2 variants of concern and variants under investigation in England - Technical briefing 10 (PDF) (Report). London: Public Health England. 7 May 2021. Retrieved 5 June 2021. A variant first detected in India was designated under investigation on 1 April 2021 as VUI-21APR-01 (B.1.617.1). Open Government Licence logo.svg  This article incorporates text published under the British Open Government Licence  v3.0:
  5. 1 2 3 "Spike Variants: Kappa variant, aka B.1.617.1". covdb.stanford.edu. Stanford University Coronavirus Antiviral & Resistance Database. 1 July 2021. Retrieved 3 July 2021.
  6. 1 2 3 4 SARS-CoV-2 variants of concern and variants under investigation in England - Technical briefing 9 (PDF) (Report). London: Public Health England. 22 April 2021. Retrieved 9 June 2021. Open Government Licence logo.svg  This article incorporates text published under the British Open Government Licence  v3.0:
  7. 1 2 "Dedicated 21A/S:154K Nextstrain build". covariants.org. 8 June 2021. Retrieved 11 June 2021.
  8. Nuki, Paul; Newey, Sarah (16 April 2021). "Arrival of India's 'double mutation' adds to variant woes, but threat posed remains unclear" . The Telegraph. ISSN   0307-1235. Archived from the original on 12 January 2022. Retrieved 7 June 2021.
  9. Starr, Tyler N.; Greaney, Allison J.; Dingens, Adam S.; Bloom, Jesse D. (April 2021). "Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016". Cell Reports Medicine. 2 (4) 100255. doi: 10.1016/j.xcrm.2021.100255 . PMC   8020059 . PMID   33842902.
  10. Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Sincuir Martinez, Jorge M.; Plummer, Jasmine T.; Vail, Eric (6 April 2021). "Emergence of a Novel SARS-CoV-2 Variant in Southern California". JAMA. 325 (13): 1324–1326. doi: 10.1001/jama.2021.1612 . PMC   7879386 . PMID   33571356.
  11. 1 2 Haseltine, William. "An Indian SARS-CoV-2 Variant Lands In California. More Danger Ahead?". Forbes. Retrieved 7 June 2021.
  12. Harvey, WT; Carabelli, AM; Jackson, B; Gupta, RK; Thomson, EC; Harrison, EM; et al. (2021). "SARS-CoV-2 variants, spike mutations and immune escape". Nat Rev Microbiol. 19 (7): 409–424. doi:10.1038/s41579-021-00573-0. PMC   8167834 . PMID   34075212. For example, recently detected viruses of lineage B.1.617.1 were anticipated to show altered antigenicity due to the presence of the substitutions L452R and E484Q, which have been described as affecting antibody recognition.
  13. "SARS-CoV-2 Variant Classifications and Definitions". cdc.org. Centers for Disease Control and Prevention. 11 February 2020. Retrieved 7 June 2021.
  14. "SARS-CoV-2 variants of concern as of 3 June 2021". European Centre for Disease Prevention and Control. 3 June 2021. Retrieved 8 June 2021.
  15. Dr. Sanchari Sinha Dutta, Ph.D (15 March 2021). "D614G Mutation in SARS-CoV-2 Spike Protein". News Medical. Retrieved 8 June 2021.
  16. Korber, Bette; Fischer, Will M.; Gnanakaran, Sandrasegaram; Yoon, Hyejin; Theiler, James; Abfalterer, Werner; et al. (20 August 2020). "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus". Cell. 182 (4): 812–827. doi:10.1016/j.cell.2020.06.043. PMC   7332439 . PMID   32697968.
  17. "SARS-CoV-2 Variant Classifications and Definitions". cdc.gov. 4 June 2021. Retrieved 8 June 2021. These variants share one specific mutation called D614G... ...There is evidence that variants with this mutation spread more quickly than viruses without this mutation.
  18. "Weekly epidemiological update on COVID-19 - 11 May 2021" (PDF). World Health Organization. 11 May 2021. p. 4. Retrieved 8 June 2021.
  19. "Weekly epidemiological update on COVID-19 - 25 May 2021" (PDF). World Health Organization. 25 May 2021. p. 10. Retrieved 8 June 2021.
  20. "B.1.617 Covid variant, first found in India, now in 53 countries: WHO". Business Standard . India. 27 May 2021. Retrieved 8 June 2021. According to it, B.1.617.1 is found in 41 countries...
  21. "Variants: distribution of cases data". gov.uk. Public Health England. 9 February 2021. Retrieved 8 June 2021. Open Government Licence logo.svg  This article incorporates text published under the British Open Government Licence  v3.0:
  22. Taylor, Josh (6 June 2021). "Where did Australia's first cases of the Covid Delta variant come from and how infectious is it?". The Guardian . Melbourne. Retrieved 8 June 2021.
  23. Baro, Dimple (11 July 2021). "All you need to know about the COVID-19 Kappa variant". EastMojo.
  24. Davey, Melissa (2 June 2021). "Experts dispute Victoria claim that Kappa variant is more infectious than previous Covid outbreaks". The Guardian . Victoria. Retrieved 9 June 2021.
  25. "Coronavirus: AstraZeneca, Pfizer vaccines effective against Delta, Kappa variants, shows study". 23 June 2021.
  26. "Covaxin neutralises double mutant strain of SARS-CoV-2: ICMR study". 21 April 2021.
  27. "Small studies indicate Moderna COVID-19 vaccine may be effective against Delta, Kappa and Eta variants". July 2021.
  28. "GISAID - hCov19 Variants". www.gisaid.org. Retrieved 13 September 2021.