SARS-CoV-2 Kappa variant

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For lineage B.1.617.2, see SARS-CoV-2 Delta variant.

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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 known to have been detected in India in December 2020, though it may have existed in China but may have not been disclosed.[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]

Mutations

  • SARS-CoV-2 Kappa variant.svg

    Amino acid mutations of SARS-CoV-2 Kappa variant plotted on a genome map of SARS-CoV-2 with a focus on the spike.[5]

Defining mutations in
SARS-CoV-2 Kappa variant
Gene Nucleotide[6] Amino acid[6][7]
ORF1ab C3457T -
C4957T T1567I
A11201G T3646A
G17523T M5753I
A20396G K6711R
P314L
G1129C
M1352I
K2310R
S2312A
Spike T21895C -
T21895C E154K
T22917G L452R
G23012C E484Q
D614G
C23604G P681R
Q1071H
N G28881T R203M
D377Y
M I82S
orf3a C25469T S26L
orf1a T1567I
T3646A
orf7a T27638C V82A
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]

  • L452R. The substitution at position 452, a leucine-to-arginine substitution. This exchange confers stronger affinity of the spike protein for the ACE2 receptor along with decreased recognition capability of the immune system.[9][10]
  • E484Q. The substitution at position 484, a glutamic acid-to-glutamine substitution. This alteration confers the variant stronger binding potential to Angiotensin-converting enzyme 2, as well as better ability to evade hosts' immune systems.[11][12]
  • P681R. The substitution at position 681, a proline-to-arginine substitution.[13][11]

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

  • D614G. This is a substitution at position 614, an aspartic acid-to-glycine substitution.[15] Other variants which have the D614G mutation include the Beta and Delta variants, and the mutation is associated with increased infectivity.[16][17]

Two other mutations, 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]

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.[23]

Statistics

Cases by country (Updated as of 7 July 2021) GISAID[24]
Country Confirmed cases Collection date
India 3,693 26 May 2021
United Kingdom 517 31 May 2021
USA 299 24 June 2021
Canada 266 12 May 2021
Ireland 170 8 June 2021
Australia 112 15 June 2021
Germany 106 22 June 2021
Singapore 59 13 May 2021
Denmark 28 31 May 2021
Netherlands 27 12 June 2021
Japan 27 7 May 2021
Angola 24 20 April 2021
France 16 20 May 2021
Belgium 16 13 May 2021
China 13 18 April 2021
Qatar 12 17 May 2021
South Korea 12 27 April 2021
Switzerland 10 4 May 2021
Portugal 9 4 May 2021
Italy 9 24 May 2021
Bahrain 8 10 April 2021
Mexico 8 2 June 2021
South Africa 8 18 June 2021
Finland 7 23 May 2021
Luxembourg 6 26 April 2021
Spain 5 19 May 2021
Sweden 5 17 April 2021
Ghana 5 20 April 2021
Kenya 5 29 April 2021
Czech Republic 4 4 May 2021
Jordan 4 25 April 2021
Myanmar 4 2 June 2021
New Zealand 4 8 April 2021
Malaysia 4 1 June 2021
Indonesia 3 29 April 2021
Guadeloupe 2 10 March 2021
Malawi 2 30 April 2021
Nepal 2 9 May 2021
Sint Maarten 2 3 April 2021
Botswana 2 1 June 2021
Kuwait 1
Austria 1
Cambodia 1 5 April 2021
Curaçao 1 23 April 2021
Greece 1 6 April 2021
Slovakia 1 19 April 2021
Slovenia 1 6 April 2021
Thailand 1 26 April 2021
Uganda 1 26 March 2021
Zambia 1 2 May 2021
World (50 countries) Total: 5,525 Total as of 1 July 2021

See also

References

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  4. ↑ Lua error in package.lua at line 80: module 'strict' not found. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
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  6. ↑ 6.0 6.1 6.2 6.3 Lua error in package.lua at line 80: module 'strict' not found. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  7. ↑ 7.0 7.1 Lua error in package.lua at line 80: module 'strict' not found.
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  21. ↑ Lua error in package.lua at line 80: module 'strict' not found. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  22. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  23. ↑ Lua error in package.lua at line 80: module 'strict' not found.
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