SARS-CoV-2 Kappa variant

Source: Wikipedia, the free encyclopedia.

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]

Mutations

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]

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]

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 13 September 2021) GISAID[24]
Country Confirmed cases Collection date
 India 4,437 26 May 2021
 United Kingdom 545 31 May 2021
 USA 308 24 June 2021
 Canada 372 12 May 2021
 Ireland 206 8 June 2021
 Australia 128 15 June 2021
 Germany 102 22 June 2021
 Singapore 59 13 May 2021
 Denmark 28 31 May 2021
 Netherlands 27 12 June 2021
 Japan 27 7 May 2021
 Angola 6 20 April 2021
 France 16 20 May 2021
 Belgium 17 13 May 2021
 China 13 18 April 2021
 Qatar 7 17 May 2021
 South Korea 12 27 April 2021
  Switzerland 10 4 May 2021
 Portugal 9 4 May 2021
 Italy 19 24 May 2021
 Bahrain 8 10 April 2021
 Mexico 7 2 June 2021
 South Africa 15 18 June 2021
 Finland 11 23 May 2021
 Luxembourg 10 26 April 2021
 Spain 5 19 May 2021
 Sweden 5 17 April 2021
 Ghana 5 20 April 2021
 Kenya 7 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 2 29 April 2021
 Guadeloupe 2 10 March 2021
   Nepal 2 9 May 2021
 Sint Maarten 2 3 April 2021
 Austria 2 1 August 2021
 Curaçao 1 23 April 2021
 Greece 1 6 April 2021
 Slovakia 1 19 April 2021
 Slovenia 2 6 April 2021
 Thailand 1 26 April 2021
 Uganda 1 26 March 2021
 Zambia 1 2 May 2021
 Romania 1 5 May 2021
 Morocco 1 22 April 2021
 Cayman Islands 3 16 April 2021
 Poland 1 6 May 2021
 Turkey 1 12 March 2021
 Brazil 2 10 February 2021
 Israel 2 2 January 2021
 Saudi Arabia 1 14 April 2021
 Russia 1 11 April 2021
 Gabon 1 14 April 2021
 Oman 2 16 May 2021
 Nigeria 1 21 April 2021
World (58 countries) Total: 6,476 Total as of 13 September 2021

See also

References

  1. ^ "Tracking SARS-CoV-2 variants". www.who.int. 31 May 2021. Retrieved 5 June 2021.
  2. ^ a b "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. ^ 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). This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  5. ^ a b c "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. ^ a b c d 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. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  7. ^ a b "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. 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. ^ a b 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. This article contains OGL licensed text 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. ^ 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.
  24. ^ "GISAID - hCov19 Variants". www.gisaid.org. Retrieved 13 September 2021.