SARS-CoV-2 Kappa variant

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
GeneNucleotide[6]Amino acid[6][7]
ORF1abC3457T-
C4957TT1567I
A11201GT3646A
G17523TM5753I
A20396GK6711R
P314L
G1129C
M1352I
K2310R
S2312A
SpikeT21895C-
T21895CE154K
T22917GL452R
G23012CE484Q
D614G
C23604GP681R
Q1071H
NG28881TR203M
D377Y
MI82S
ORF3aC25469TS26L
ORF1aT1567I
T3646A
ORF7aT27638CV82A
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] 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

Vaccines are effective against the Kappa variant, albeit to a lower extent than against the original strain.

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 13 September 2021) GISAID[28]
CountryConfirmed casesCollection date
 India4,43726 May 2021
 United Kingdom54531 May 2021
 USA30824 June 2021
 Canada37212 May 2021
 Ireland2068 June 2021
 Australia12815 June 2021
 Germany10222 June 2021
 Singapore5913 May 2021
 Denmark2831 May 2021
 Netherlands2712 June 2021
 Japan277 May 2021
 Angola620 April 2021
 France1620 May 2021
 Belgium1713 May 2021
 China1318 April 2021
 Qatar717 May 2021
 South Korea1227 April 2021
  Switzerland104 May 2021
 Portugal94 May 2021
 Italy1924 May 2021
 Bahrain810 April 2021
 Mexico72 June 2021
 South Africa1518 June 2021
 Finland1123 May 2021
 Luxembourg1026 April 2021
 Spain519 May 2021
 Sweden517 April 2021
 Ghana520 April 2021
 Kenya729 April 2021
 Czech Republic44 May 2021
 Jordan425 April 2021
 Myanmar42 June 2021
 New Zealand48 April 2021
 Malaysia41 June 2021
 Indonesia229 April 2021
 Guadeloupe210 March 2021
   Nepal29 May 2021
 Sint Maarten23 April 2021
 Austria21 August 2021
 Curaçao123 April 2021
 Greece16 April 2021
 Slovakia119 April 2021
 Slovenia26 April 2021
 Thailand126 April 2021
 Uganda126 March 2021
 Zambia12 May 2021
 Romania15 May 2021
 Morocco122 April 2021
 Cayman Islands316 April 2021
 Poland16 May 2021
 Turkey112 March 2021
 Brazil210 February 2021
 Israel22 January 2021
 Saudi Arabia114 April 2021
 Russia111 April 2021
 Gabon114 April 2021
 Oman216 May 2021
 Nigeria121 April 2021
 Philippines18 November 2021
 World (58 countries)Total: 6,476Total 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. 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. ^ 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. ^ 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".
  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.

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