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

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 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.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

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