SARS-CoV-2 Kappa 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 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]

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]
CountryConfirmed casesCollection date
Flag of India.svg India4,43726 May 2021
Flag of the United Kingdom.svg United Kingdom54531 May 2021
Flag of the United States.svg USA30824 June 2021
Flag of Canada (Pantone).svg Canada37212 May 2021
Flag of Ireland.svg Ireland2068 June 2021
Flag of Australia (converted).svg Australia12815 June 2021
Flag of Germany.svg Germany10222 June 2021
Flag of Singapore.svg Singapore5913 May 2021
Flag of Denmark.svg Denmark2831 May 2021
Flag of the Netherlands.svg Netherlands2712 June 2021
Flag of Japan.svg Japan277 May 2021
Flag of Angola.svg Angola620 April 2021
Flag of France.svg France1620 May 2021
Flag of Belgium (civil).svg Belgium1713 May 2021
Flag of the People's Republic of China.svg China1318 April 2021
Flag of Qatar.svg Qatar717 May 2021
Flag of South Korea.svg South Korea1227 April 2021
Flag of Switzerland.svg  Switzerland104 May 2021
Flag of Portugal.svg Portugal94 May 2021
Flag of Italy.svg Italy1924 May 2021
Flag of Bahrain.svg Bahrain810 April 2021
Flag of Mexico.svg Mexico72 June 2021
Flag of South Africa.svg South Africa1518 June 2021
Flag of Finland.svg Finland1123 May 2021
Flag of Luxembourg.svg Luxembourg1026 April 2021
Flag of Spain.svg Spain519 May 2021
Flag of Sweden.svg Sweden517 April 2021
Flag of Ghana.svg Ghana520 April 2021
Flag of Kenya.svg Kenya729 April 2021
Flag of the Czech Republic.svg Czech Republic44 May 2021
Flag of Jordan.svg Jordan425 April 2021
Flag of Myanmar.svg Myanmar42 June 2021
Flag of New Zealand.svg New Zealand48 April 2021
Flag of Malaysia.svg Malaysia41 June 2021
Flag of Indonesia.svg Indonesia229 April 2021
Flag of France.svg Guadeloupe210 March 2021
Flag of Nepal.svg   Nepal29 May 2021
Flag of Sint Maarten.svg Sint Maarten23 April 2021
Flag of Austria.svg Austria21 August 2021
Flag of Curacao.svg Curaçao123 April 2021
Flag of Greece.svg Greece16 April 2021
Flag of Slovakia.svg Slovakia119 April 2021
Flag of Slovenia.svg Slovenia26 April 2021
Flag of Thailand.svg Thailand126 April 2021
Flag of Uganda.svg Uganda126 March 2021
Flag of Zambia.svg Zambia12 May 2021
Flag of Romania.svg Romania15 May 2021
Flag of Morocco.svg Morocco122 April 2021
Flag of the Cayman Islands.svg Cayman Islands316 April 2021
Flag of Poland.svg Poland16 May 2021
Flag of Turkey.svg Turkey112 March 2021
Flag of Brazil.svg Brazil210 February 2021
Flag of Israel.svg Israel22 January 2021
Flag of Saudi Arabia.svg Saudi Arabia114 April 2021
Flag of Russia.svg Russia111 April 2021
Flag of Gabon.svg Gabon114 April 2021
Flag of Oman.svg Oman216 May 2021
Flag of Nigeria.svg Nigeria121 April 2021
World (58 countries)Total: 6,476Total as of 13 September 2021

See also

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