SARS-CoV-2 Kappa variant

File: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.{{cite web |url=https://covdb.stanford.edu/page/mutation-viewer/#sec_kappa |title=Spike Variants: Kappa variant, aka B.1.617.1 |date=1 July 2021 |website=covdb.stanford.edu |publisher=Stanford University Coronavirus Antiviral & Resistance Database |access-date=2021-07-03}}

class="wikitable mw-collapsible autocollapse" align="right" style="text-align: center;" |+ {{nowrap|Defining mutations in SARS-CoV-2 Kappa variant{{Break}} }} ! Gene ! Nucleotide ! Amino acid
rowspan="10"| ORF1ab | C3457T || -
C4957T	T1567I
A11201G	T3646A
G17523T	M5753I
A20396G	K6711R
	P314L
	G1129C
	M1352I
	K2310R
	S2312A
rowspan="7"| Spike | T21895C || -
T21895C	E154K
T22917G	L452R
G23012C	E484Q
	D614G
C23604G	P681R
	Q1071H
rowspan="2"| N | G28881T || R203M
	D377Y
rowspan="1"| M | || I82S
rowspan="1"| ORF3a | C25469T || S26L
rowspan="2"| ORF1a | || T1567I
	T3646A
rowspan="1"| ORF7a | T27638C || V82A
style="text-align:left;" class="sortbottom" | colspan="3" | Source: covariants.org{{cite web |url=https://covariants.org/variants/21A.S.154K |title=Dedicated 21A/S:154K Nextstrain build |date=8 June 2021 |website=covariants.org |access-date=2021-06-11}} and PHE Technical Briefing 9

The Kappa variant has three notable alterations in the amino-acid sequences, all of which are in the virus's spike protein code.

The three notable substitutions are: L452R, E484Q, P681R{{Cite news|last1=Nuki|first1=Paul|last2=Newey|first2=Sarah|date=2021-04-16|title=Arrival of India's 'double mutation' adds to variant woes, but threat posed remains unclear|language=en-GB|work=The Telegraph|url=https://www.telegraph.co.uk/global-health/science-and-disease/arrival-indias-double-mutation-adds-variant-woes-threat-posed/ |archive-url=https://ghostarchive.org/archive/20220112/https://www.telegraph.co.uk/global-health/science-and-disease/arrival-indias-double-mutation-adds-variant-woes-threat-posed/ |archive-date=12 January 2022 |url-access=subscription |url-status=live|access-date=2021-06-07|issn=0307-1235}}{{cbignore}}

• 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.{{cite journal |last1=Starr |first1=Tyler N. |last2=Greaney |first2=Allison J. |last3=Dingens |first3=Adam S. |last4=Bloom |first4=Jesse D. |title=Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016 |journal=Cell Reports Medicine |date=April 2021 |volume=2 |issue=4 |pages=100255 |doi=10.1016/j.xcrm.2021.100255 |pmid=33842902 |pmc=8020059 |doi-access=free |access-date=}}{{cite journal |last1=Zhang |first1=Wenjuan |last2=Davis |first2=Brian D. |last3=Chen |first3=Stephanie S. |last4=Sincuir Martinez |first4=Jorge M. |last5=Plummer |first5=Jasmine T. |last6=Vail |first6=Eric |title=Emergence of a Novel SARS-CoV-2 Variant in Southern California |journal=JAMA |date=6 April 2021 |volume=325 |issue=13 |pages=1324–1326 |doi=10.1001/jama.2021.1612|pmid=33571356 |pmc=7879386 |doi-access=free }}
• 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.{{cite journal |last1=Harvey |first1=WT |last2=Carabelli |first2=AM |last3=Jackson |first3=B |last4=Gupta |first4=RK |last5=Thomson |first5=EC |last6=Harrison |first6=EM |last7=Ludden |first7=C |last8=Reeve |first8=R |last9=Rambaut |first9=A |last10=Peacock |first10=SJ |last11=Robertson |first11=DL |display-authors=6 |title=SARS-CoV-2 variants, spike mutations and immune escape |url= |journal=Nat Rev Microbiol |year=2021 |volume= 19|issue= 7|pages= 409–424|doi=10.1038/s41579-021-00573-0 |pmid=34075212 |pmc=8167834 |quote=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.}}
• P681R. The substitution at position 681, a proline-to-arginine substitution.{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html |title=SARS-CoV-2 Variant Classifications and Definitions |website=cdc.org |date=11 February 2020 |publisher=Centers for Disease Control and Prevention|access-date=2021-06-07}}{{cite news |last1=Haseltine |first1=William |title=An Indian SARS-CoV-2 Variant Lands In California. More Danger Ahead? |url=https://www.forbes.com/sites/williamhaseltine/2021/04/12/an-indian-sars-cov-2-variant-lands-in-california-more-danger-ahead/?sh=1ff3056b3b29 |access-date=2021-06-07 |work=Forbes |language=en}}

The European Centre for Disease Prevention and Control (ECDC) also list a fourth spike mutation of interest:{{Cite web|title=SARS-CoV-2 variants of concern as of 3 June 2021|date=3 June 2021|url=https://www.ecdc.europa.eu/en/covid-19/variants-concern|access-date=2021-06-08|website=European Centre for Disease Prevention and Control }}

• D614G. This is a substitution at position 614, an aspartic acid-to-glycine substitution.{{cite news |last= Dr. Sanchari Sinha Dutta, Ph.D |date=15 March 2021 |title=D614G Mutation in SARS-CoV-2 Spike Protein |url=https://www.news-medical.net/health/D614G-Mutation.aspx |work=News Medical |location= |access-date=2021-06-08}} Other variants which have the D614G mutation include the Beta and Delta variants, and the mutation is associated with increased infectivity.{{cite journal |last1=Korber |first1=Bette |last2=Fischer |first2=Will M. |last3=Gnanakaran |first3=Sandrasegaram |last4=Yoon |first4=Hyejin |last5=Theiler |first5=James |last6=Abfalterer |first6=Werner |last7=Hengartner |first7=Nick |last8=Giorgi |first8=Elena E. |last9=Bhattacharya |first9=Tanmoy |last10=Foley |first10=Brian |last11=Hastie |first11=Kathryn M. |last12=Parker |first12=Matthew D. |last13=Partridge |first13=David G. |last14=Evans |first14=Cariad M. |last15=Freeman |first15=Timothy M. |last16=de Silva |first16=Thushan I. |last17=McDanal |first17=Charlene |last18=Perez |first18=Lautaro G. |last19=Tang |first19=Haili |last20=Moon-Walker |first20=Alex |last21=Whelan |first21=Sean P. |last22=LaBranche |first22=Celia C.|last23=Saphire |first23=Erica O. |last24=Montefiori |first24=David C. |display-authors=6 |date=20 August 2020 |title=Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus |url= |journal=Cell |volume=182 |issue=4 |pages=812–827 |doi=10.1016/j.cell.2020.06.043 |pmid=32697968 |pmc=7332439 }}{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html |title=SARS-CoV-2 Variant Classifications and Definitions |author= |date=4 June 2021 |website=cdc.gov |access-date=2021-06-08 |quote=These variants share one specific mutation called D614G... ...There is evidence that variants with this mutation spread more quickly than viruses without this mutation.}}

The two other mutations which can be found closer to either end of the spike region are T95I and Q1071H.

The Kappa variant was first identified in India in December 2020.

By 11 May 2021, the WHO Weekly Epidemiological Update had reported 34 countries with detections of the subvariant,{{cite web|url=https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210511_weekly_epi_update_39.pdf?sfvrsn=b66ba70d_11&download=true|title=Weekly epidemiological update on COVID-19 - 11 May 2021|date=11 May 2021 |website=World Health Organization|page=4|access-date=8 June 2021}} however by 25 May 2021, the number of countries had risen to 41.{{cite web|url=https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210525_weekly_epi_update_41.pdf?sfvrsn=d602902c_6&download=true|title=Weekly epidemiological update on COVID-19 - 25 May 2021|date=25 May 2021 |website=World Health Organization|page=10|access-date=8 June 2021}}{{cite news |author= |title=B.1.617 Covid variant, first found in India, now in 53 countries: WHO |url=https://www.business-standard.com/article/current-affairs/b-1-617-covid-variant-first-found-in-india-now-in-53-countries-who-121052700342_1.html |work=Business Standard |location=India |date=27 May 2021 |access-date=2021-06-08 |quote=According to it, B.1.617.1 is found in 41 countries...}} {{As of|2021|May|19}}, the United Kingdom had detected a total of 418 confirmed cases of the SARS-CoV-2 Kappa variant.{{cite web |url=https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data |title=Variants: distribution of cases data |author= |date=9 February 2021 |website=gov.uk |publisher=Public Health England |access-date=2021-06-08 |language=en}} {{OGL-attribution|version=3.0}} On 6 June 2021, a cluster of 60 cases identified in the Australian city of Melbourne were linked to the Kappa variant.{{cite news |last=Taylor |first=Josh |date=6 June 2021 |title=Where did Australia's first cases of the Covid Delta variant come from and how infectious is it? |url=https://www.theguardian.com/australia-news/2021/jun/04/where-did-australias-first-cases-of-the-delta-variant-come-from-and-how-infectious-is-it |work=The Guardian |location=Melbourne |access-date=2021-06-08}} According to GISAID in July 2021, India had submitted more genetic samples of the Kappa variant than any other country.{{cite news |last1=Baro |first1=Dimple |title=All you need to know about the COVID-19 Kappa variant |url=https://www.eastmojo.com/coronavirus-updates/2021/07/11/all-you-need-to-know-about-the-covid-19-kappa-variant/ |work=EastMojo |date=11 July 2021}}

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.{{cite report |author= |title=SARS-CoV-2 variants of concern and variants under investigation in England - Technical briefing 9 |url=https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/979818/Variants_of_Concern_VOC_Technical_Briefing_9_England.pdf |location=London |publisher=Public Health England |date=22 April 2021 |access-date=2021-06-09 |language=en}} {{OGL-attribution|version=3.0}}

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.{{cite news |last=Davey |first=Melissa |date=2 June 2021 |title=Experts dispute Victoria claim that Kappa variant is more infectious than previous Covid outbreaks |url=https://www.theguardian.com/australia-news/2021/jun/02/experts-dispute-victoria-claim-that-kappa-variant-is-more-infectious-than-previous-covid-outbreaks |work=The Guardian |location=Victoria |access-date=2021-06-09}}

Vaccine efficacy

Vaccines are effective against the Kappa variant, albeit to a lower extent than against the original strain.{{cn|date=July 2024}}

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.{{Cite web|url=https://scroll.in/latest/998317/coronavirus-astrazeneca-pfizer-vaccines-effective-against-delta-kappa-variants-shows-study|title = Coronavirus: AstraZeneca, Pfizer vaccines effective against Delta, Kappa variants, shows study| date=23 June 2021 }}

Covaxin was also found to be effective against the Kappa variant (B.1.617.1) as for other variants.{{Cite web|url=https://indianexpress.com/article/india/covaxin-neutralises-double-mutant-strain-icmr-study-7282835/|title=Covaxin neutralises double mutant strain of SARS-CoV-2: ICMR study|date=21 April 2021}}

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.{{Cite web|url=https://homelandprepnews.com/stories/70786-small-studies-indicate-moderna-covid-19-vaccine-may-be-effective-against-delta-kappa-and-eta-variants/?amp|title = Small studies indicate Moderna COVID-19 vaccine may be effective against Delta, Kappa and Eta variants|date = July 2021}}

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