SARS-CoV-2 Beta variant: Difference between revisions
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| C1059T || T265I<!--ceil((1059 - 265) / 3)--> |
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| C3037T<sup>1</sup> || F924<sup>2</sup> |
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| G5230T || K1655N |
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| C14408T<sup>1</sup> || |
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Footnote: <sup>1</sup>Presented in parent lineage B.1. |
Footnote: <sup>1</sup>Presented in parent lineage B.1; <sup>2</sup>[[Synonymous substitution]]. |
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Source: {{harvp|Tegally et al.|loc=supplementary Fig S8}} |
Source: {{harvp|Tegally et al.|loc=supplementary Fig S8}} |
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Revision as of 17:18, 5 January 2021
The 501.V2 variant, or simply 501.V2, is a variant of SARS-CoV-2—the virus that causes COVID-19. The variant was first detected in the Nelson Mandela Bay[1] metropolitan area of the Eastern Cape province of South Africa[2] and reported by the country's health department on 18 December 2020.[3]
Variant
| Gene | Nucleotide | Amino acid |
|---|---|---|
| ORF1ab | C1059T | T265I |
| C3037T1 | F9242 | |
| G5230T | K1655N | |
| C8660T | H2799Y | |
| C8964T | S2900L | |
| A10323G | K3353R | |
| G13843T | D4527Y | |
| C14408T1 | P4715L | |
| C17999T | T5912I | |
| Spike | C21614T | L18F |
| A21801C | D80A | |
| A22206G | D215G | |
| G22299T | R246I | |
| G22813T | K417N | |
| G23012A | E484K | |
| A23063T | N501Y | |
| A23403G1 | D614G | |
| G23664T | A701V | |
| ORF3a | G25563T | Q57H |
| C25904T | S171L | |
| E | C26456T | P71L |
| N | C28887T | T205I |
|
Footnote: 1Presented in parent lineage B.1; 2Synonymous substitution. Source: Tegally et al., supplementary Fig S8 | ||
Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more powerful in such cases.[4][5] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 pandemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[3][4]
Scientists noted that the variant contains several mutations that allows it to attach more easily to human cells because of three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y[3][6] (a change from asparagine (N) to tyrosine (Y)[7] in amino-acid position 501), K417N, and E484K.[8][9] Two of these mutations (E484K and N501Y) are within the receptor-binding motif (RBM) of the receptor-binding domain (RBD).[10][11]
The N501Y mutation has also been detected in the United Kingdom.[3][12] Two mutations found in 501.v2, E484K and K417N, are not found in Variant of Concern 202012/01. Also, 501.v2 does not have the 69-70del mutation found in the other variant.[13][6]
Detection
The new variant was uncovered by whole genome sequencing. Several genomic sequences from this lineage were submitted to the GISAID sequence database, for example sequence accession EPI_ISL_678597.[14][better source needed]
Spread
On 23 December, Matt Hancock announced that two people who had travelled from South Africa to the UK were infected with 501.V2.[13][15] On 28 December, the variant had been detected in two individuals in Switzerland [16] and in one individual in Finland.[17] On 29 December, the strain had been detected in a visitor from South Africa to Japan,[18] and in one overseas traveller in Queensland, Australia.[19] On 30 December, the variant has been detected in Zambia.[20] On 31 December, it has also been detected in France, in a passenger returning from South Africa.[21] On 2 January 2021, the first case of this variant has been detected in South Korea.[22]
Vaccine evasion
On 4 January 2021, The Telegraph reported that Oxford immunologist Sir John Bell believed there was "a big question mark" over the new South African variant's potential resistance to COVID-19 vaccines, raising fears that vaccines might not work as effectively on the variant strain.[23] The same day, professor of vaccinology Shabir Madhi commented to CBS News that "it's not a given" that the new 501.V2 variant would be able to evade the vaccines, but that it should be considered that they "might not have the full efficacy".[24] The additional mutations to the spike protein in variant 501.V2 were raised as a concerning factor by Simon Clarke, an associate professor in cellular microbiology at the University of Reading, in that they "may make the virus less susceptible to the immune response triggered by the vaccines".[25] Lawrence Young, a virologist at Warwick University, also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[25]
See also
- Variant of Concern 202012/01, also called B1.1.7., a variant of the SARS-CoV-2 virus found in the United Kingdom
- Cluster 5, a variant of the SARS-CoV-2 virus found in Denmark
- Variants of SARS-CoV-2
References
- ^ "SA reaches grim milestone of 1 million Covid-19 cases". www.iol.co.za. Retrieved 29 December 2020.
- ^ "Covid: South Africa passes one million infections as cases surge". BBC News. 28 December 2020. Retrieved 29 December 2020.
- ^ a b c d "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
N501Y...has been found in other countries, including the United Kingdom
- ^ a b Wroughton, Lesley; Bearak, Max (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Archived from the original on 27 December 2020. Retrieved 20 December 2020.
- ^ Mkhize, Dr Zwelini (18 December 2020). "Update on Covid-19 (18th December 2020)" (Press release). South Africa. COVID-19 South African Online Portal. Retrieved 23 December 2020.
Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick.
- ^ a b Abdool Karim, Salim (19 December 2020). "The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant". Scribd. CAPRISA. p. 11. Retrieved 24 December 2020.
- ^ For a list of the symbols used for the α-amino acids incorporated into protein under mRNA direction, see: "Nomenclature and Symbolism for Amino Acids and Peptides". IUPAC-IUB Joint Commission on Biochemical Nomenclature. 1983. Archived from the original on 9 October 2008. Retrieved 5 March 2018.
- ^ Statement of the WHO Working Group on COVID-19 Animal Models (WHO-COM) about the UK and South African SARS-CoV-2 new variants (PDF), World Health Organization, 22 December 2020, retrieved 23 December 2020
- ^ Lowe, Derek (22 December 2020). "The New Mutations". In The Pipeline. American Association for the Advancement of Science. Retrieved 23 December 2020.
I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
- ^ "Expert reaction to South African variant of SARS-CoV-2]". Retrieved 26 December 2020.
- ^ . doi:10.1101/2020.12.21.20248640.
{{cite journal}}: Cite journal requires|journal=(help); Missing or empty|title=(help) - ^ "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Retrieved 23 December 2020.
- ^ a b "Expert reaction to South African variant of SARS-CoV-2, as mentioned by Matt Hancock at the Downing Street press briefing". Science Media Centre. 23 December 2020. Retrieved 24 December 2020.
The South African variant '501.V2' is characterised by N501Y, E484K and K417N mutations in the S protein – so it shares the N501Y mutation with the UK variant, but the other two mutations are not found in the UK variant. Similarly, the South African variant does not contain the 69-70del mutation that is found in the UK variant.
- ^ "COVID-19 GISAID Acknowledgement Threat Assessment UK variant" (PDF). ecdc.europa.eu. GISAID. 20 December 2020. p. 9. Retrieved 29 December 2020.
EPI_ISL_678594, EPI_ISL_678596, EPI_ISL_678597. Netcare. KRISP, KZN Research Innovation and Sequencing Platform. Giandhari J, Pillay S, Lessells R, Chimukangara B, Mdlalose K, York D, Khan S, Tegally H, Wilkinson E, de Oliveira T.
- ^ Sample, Ian; Grover, Natalie (23 December 2020). "South African Covid-19 variant has reached the UK, says Matt Hancock". The Guardian. London. Retrieved 4 January 2021.
- ^ "South African Covid variant discovered in Switzerland". BusinessInsider. Retrieved 29 December 2020.
- ^ "Update: New UK, South African variant Covid strains detected in Finland". Yle News. Retrieved 29 December 2020.
- ^ "South African coronavirus variant found in Japan". News24. Retrieved 29 December 2020.
- ^ "First case of 'more contagious' coronavirus strain detected in Australia". 9 News. 29 December 2020.
- ^ "Second COVID-19 wave confirmed in Zambia". Xinhua News Agency. 30 December 2020.
- ^ "France detects first case of South African strain of Covid-19". France24. 31 December 2020.
- ^ "남아공 '변이 코로나' 첫 국내 확인…영국발 변이도 4건 추가" [South Africa's 'mutant corona' first confirmed in Korea... 4 additional variations from UK] (in Korean). Donga Ilbo. 2 January 2021.
- ^ Knapton, Sarah (4 January 2021). "South African variant may evade vaccines and testing, warn scientists". Retrieved 5 January 2021.
- ^ Carter, Sarah (4 January 2021). "COVID vaccines "might not" work as well on South African strain, scientists warn". CBS News. Johannesburg. Retrieved 5 January 2021.
- ^ a b "UK scientists worry vaccines may not protect against S.African coronavirus variant". Reuters. 4 January 2021. Retrieved 5 January 2021.