501.V2 variant

From Wikipedia the free encyclopedia

Countries with confirmed cases of 501.V2 as of 20 January 2021, excluding South Africa
  10 – 49 confirmed cases
  5 - 9 confirmed cases
  2 - 4 confirmed cases
  1 confirmed case
  It has cases, but there are no precise figures
  Suspicious cases
  No confirmed cases, no population, or no data available
Note: The amount of gene sequencing varies widely between countries, with the UK having sequenced approximately as many SARS-CoV-2 genomes as the rest of the world combined. This is reflected in the number of confirmed cases.

The 501.V2 variant, also known as 20C/501Y.V2, B.1.351 lineage[1] and South African COVID-19 variant,[2] is a variant of SARS-CoV-2, the virus that causes COVID-19. The variant was first detected in the Nelson Mandela Bay[3] metropolitan area of the Eastern Cape province of South Africa[4] and reported by the country's health department on 18 December 2020.[5]

Variant[edit]

Mutational profile of 501.V2
(change of amino acid only)
Gene Nucleotide Amino acid
ORF1ab C1059T T265I
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.

Source: Tegally et al. (2020), supplementary Fig S8

Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and more frequently causes serious illness in such cases than other variants.[6][7] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 pandemic in the country, as the variant spreads faster than other earlier variants of the virus.[5][6]

Scientists noted that the variant is able 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[5][8] (a change from asparagine (N) to tyrosine (Y)[9] in amino-acid position 501), K417N, and E484K.[10][11] Two of these mutations, E484K and N501Y, are within the receptor-binding motif (RBM) of the receptor-binding domain (RBD).[12][13]

The N501Y mutation has also been detected in the United Kingdom.[5][14] 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.[15][8]

Detection[edit]

The new variant was uncovered by whole genome sequencing. Several genomic sequences from this lineage were submitted to the GISAID sequence database.[16][better source needed]

International spread[edit]

On 23 December, UK health minister Matt Hancock announced that two people who had travelled from South Africa to the UK were infected with 501.V2.[15][17] On 28 December, the variant had been detected in two people in Switzerland[18] and in one in Finland.[19] On 29 December, the strain had been detected in a visitor from South Africa to Japan,[20] and in one overseas traveller to Queensland, Australia.[21] On 30 December the variant was detected in Zambia.[22] On 31 December it was also detected in France, in a passenger returning from South Africa.[23] On 2 January 2021, the first case of this variant was detected in South Korea.[24] Austria reported their first case of this variant, along with four cases of the UK variant on 4 January.[25] The Republic of Botswana also detected their first case on 4 January.[26] The People's Republic of China reported the first case of this variant in southern Guangdong province on 6 January.[27]

On 8 January 2021, the Republic of Ireland reported the detection of 3 cases, all linked to travel from South Africa.[28] On the same day a case of reinfection with the new variant by a woman who had had COVID-19 was reported from Brazil, the first such reinfection reported in the world.[29] Canada reported the first case of this variant in Alberta on 9 January,[30] and Israel reported four cases, all of which were imported in people travelling from South Africa.[31] New Zealand reported the first case of this variant on 10 January.[32][33] On 12 January, Germany reported the detection of the mutation in six people from three different households.[34] The same day, it was reported that the United Kingdom had a total of 29 cases, two of which were previously reported.[35] The following day, Belgium reported the first case in a person from West Flanders with no travel history,[36] Israel reported four further cases,[37] and Taiwan reported the first case in a Swazi man in his 30s who had tested positive for COVID-19 on 1 January.[38]

On 14 January, Germany detected a further case[39] and the following day, Canada reported a second case of the mutation which was detected in the Canadian province of British Columbia.[40] A further case was reported in Germany the same day.[41] Denmark reported the first case on 16 January as Israel discovered a further four cases.[42][43] On 17 January, Israel reported another four cases bringing their total number of cases of this variant to 20.[44] Two further cases were reported in The Netherlands on 18 January bringing the country's total to three.[45] On 23 January, Panama detected its first case of the strain in a person from Zimbabwe, who had traveled from South Africa.[46] Also on 23 January, Belgium reported at least 15 cases of the variant in Ostend.[47]

Vaccine evasion[edit]

On 4 January 2021 UK newspaper 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 that variant strain.[48] 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".[49] 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".[50] Lawrence Young, a virologist at Warwick University, also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[50]

On 7 January 2021 it was reported that Pfizer researchers had found the Pfizer and BioNTech COVID-19 vaccine in tests involving 20 blood assays to be capable of affording protection against one of the 501.V2 variant mutations (N501Y, shared with variant B1.1.7). Further investigation was to be undertaken to ascertain the level of protection involved.[51]

E484K mutation[edit]

The E484K amino acid change, a receptor-binding-domain (RBD) mutation, was reported to be "associated with escape from neutralising antibodies" which could adversely affect the efficacy of spike protein-dependent COVID vaccines.[52][53] The E484K spike mutation was linked to a case of reinfection with the 501.V2 variant of SARS-CoV-2 in Brazil, believed by researchers to be the first such case of reinfection involving this mutation.[29] The possibility of an alteration in antigenicity was referred to as an "escape mutation" from a monoclonal antibody with the capability of neutralising the spike protein variants of SARS-CoV-2.[54][55]

Statistics[edit]

Cases by country (Updated as of 24 January 2021)
Country Confirmed cases Date References
 South Africa 520 8 October 2020 [56]
 United Kingdom 2
27
38
6
5
78 (total)
23 December 2020
12 January 2021
20 January 2021
22 January 2021
23 January 2021
[57]
[35]
[56]
[56]
[56]
  Switzerland 2
31
28 December 2020
21 January 2021
[18]
[58]
 Finland 1
1
28 December 2020
20 January 2021
[19]
[56]
 Japan 1 29 December 2020 [20]
 Australia 1
5
1
29 December 2020
20 January 2021
22 January 2021
[21]
[56]
[56]
 Zambia 1 30 December 2020 [59]
 France 1
4
5
31 December 2020
20 January 2021
20 January 2021
[60]
[56]
[61]
 South Korea 1
1
2 January 2021
18 January 2021
[24]
[62]
 Sweden 1
1
2 January 2021
20 January 2021
[63]
[64]
 Norway 1 4 January 2021 [65]
 China 1 6 January 2021 [27]
 Austria 1 4 January 2021 [66]
 Botswana 1
5
4 January 2021
20 January 2021
[26]
[56]
 Ireland 3 8 January 2021 [28]
 Brazil 1 8 January 2021 [29]
 The Netherlands 1
2
8 January 2021
18 January 2021
[67]
[45]
 Canada 1
1
8 January 2021
15 January 2021
[68]
[40]
 Israel 4
4
4
8
2
22 (total)
9 January 2021
13 January 2021
16 January 2021
17 January 2021
21 January 2021
[31]
[37]
[43]
[44]
[69][70]
 New Zealand 1 10 January 2021 [32][33]
 Germany 6
1
1
12 January 2021
14 January 2021
15 January 2021
[34]
[39]
[41]
 Belgium 1
5
15
13 January 2021
20 January 2021
23 January 2021
[36]
[56]
[47]
 Taiwan 1 13 January 2021 [38]
 Denmark 1 16 January 2021 [42]
 Spain 1 22 January 2021 [56]
 Kenya 2 22 January 2021 [71]
 Portugal 1 22 January 2021 [72]
 Panama 1 23 January 2021 [46]
 UAE 5 23 January 2021 [56]
World (29 countries) 738

See also[edit]

References[edit]

  1. ^ "Emerging SARS-CoV-2 Variants". Centers for Disease Control and Prevention. 3 January 2021.
  2. ^ For a list of sources, refer to South African COVID-19 variant.
  3. ^ "SA reaches grim milestone of 1 million Covid-19 cases". www.iol.co.za. Retrieved 29 December 2020.
  4. ^ "Covid: South Africa passes one million infections as cases surge". BBC News. 28 December 2020. Retrieved 29 December 2020.
  5. ^ 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
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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
  11. ^ 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.
  12. ^ "Expert reaction to South African variant of SARS-CoV-2". Science Media Centre. Retrieved 26 December 2020.
  13. ^ Tegally, Houriiyah; Wilkinson, Eduan; Giovanetti, Marta; Iranzadeh, Arash; Fonseca, Vagner; Giandhari, Jennifer; Doolabh, Deelan; Pillay, Sureshnee; San, Emmanuel James; Msomi, Nokukhanya; Mlisana, Koleka; von Gottberg, Anne; Walaza, Sibongile; Allam, Mushal; Ismail, Arshad; Mohale, Thabo; Glass, Allison J.; Engelbrecht, Susan; Van Zyl, Gert; Preiser, Wolfgang; Petruccione, Francesco; Sigal, Alex; Hardie, Diana; Marais, Gert; Hsiao, Marvin; Korsman, Stephen; Davies, Mary-Ann; Tyers, Lynn; Mudau, Innocent; et al. (2020). Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa (Report). doi:10.1101/2020.12.21.20248640. S2CID 229348551.
  14. ^ "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Retrieved 23 December 2020.
  15. ^ 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.
  16. ^ "Risk Assessment: Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA". www.ecdc.europa.eu. 29 December 2020. Retrieved 23 January 2021. This variant was first observed in samples from October, and since then more than 300 cases with the 501.V2 variant have been confirmed by whole genome sequencing (WGS) in South Africa
  17. ^ 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.
  18. ^ a b "South African Covid variant discovered in Switzerland". BusinessInsider. Retrieved 29 December 2020.
  19. ^ a b "Update: New UK, South African variant Covid strains detected in Finland". Yle News. Retrieved 29 December 2020.
  20. ^ a b "South African coronavirus variant found in Japan". News24. Retrieved 29 December 2020.
  21. ^ a b "First case of 'more contagious' coronavirus strain detected in Australia". 9 News. 29 December 2020.
  22. ^ "Second COVID-19 wave confirmed in Zambia". Xinhua News Agency. 30 December 2020.
  23. ^ "France detects first case of South African strain of Covid-19". France24. 31 December 2020.
  24. ^ a b "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.
  25. ^ "British, South African corornavirus mutations detected in Austria". Reuters. Berlin. 4 January 2021. Retrieved 6 January 2021.
  26. ^ a b "Botswana government adjusts national lockdown regulations". SABC News. South Africa. 4 January 2021. Retrieved 11 January 2021. ...the new strain of the COVID-19 virus, known as 501V2 variant, has been detected in Botswana.
  27. ^ a b "Factbox-Coronavirus variants, first found in UK and South Africa, spread worldwide". Reuters. 8 January 2021. Retrieved 16 January 2021.
  28. ^ a b "Statement from the National Public Health Emergency Team - Friday 8 January". Government of Ireland. Department of Health. 8 January 2021. Retrieved 8 January 2021.
  29. ^ a b c "South African coronavirus variant detected in reinfection case in Brazil". www.reuters.com. 8 January 2021. Retrieved 11 January 2021.
  30. ^ "First case of South African COVID-19 variant detected in Canada". dailyhive.com. 9 January 2021. Retrieved 11 January 2021.
  31. ^ a b "Israel records 4 cases of S. African COVID-19 variant". Ynet. 9 January 2021. Retrieved 12 January 2021.
  32. ^ a b "coronavirus-very-contagious-south-africa-variant-now-in-new-zealand". www.newshub.co.nz.
  33. ^ a b Martin, Hannah; Hunt, Tom (10 January 2021). "Covid-19: Health officials confirm 31 new cases of coronavirus, first case of South African variant found". Stuff (website). New Zealand. Retrieved 13 January 2021.
  34. ^ a b Gebauer, Mathhias. "Coronavirus: Südafrikanische Virus-Mutation auch in Deutschland nachgewiesen" [South African virus mutation also detected in Germany]. Der Spiegel (in German). Retrieved 13 January 2021. Mittlerweile gebe es sechs Virusnachweise bei sechs Personen aus drei Haushalten, teilte das Ministerium mit. (There are now six virus detections in six people from three households, the ministry said.)
  35. ^ a b Sample, Ian (12 January 2021). "Public Health England steps up surveillance of South African Covid variant". The Guardian. London. Retrieved 16 January 2021. Scientists are particularly concerned about the South African variant, named B1351... ...At least 29 cases in the UK and three in Ireland have been recorded.
  36. ^ a b Alexander Verstraete (13 January 2021). "Eerste geval met Zuid-Afrikaanse coronavariant bevestigd in ons land net als 8 nieuwe gevallen van Britse variant" [First case with South African corona variant confirmed in our country as well as 8 new cases of British variant]. VRT. Retrieved 13 January 2021.
  37. ^ a b "Four Additional Cases of the South African Variant Detected". Ministry of Health (Israel). 13 January 2021. Retrieved 15 January 2021.
  38. ^ a b "Taiwan reports first case of mutant South African Covid strain". Taiwan News. Taipei. 13 January 2021. Retrieved 15 January 2021.
  39. ^ a b "Corona-Mutante aus Südafrika in Hamburg entdeckt" [Corona mutant from South Africa discovered in Hamburg]. www.t-online.de (in German). Retrieved 14 January 2021.
  40. ^ a b Little, Simon (15 January 2021). "B.C. becomes 2nd province to identify South African COVID-19 variant". Global News. British Columbia. Retrieved 15 January 2021.
  41. ^ a b "Südafrika-Corona-Mutation jetzt auch in Hessen nachgewiesen" [South Africa Corona mutation now also detected in Hesse]. AerzteZeitung.de (in German). Retrieved 16 January 2021.
  42. ^ a b "Det første tilfælde af ny covid-19-variant er nu fundet i Danmark" [The first case of a new covid-19 variant has now been found in Denmark]. ssi.dk (in Danish). Retrieved 16 January 2021.
  43. ^ a b "Health Ministry reports 4 more cases of South African virus variant". The Times of Israel. 16 January 2021. Retrieved 16 January 2021.
  44. ^ a b "Gov't votes to require all Dubai returnees to isolate in COVID-19 hotels". The Jerusalem Post. 17 January 2021. Retrieved 17 January 2021. There are 20 known cases of the variant in the country that resulted from seven chains of infection.
  45. ^ a b Klaassen, Niels (18 January 2021). "Berekening van Nederlandse expertengroep: "Eén op tien heeft nu Britse coronavariant, mogelijk derde golf in maart"" [Calculation of Dutch expert group: "One in ten now has British corona variant, possibly third wave in March"]. HLN (in Dutch). The Netherlands. Retrieved 18 January 2021. Verder zijn er inmiddels drie gevallen van de Zuid-Afrikaanse variant bekend, een andere besmettelijke mutatie van het coronavirus. (Furthermore, three cases of the South African variant, another contagious mutation of the coronavirus, are now known.)
  46. ^ a b "Panama detects first case of South Africa COVID-19 variant - health ministry". www.reuters.com. 23 January 2021. Retrieved 23 January 2021.
  47. ^ a b "At least 15(sic) cases of South African variant in Ostend". VRT. 23 January 2021. Retrieved 23 January 2021.
  48. ^ Knapton, Sarah (4 January 2021). "South African variant may evade vaccines and testing, warn scientists". www.telegraph.co.uk.
  49. ^ Carter, Sarah (4 January 2021). "COVID vaccines "might not" work as well on South African strain, scientists warn". CBS News. Johannesburg.
  50. ^ a b "UK scientists worry vaccines may not protect against S.African coronavirus variant". Reuters. 4 January 2021. Retrieved 5 January 2021.
  51. ^ Geddes, Linda (8 January 2021). "Pfizer vaccine protects against new Covid variants, study suggests". The Guardian.
  52. ^ "New virus mutation raises vaccine questions". France 24. Paris. 13 January 2021. Retrieved 13 January 2021.
  53. ^ Callaway, Ewen (7 January 2021). "Could new COVID variants undermine vaccines? Labs scramble to find out". Nature. Retrieved 17 January 2021. Chief among those is another receptor-binding-domain mutation, called E484K, that de Oliveira’s team has identified in the 501Y.V2 variant.
  54. ^ Weisblum, Yiska; Schmidt, Fabian; Zhang, Fengwen; Dasilva, Justin; Poston, Daniel; Lorenzi, Julio CC; Muecksch, Frauke; Rutkowska, Magdalena; Hoffmann, Hans-Heinrich; Michailidis, Eleftherios; Gaebler, Christian; Agudelo, Marianna; Cho, Alice; Wang, Zijun; Gazumyan, Anna; Cipolla, Melissa; Luchsinger, Larry; Hillyer, Christopher D.; Caskey, Marina; Robbiani, Davide F.; Rice, Charles M.; Nussenzweig, Michel C.; Hatziioannou, Theodora; Bieniasz, Paul D. (20 October 2020). "Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants". eLife. 9. doi:10.7554/eLife.61312. PMC 7723407. PMID 33112236.
  55. ^ "Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil" (PDF) (Press release). Japan: NIID (National Institute of Infectious Diseases). 12 January 2021. Retrieved 16 January 2021.
  56. ^ a b c d e f g h i j k l Global Report B.1.351 (Report). cov-lineages.org. 20 January 2021. Retrieved 20 January 2021.
  57. ^ "Confirmed cases of COVID-19 variant from South Africa identified in UK". Government of the United Kingdom. Retrieved 23 December 2020.
  58. ^ Mäder, Nick. "Coronavirus in St. Moritz: 31 Personen mit Mutation infiziert". Nau (in German). Retrieved 21 January 2021.
  59. ^ "Zambia experiences second wave of Covid-19 as variant linked to new strain in South Africa isolated". Luksaka Times. 30 December 2020. Retrieved 8 January 2021.
  60. ^ "France has detected its first case of the South African variant of coronavirus, the health ministry said on Thursday". France 24. France. 31 December 2020. Retrieved 8 January 2021.
  61. ^ "Coronavirus (COVID-19) - L'épidémie de COVID-19 en France". santepubliquefrance.fr (in French). Santé publique France. 20 January 2021. Retrieved 22 January 2021. 10 cas d'infections au variant 501Y.V2 (Afrique du Sud) ont été rapportés en France.
  62. ^ "S. Korea reports 1st COVID-19 variant case from Brazil". Yonhap News Agency. 18 January 2021. Retrieved 20 January 2021. The latest discovery brings the total caseload of new coronavirus variants to... ...two with the South African variant...
  63. ^ Nya fall konstaterade av de brittiska och sydafrikanska virusvarianterna [New cases found of the British and South African virus variants], Folkhälsomyndigheten, 2 January 2021, retrieved 16 January 2021
  64. ^ "Nya varianter av SARS-CoV-2 (december 2020– )" [New variants of SARS-CoV-2 (December 2020–)] (in Swedish). Folkhälsomyndigheten. 19 January 2021. Retrieved 20 January 2021. Två fall har bekräftats i Sverige, fallen är kopplade till resande från Sydafrika. Two cases have been confirmed in Sweden, the cases are linked to travelers from South Africa.
  65. ^ "Ny variant av viruset fra Sør-Afrika påvist hos reisende til Norge" [New variant of the virus from South Africa detected in travellers to Norway]. fhi.no (in Norwegian). Retrieved 16 January 2021.
  66. ^ Ellyatt, Holly (6 January 2021). "Covid variant found in South Africa is worrying experts: Here's what we know so far". CNBC. Retrieved 8 January 2021.
  67. ^ "South African coronavirus variant found in the Netherlands". RIVM. 8 January 2021. Retrieved 11 January 2021.
  68. ^ "Alberta reports Canada's 1st case of coronavirus variant found in South Africa". CBC News. 8 January 2021. Retrieved 9 January 2021.
  69. ^ Ran Balicer [@RanBalicer] (21 January 2021). "Israel update: Vaccines, Covid, Variants" (Tweet) – via Twitter.
  70. ^ "10 Additional Cases of the South African Variant". gov.il. Ministry of Health. 20 January 2021. Retrieved 22 January 2021.
  71. ^ "Kenya says it has detected SA COVID-19 variant". eNCA. South Africa. 22 January 2021. Retrieved 22 January 2021.
  72. ^ "Coronavirus live news: France death toll surpasses 72,000; Brazil variant found in Germany". The Guardian. London. 22 January 2021. Retrieved 22 January 2021. The first case of the South African coronavirus variant was identified in Portugal on Friday...