501.V2 variant

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File:501.V2 Variant Cases Map 15 January 2021.png
Countries with confirmed cases of 501.V2 as of 15 January 2021, excluding South Africa
  5 - 9 Confirmed cases
  2 - 4 Confirmed cases
  1 Confirmed cases
  It has cases, but there are no precise figures
  Suspicious cases
  No confirmed cases, no population, or no data available

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

(change of amino acid only)
Mutational profile of 501.V2
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 can 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

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.[16][better source needed]

International spread

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]

Vaccine evasion

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.[46] 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".[47] 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".[48] Lawrence Young, a virologist at Warwick University, also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[48]

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.[49]

E484K mutation

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.[50][51] 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.[52][53]

Statistics

Cases by country, excluding South Africa (Updated as of 18 January 2021)
Country Confirmed cases Date References
 United Kingdom 2
27		 23 December 2020
12 January 2021		 [54]
[35]
  Switzerland 2 28 December 2020 [18]
 Finland 1 28 December 2020 [19]
 Japan 1 29 December 2020 [20]
 Australia 1 29 December 2020 [21]
 Zambia 1 30 December 2020 [55]
 France 1 31 December 2020 [56]
 South Korea 1 2 January 2021 [24]
 Sweden 1 2 January 2021 [57]
 Norway 1 4 January 2021 [58]
 China 1 6 January 2021 [27]
 Austria 1 4 January 2021 [59]
 Botswana 1 4 January 2021 [26]
 Ireland 3 8 January 2021 [28]
 Brazil 1 8 January 2021 [29]
 The Netherlands 1
2		 8 January 2021
18 January 2021		 [60]
[45]
 Canada 1
1		 8 January 2021
15 January 2021		 [61]
[40]
 Israel 4
4
4
20 (total)		 9 January 2021
13 January 2021
16 January 2021
17 January 2021		 [31]
[37]
[43]
[44]
 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 13 January 2021 [36]
 Taiwan 1 13 January 2021 [38]
 Denmark 1 16 January 2021 [42]
World (23 other countries) 83

See also

References

  1. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ For a list of sources, refer to South African COVID-19 variant.
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ 5.0 5.1 5.2 5.3 Lua error in package.lua at line 80: module 'strict' not found.
  6. ↑ 6.0 6.1 Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ 8.0 8.1 Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ For a list of the symbols used for the α-amino acids incorporated into protein under mRNA direction, see: Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  11. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  12. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ 15.0 15.1 Lua error in package.lua at line 80: module 'strict' not found.
  16. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  17. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  18. ↑ 18.0 18.1 Lua error in package.lua at line 80: module 'strict' not found.
  19. ↑ 19.0 19.1 Lua error in package.lua at line 80: module 'strict' not found.
  20. ↑ 20.0 20.1 Lua error in package.lua at line 80: module 'strict' not found.
  21. ↑ 21.0 21.1 Lua error in package.lua at line 80: module 'strict' not found.
  22. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  23. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  24. ↑ 24.0 24.1 Lua error in package.lua at line 80: module 'strict' not found.
  25. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  26. ↑ 26.0 26.1 Lua error in package.lua at line 80: module 'strict' not found.
  27. ↑ 27.0 27.1 Lua error in package.lua at line 80: module 'strict' not found.
  28. ↑ 28.0 28.1 Lua error in package.lua at line 80: module 'strict' not found.
  29. ↑ 29.0 29.1 29.2 Lua error in package.lua at line 80: module 'strict' not found.
  30. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  31. ↑ 31.0 31.1 Lua error in package.lua at line 80: module 'strict' not found.
  32. ↑ 32.0 32.1 Lua error in package.lua at line 80: module 'strict' not found.
  33. ↑ 33.0 33.1 Lua error in package.lua at line 80: module 'strict' not found.
  34. ↑ 34.0 34.1 Lua error in package.lua at line 80: module 'strict' not found.
  35. ↑ 35.0 35.1 Lua error in package.lua at line 80: module 'strict' not found.
  36. ↑ 36.0 36.1 Lua error in package.lua at line 80: module 'strict' not found.
  37. ↑ 37.0 37.1 Lua error in package.lua at line 80: module 'strict' not found.
  38. ↑ 38.0 38.1 Lua error in package.lua at line 80: module 'strict' not found.
  39. ↑ 39.0 39.1 Lua error in package.lua at line 80: module 'strict' not found.
  40. ↑ 40.0 40.1 Lua error in package.lua at line 80: module 'strict' not found.
  41. ↑ 41.0 41.1 Lua error in package.lua at line 80: module 'strict' not found.
  42. ↑ 42.0 42.1 Lua error in package.lua at line 80: module 'strict' not found.
  43. ↑ 43.0 43.1 Lua error in package.lua at line 80: module 'strict' not found.
  44. ↑ 44.0 44.1 Lua error in package.lua at line 80: module 'strict' not found.
  45. ↑ 45.0 45.1 Lua error in package.lua at line 80: module 'strict' not found.
  46. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  47. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  48. ↑ 48.0 48.1 Lua error in package.lua at line 80: module 'strict' not found.
  49. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  50. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  51. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  52. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  53. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  54. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  55. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  56. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  57. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  58. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  59. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  60. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  61. ↑ Lua error in package.lua at line 80: module 'strict' not found.
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