501.V2 variant

The 501Y.V2 variant, also known as 20H/501Y.V2 (formerly 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]

Countries with confirmed cases of 501.V2 as of 29 January 2021
  100 - 999 confirmed cases
  50 - 99 confirmed cases
  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 that 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.

Detection

The new variant was uncovered by whole genome sequencing. Several genomic sequences from this lineage were submitted to the GISAID sequence database.[6]

Variant

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.[7][8] 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][7]

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][9] (a change from asparagine (N) to tyrosine (Y)[10] in amino-acid position 501), K417N, and E484K.[11][12] Two of these mutations, E484K and N501Y, are within the receptor-binding motif (RBM) of the receptor-binding domain (RBD).[13][14]

The N501Y mutation has also been detected in the United Kingdom.[5][15] 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.[9][16]

International spread
Mutational profile of 501.V2
(change of amino acid only)
Gene Nucleotide Amino acid
ORF1ab C1059TT265I
G5230TK1655N
C8660TH2799Y
C8964TS2900L
A10323GK3353R
G13843TD4527Y
C14408T1P4715L
C17999TT5912I
Spike C21614TL18F
A21801CD80A
A22206GD215G
G22299TR246I
G22813TK417N
G23012AE484K
A23063TN501Y
A23403G1D614G
G23664TA701V
ORF3a G25563TQ57H
C25904TS171L
E C26456TP71L
N C28887TT205I

Footnote: 1Presented in parent lineage B.1.

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

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.[16][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 travelled from South Africa.[46] Also on 23 January, Belgium reported at least 15 cases of the variant in Ostend.[47] On 26 January, the Republic of Ireland reported the detection of 6 further cases.[48] The United States reported its first cases of the variant on 28 January 2021, in the state of South Carolina.[49]On 27 January, Israel reported 3 more cases which were the first cases of the variant from samples that were collected in the community randomly, without knowing the source of infection.[50] On 31 January, Israel reported its first case of reinfection with the new variant by a man who returned from Turkey. [51]

On 1 February 2021, the United Kingdom Secretary of State for Health and Social Care reported the random detection of 11 cases of the variant where there was no connection to international travel.[52] The same day, the Canadian province of Ontario reported the first case of the variant in the Peel Region, with a similar absence of travel history and no contact with anyone who had recently been abroad.[53]

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.[54] 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".[55] 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".[56] Lawrence Young, a virologist at Warwick University, also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[56]

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.[57]

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.[58][59] 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.[60][61] This suggests that existing vaccines can and should be updated to counter the new strains without recourse to phased trials. Moderna is planning to test an alternate mRNA-1273 vaccine version specially designed to protect against 501.V2.[62] It is reported that NVX-CoV2373 is 60% effective against 501.V2.[63] According to a clinical study of the Ad26.COV2.S vaccine, its effectiveness in southern Africa is 15% lower than in the United States (57% and 72%, respectively), the difference is probably associated with the prevalence of the 501.V2 strain in South Africa.[64] One more vaccine study (related to NVX-CoV2373 by Novavax) showed 60% efficacy (for HIV-negative participants) in South Africa, compared to 90% efficacy in Britain.[65] According to Reuters, Pfizer vaccine is only slightly less effective against 501.V2.[66]

On 6 February 2021, The Financial Times reported that provisional trial data from a study undertaken by South Africa's University of the Witwatersrand in conjunction with Oxford University demonstrated reduced efficacy of the Oxford–AstraZeneca COVID-19 vaccine against the 501.V2 variant.[67] The study found that in a sample size of 2,000 the AZD1222 vaccine afforded only "minimal protection" in all but the most severe cases of COVID-19.[68] On 7 February 2021, the Minister for Health for South Africa suspended the planned deployment of around 1 million doses of the vaccine whilst they examine the data and await advice on how to proceed.[69]

Statistics
Cases by country (Updated as of 5 February 2021)
Country Confirmed cases Date References
 South Africa520
4
1
-6
30
549 (total)		8 October 2020
25 January 2021
29 January 2021
30 January 2021
3 February 2021

[70]
[70]
[70]
[70]
[70]

 United Kingdom2
27
38
6
5
1
7
4
4
11
7
112 (total)		23 December 2020
12 January 2021
20 January 2021
22 January 2021
23 January 2021
25 January 2021
26 January 2021
27 January 2021
28 January 2021
1 February 2021
5 February 2021

[71]
[35]
[70]
[70]
[70]
[70]
[70]
[70]
[70]
[72]
[70]

  Switzerland2
31
33 (total)		28 December 2020
21 January 2021

[18]
[73]

 Finland1
1
2 (total)		28 December 2020
20 January 2021

[19]
[70]

 Japan129 December 2020[20]
 Australia1
5
1
1
2
10 (total)		29 December 2020
20 January 2021
22 January 2021
29 January 2021
5 February 2021

[21]
[70]
[70]
[70]
[70]

 Zambia130 December 2020[74]
 France1
4
5
1
1
12
1
25 (total)		31 December 2020
20 January 2021
20 January 2021
27 January 2021
2 February 2021
3 February 2021
5 February 2021

[75]
[70]
[76]
[70]
[70]
[70]
[70]

 South Korea1
1
2 (total)		2 January 2021
18 January 2021

[24]
[77]

 Sweden1
1
1
3
6 (total)		2 January 2021
20 January 2021
26 January 2021
2 February 2021

 [78]
[79]
[80]
[81]

 Norway14 January 2021[82]
 China16 January 2021[27]
 Botswana1
5
1
3
10 (total)		4 January 2021
20 January 2021
27 January 2021
5 February 2021

[26]
[70]
[70]
[70]

 Ireland3
6
9 (total)		8 January 2021
26 January 2021

[28]
[48]

 Brazil18 January 2021[29]
 The Netherlands1
2
18
1
22 (total)		8 January 2021
18 January 2021
26 January 2021
5 February 2021

 [83]
[45]
[84]
[70]

 Canada1
1
1
3 (total)		8 January 2021
15 January 2021
1 February 2021

[85]
[40]
[53]

 Israel4
4
4
8
2
5
3
50
80 (total)		9 January 2021
13 January 2021
16 January 2021
17 January 2021
21 January 2021
24 January 2021
27 January 2021
1 February 2021

[31]
[37]
[43]
[44]
[86][87]
[88]
[50]
[89]

 New Zealand1
6
7 (total)		10 January 2021
29 January 2021

[32][33]
[70]

 Germany6
1
1
1
24
2
35 (total)		12 January 2021
14 January 2021
15 January 2021
25 January 2021
27 January 2021
29 January 2021

[34]
[39]
[41]
[70]
[90]
[91]

 Belgium1
5
15
12
33 (total)		13 January 2021
20 January 2021
23 January 2021
5 February 2021

[36]
[70]
[47]
[70]

 Taiwan113 January 2021[38]
 Denmark1
2
2
5 (total)		16 January 2021
29 January 2021
5 February 2021

[42]
[70]
[70]

 Spain122 January 2021[70]
 Kenya222 January 2021[92]
 Portugal122 January 2021[93]
 Panama123 January 2021[46]
 UAE523 January 2021[70]
 Mayotte5
2
15
22 (total)		27 January 2021
1 February 2021
2 February 2021

[70]
[70]
[70]

 USA2
1
2
5 (total)		27 January 2021
2 February 2021
3 February 2021

[70][49]
[94]
[70]

 Mozambique20
-1
19 (total)		29 January 2021
30 January 2021

[70]
[70]
 Vietnam131 January 2021[95]
 Luxembourg22 February 2021[70]
 Turkey23 February 2021[96][97]
 Austria1
75
76 (total)		4 January 2021
4 February 2021

[98]
[99]

World (35 countries)1086As of 5 February 2021

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