501.V2 variant

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Countries with confirmed cases of 501.V2 as of 5 March 2021[1]
  100 - 999 confirmed cases
  50 - 99 confirmed cases
  10 – 49 confirmed cases
  5 - 9 confirmed cases
  2 - 4 confirmed cases
  1 confirmed case
  No confirmed cases, no population, or no data available

The 501Y.V2 variant, also known as 20H/501Y.V2 (formerly 20C/501Y.V2), B.1.351 lineage[2] and colloquially known as South African COVID-19 variant,[3] is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay[4] metropolitan area of the Eastern Cape province of South Africa in October 2020,[5] which was reported by the country's health department on 18 December 2020.[6] Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay already in July or August 2020.[7]

Detection[edit]

A genomics team lead by the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal discovered the new variant.[8] It was uncovered by whole genome sequencing. Several genomic sequences from this lineage were submitted to the GISAID sequence database.[9][better source needed]

Variant[edit]

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.[10][11] 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.[6][10]

Mutations[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

There are three mutations of particular interest in the spike region of the B.1.351 genome:[12]

  • K417N
  • E484K
  • N501Y

and a further five spike mutations which have so far generated less concern:[12]

  • L18F
  • D80A
  • D215G
  • R246I
  • A701V

Away from the spike region, it also carries: K1655N, SGF 3675-3677 deletion, P71L, and T205I.[13]

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[6][14] (a change from asparagine (N) to tyrosine (Y)[15] in amino-acid position 501), K417N, and E484K.[16][17] Two of these mutations, E484K and N501Y, are within the receptor-binding motif (RBM) of the receptor-binding domain (RBD).[18][19]

The N501Y mutation has also been detected in the United Kingdom.[6][20] 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.[14][21]

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.[21][22] On 28 December, the variant had been detected in two people in Switzerland[23] and in one in Finland.[24] On 29 December, the strain had been detected in a visitor from South Africa to Japan,[25] and in one overseas traveller to Queensland, Australia.[26] On 30 December the variant was detected in Zambia.[27] On 31 December it was also detected in France, in a passenger returning from South Africa.[28] On 2 January 2021, the first case of this variant was detected in South Korea.[29] Austria reported their first case of this variant, along with four cases of the UK variant on 4 January.[30] The Republic of Botswana also detected their first case on 4 January.[31] The People's Republic of China reported the first case of this variant in southern Guangdong province on 6 January.[32]

On 8 January 2021, the Republic of Ireland reported the detection of 3 cases, all linked to travel from South Africa.[33] 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.[34] Canada reported the first case of this variant in Alberta on 9 January,[35] and Israel reported four cases, all of which were imported in people travelling from South Africa.[36] New Zealand reported the first case of this variant on 10 January.[37][38] On 12 January, Germany reported the detection of the mutation in six people from three different households.[39] The same day, it was reported that the United Kingdom had a total of 29 cases, two of which were previously reported.[40] The following day, Belgium reported the first case in a person from West Flanders with no travel history,[41] Israel reported four further cases,[42] and Taiwan reported the first case in a Swazi man in his 30s who had tested positive for COVID-19 on 1 January.[43]

On 14 January, Germany detected a further case[44] and the following day, Canada reported a second case of the mutation which was detected in the Canadian province of British Columbia.[45] A further case was reported in Germany the same day.[46] Denmark and Réunion reported their first cases on 16 January as Israel discovered a further four cases.[47][48][49] On 17 January, Israel reported another four cases bringing their total number of cases of this variant to 20.[50] Two further cases were reported in The Netherlands on 18 January bringing the country's total to three.[51] Ghana reported its first case of the variant on 19 January.[52] On 23 January, Panama detected its first case of the strain in a person from Zimbabwe, who had travelled from South Africa.[53] Also on 23 January, Belgium reported at least 15 cases of the variant in Ostend,[54] while 6 cases were confirmed in the Comoros.[55] On 26 January, the Republic of Ireland reported the detection of 6 further cases.[56] The United States reported its first cases of the variant on 28 January 2021, in the state of South Carolina.[57] 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.[58] Preliminary data reported by Africa CDC on 29 January indicated that the variant had reached Ghana.[59] On 31 January, Israel reported its first case of reinfection with the new variant by a man who returned from Turkey.[60]

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.[61] 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.[62] On 8 February, the Republic of Ireland reported the detection of 2 further cases.[63]

On 8 February 2021, Austria detected the greatest outbreak of 501.V2 variant in Europe so far. A total of 293 confirmed cases and 200 suspected cases have been identified through sequencing, most of them will be confirmed in all probability. All of the cases were found in the Tirol region, where nearly 9% of the positive PCR tests were identified as the 501.V2 variant by sequencing.[64] The active cases were estimated at around 140. After a week of public discussion and political pressure about a possible quarantine of Tirol, the government of Austria abstained from isolating the areas of concern, instead making a formal plea to reduce movement in and out of the region and go for testing after visiting Tirol.[65] Tirolean officials stated their intention to relax the lockdown rules in Tirol in keeping with the rest of Austria.[66]

On 22 February, the Israeli Health Ministry stated that the variant had been genetically sequenced in just under 1% of 3,000 community samples.[67] Later on, Israel reported a total of 444 cases of the variant, making is the highest infection rate in the world outside South Africa.[68] On 25 February, the Republic of Ireland reported the detection of 4 further cases.[69] By late February, Turkey had 49 cases of the 501.V2 variant.[70]

On 3 March 2021, the Philippines confirmed its first 6 new cases of the South African variant, with 3 patients from Pasay City with no travel history, and 3 with travel histories from Qatar and UAE.[71] On 5 March 2021, Romania reported its first two cases of the South African variant, coming from two patients in Bucharest and Pitești.[72]

On 23 March 2021, Lithuania confirmed its first 2 new cases of the South African strain, 1 in Kaunas county and 1 in Vilnius. There are 10 more suspected cases of it. The infected people said, that they didn't travel anywhere.[73] On 26 March there were 3 more cases confirmed, which means that virus is successfully spreading inside.

On 01 Apr 2021, Malaysia detected the South Africa B.1.351 Covid-19 variant in several cases in the country. The health ministry said two cases are believed to be from the Jalan Lima cluster, involving an employee of a based at the Kuala Lumpur International Airport (KLIA).[74] While others cases sparse mainly in Selangor. As of 1st of April, a total of nine cases involving the variant is reported.[75]

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.[76] The same day Shabir Madhi, professor of vaccinology at the University of the Witwatersrand, 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".[77] 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".[78] Lawrence Young, a virologist at Warwick University, also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[78]

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.[79][80] 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.[34] The possibility of an alteration in antigenicity was referred to as an "escape mutation" from a monoclonal antibody with the capability of neutralizing the spike protein variants of SARS-CoV-2.[81][82] This suggests that existing vaccines can and should be updated to counter the new strains without recourse to phased trials.

Johnson & Johnson (Ad26.COV2.S)[edit]

In January, Johnson & Johnson, which held trials for its Ad26.COV2.S vaccine in South Africa, reported the level of protection against moderate to severe COVID-19 infection was 72% in the United States, but 57% in South Africa.[83]

Johnson & Johnson Vaccine at O.R Tambo International Airport

Oxford–AstraZeneca (AZD1222)[edit]

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. 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.[84]

On 7 February 2021, the South African government suspended the planned deployment of around 1 million doses of the vaccine whilst they examined the data and awaited advice on how to proceed.[85] The South African government subsequently cancelled the use of the vaccine, selling its supply to other African countries, and switched its vaccination program to use the Johnson & Johnson COVID-19 vaccine.[86][87]

AstraZeneca vaccines being offloaded in South Africa

Sputnik V (Gam-COVID-Vac)[edit]

The South African Health Products Regulatory Authority (SAHPRA) has confirmed that it has received documentation for the vaccine developed by the Gamaleya Institute in Russia.[88]

Sputnik V is one of three Covid vaccines worldwide with an efficacy higher than 90% in symptomatic cases. They are still in the process of testing its effectiveness against the 501.V2 variant.[89]

Pfizer–BioNTech (BNT162b2)[edit]

On 17 February 2021, Pfizer announced that neutralisation activity was reduced by two thirds for the 501.V2 variant, whilst refraining from making claims about the efficacy of the vaccine in preventing illness as a result of this variant.[90]

On 16 March 2021, The South African Health Products Regulatory Authority (SAHPRA) approved the Pfizer-BioNTech vaccine for section 21 Emergency Use Authorisation.[91]

Pfizer–BioNTech vaccine

On 1 April 2021, an update on a South African vaccine trial stated that the vaccine was 100% effective so far (i.e., vaccinated participants saw no cases), with six of nine infections in the placebo control group being the B.1.351 variant.[92] However, nine days later, an Israeli study found that the variant was present even in people who had received both shots of the vaccine, its prevalence a disproportionate, eight-fold increase amongst vaccinated individuals in comparison to wild strains.[93]

Moderna (mRNA-1273)[edit]

In February, Moderna reported that the current vaccine produced only one sixth of the antibodies in response to the South African variant compared with the original virus. They have launched a trial of a new vaccine to tackle the South African 501.V2 variant.[94]

Sinopharm (BBIBP-CorV)[edit]

Other African countries have begun the roll out of the Sinopharm, with Morocco, Egypt, The Seychelles and Zimbabwe starting the mass rollout.[95] So far, the vaccine has proven resistant to the 501.V2 variant, as demonstrated in Zimbabwe.[96] On 02 February 2021, a preprint paper announced that neutralisation activity was reduced by 1.6 fold for the 501.V2 variant, which is a smaller drop compared to mRNA vaccines Pfizer(3-fold) and Moderna(6-fold).[97]

CoronaVac (Sinovac)[edit]

CoronaVac is yet to be approved for use by the South African Health Products Authority (SAHPRA).[98] So far, Sinovac has offered to supply South Africa with 5 million doses of the vaccine.[99]

Covaxin (BBV152)[edit]

Bharat Biotech, producers of the Covaxin vaccine have said that they can modify the vaccine against the South African variant of the coronavirus within 15 days.[100]

CoviVac (КовиВак)[edit]

The CoviVac vaccine Information has not been delivered to the South African government yet.[101]

EpiVacCorona (EpiVacCorona)[edit]

The EpiVacCorona vaccine Information has not been delivered to the South African government yet.[102]

RBD-Dimer (ZF2001)[edit]

The RBD-Dimer vaccine Information is in the process of being delivered to the South African government.[103]

Novavax (NVX-CoV2373)[edit]

A study on the NVX-CoV2373 Novavax vaccine showed 60% efficacy (for HIV-negative participants) in South Africa, compared to 90% efficacy in Britain.[104]

ImmunityBio (ImmunityBio)[edit]

The BioVac Institute, a state-backed South African vaccine company, plans to use a deal it won to manufacture coronavirus vaccines. The contract with American based ImmunityBio Inc is currently conducting phase 1 vaccine trials with their hAd5 vaccine in the United States and South Africa.[105]

ImmunityBio and BioVac plan to distribute the vaccines throughout South Africa and Africa.[106][107]

Statistics[edit]

Cases by country (Updated as of 11 April 2021)
Country Confirmed cases First detection References
 South Africa 1738 8 October 2020 [1]
 United Kingdom 533 23 December 2020 [108][40][1][109][110]
  Switzerland 123 28 December 2020 [23][111][1]
 Finland 17 28 December 2020 [24][1][112]
 Japan 22 29 December 2020 [25][1]
 Australia 38 29 December 2020 [26][1]
 Zambia 31 30 December 2020 [113][1]
 France 512 31 December 2020 [114][1][115]
 South Korea 5 2 January 2021 [29][116][1]
 Sweden 299 2 January 2021 [1][117][118][119][120][121][122]
 Norway 190 4 January 2021 [123][1]
 Botswana 54 4 January 2021 [31][1]
 China 1 6 January 2021 [32]
 Ireland 43 8 January 2021 [33][56][63][124][125][1]
 The Netherlands 329 8 January 2021 [126][51][127][1]
 Canada 354 8 January 2021 [128][45][62][129]
 Israel 444 9 January 2021 [36][42][49][50][130]
[131][132][58][133][68]
 New Zealand 23 10 January 2021 [37][38][1]
 Germany 651 12 January 2021 [39][44][46][1][134][135]
 Belgium 654 13 January 2021 [41][1][54]
 Taiwan 1 13 January 2021 [43]
 Denmark 14 16 January 2021 [47][1]
 Spain 34 22 January 2021 [1]
 Kenya 37 22 January 2021 [136][1]
 Portugal 51 22 January 2021 [137][1]
 Panama 2 23 January 2021 [53]
 UAE 5 23 January 2021 [1]
 Comoros 6 23 January 2021 [55]
 Mayotte 353 27 January 2021 [1]
 USA 424 27 January 2021 [1][57][138]
 Mozambique 58 29 January 2021 [1]
 Vietnam 1 31 January 2021 [139]
 Luxembourg 227 2 February 2021 [1]
 Turkey 112 3 February 2021 [140][141][1][70]
 Austria 438 4 January 2021 [142][143][144][145]
 Bangladesh 45 8 February 2021 [1]
 Ghana 4 6 January 2021 [1][146]
 Greece 7 17 February 2021 [147]
 Malta 1 16 February 2021 [148]
 Singapore 71 16 February 2021 [1]
 Thailand 6 16 February 2021 [1]
 Réunion 16 16 January 2021 [48][1]
 Italy 26 20 February 2021 [1]
 DRC 1 22 January 2021 [1]
 Czech Republic 15 25 February 2021 [1][149]
 Rwanda 11 28 February 2021 [1]
 Costa Rica 2 28 February 2021 [1]
 Slovenia 26 28 February 2021 [1]
 Philippines 344 2 March 2021 [150][151][152][153][154][155]
 Croatia 7 3 March 2021 [1]
 India 11 17 February 2021 [156][1]
 Malawi 152 8 February 2021 [1][157]
 Romania 2 5 March 2021 [72]
 Brunei 1 6 March 2021 [1]
 Poland 12 10 March 2021 [1]
 Zimbabwe 196 13 March 2021 [1]
 Eswatini 20 13 March 2021 [1]
 Mauritius 2 13 March 2021 [1]
 Monaco 1 13 March 2021 [1]
 Guadeloupe 1 13 March 2021 [1]
 Cameroon 1 13 March 2021 [1]
 Slovakia 10 18 March 2021 [1]
 Russia 3 18 March 2021 [1]
 Sri Lanka 3 8 April 2021 [1][158]
 Aruba 2 18 March 2021 [1]
 Malaysia 9 18 March 2021 [1]
 Lesotho 14 21 March 2021 [1]
 Lithuania 5 23 March 2021 [73]
 Estonia 3 24 March 2021 [1]
 Angola 7 29 March 2021 [1]
 Ukraine 1 April 2021 [159]
 Jordan 2 4 April 2021 [1]
 Brazil 1 4 April 2021 [1]
 Togo 1 9 April 2021 [1]
World (74 countries) Total: 8,876 Total as of 11 April 2021

See Also[edit]

References[edit]

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External links[edit]