Wikipedia

SARS-CoV-2 Beta variant

(Redirected fromB.1.351)
This article is about the Beta variant of the SARS-CoV-2 virus that causes COVID-19. Not to be confused with the genus ofBetacoronavirus.
Main article:Variants of SARS-CoV-2

TheBeta variant,[1][2](B.1.351),[a]was[5][6]avariantofSARS-CoV-2,the virus that causesCOVID-19.One of severalSARS-CoV-2 variants initially believed to be of particular importance,it was first detected in theNelson Mandela Bay[7]metropolitan area of theEastern Capeprovince ofSouth Africain October 2020,[8]which was reported by the country'shealth departmenton 18 December 2020.[9]Phylogeographic analysissuggests this variant emerged in theNelson Mandela Bayarea in July or August 2020.[10]

SARS-CoV-2Variant
Beta
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom.
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom.
General details
WHO DesignationBeta
LineageB.1.351
First detectedNelson Mandela Bay,South Africa
Date reportedJuly 2020;4 years ago(2020-07)or August 2020;4 years ago(2020-08)
StatusVariant of concern
Cases map
Countries with confirmed cases of Beta variant as of 2 July 2021[1]
Legend:
1,000+ confirmed sequences
250–999 confirmed sequences
100–249 confirmed sequences
10–99 confirmed sequences
2–9 confirmed sequences
1 confirmed sequence
None or no data available
Major variants

TheWorld Health Organizationlabelled the variant as Beta variant, not to replace the scientific name but as a name for the public to commonly refer to.[11][12]The WHO considers it to be avariant of concernno longer in circulation.[5]

Names

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The variant is also known as theSouth African variant.

Mutations

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  • Amino acid mutations of SARS-CoV-2 Beta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.[13]
Mutational profile of Beta variant
(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 lineage B.1.351 genome:[14]

  • K417N
  • E484K
  • N501Y

and a further five spike mutations which have so far generated less concern:[14]

  • L18F
  • D80A
  • D215G
  • R246I
  • A701V

Away from the spike region, it also carries: K1655N, SGF 3675-3677 deletion, P71L, and T205I.[15]

Scientists noted that the variant is able to attach more easily to human cells because of three mutations in thereceptor-binding domain(RBD) in thespike glycoproteinof the virus: N501Y[9][16](a change fromasparagine(N) totyrosine(Y)[17]inamino-acidposition 501), K417N, and E484K.[18][19]Two of these mutations, E484K and N501Y, are within the receptor-binding motif (RBM) of the receptor-binding domain (RBD).[20][21]

The N501Y mutation has also been detected in the United Kingdom.[9][22]Two mutations found in the Beta variant, E484K and K417N, are not found inAlpha variant.Also, Beta does not have the 69-70del mutation found in the other variant.[16][23]

Vaccine efficacy

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See also:Oxford–AstraZeneca COVID-19 vaccine § Effectiveness,Pfizer–BioNTech COVID-19 vaccine § Effectiveness,Janssen COVID-19 vaccine § Efficacy,Moderna COVID-19 vaccine § Effectiveness,Novavax COVID-19 vaccine § Efficacy,Sinopharm BIBP COVID-19 vaccine § Variants,Sputnik V COVID-19 vaccine § Variants,CoronaVac § Variants,Covaxin § Variants,ZF2001 § Efficacy,andAbdala (vaccine) § Efficacy

On 4 January 2021, UK newspaperThe Telegraphreported that Oxford immunologistSir John Bellbelieved there was "a big question mark" over the new South African variant's potential resistance toCOVID-19 vaccines,raising fears that vaccines might not work as effectively on that variant strain.[24]The same dayShabir Madhi,professor of vaccinology at theUniversity of the Witwatersrand,commented toCBS Newsthat "it's not a given" that the new Beta variant (501.V2 variant) would be able to evade the vaccines, but that it should be considered that they "might not have the full efficacy".[25]The additional mutations to the spike protein in Beta were raised as a concerning factor by Simon Clarke, an associate professor in cellular microbiology at theUniversity of Reading,in that they "may make the virus less susceptible to the immune response triggered by the vaccines".[26]Lawrence Young, a virologist atWarwick University,also noted that the variant's multiple spike mutations "could lead to some escape from immune protection".[26]

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.[27][28]The E484K spike mutation was linked to a case of reinfection with the Beta variant ofSARS-CoV-2in 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 neutralizing the spike protein variants of SARS-CoV-2.[30][31]This suggests that existing vaccines can and should be updated to counter the new strains without recourse to phased trials.

Janssen

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In January,Johnson & Johnson,which held trials for itsJanssen(Ad26.COV2.S) vaccine inSouth Africa,reported the level of protection against moderate to severe COVID-19 infection was 72% in the United States, but 64% inSouth Africa.[32][33]

Pfizer–BioNTech

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On 17 February 2021,Pfizerannounced that neutralisation activity was reduced by two thirds for the Beta variant, whilst refraining from making claims about the efficacy of the vaccine in preventing illness as a result of this variant.[34]

On 16 March 2021, The South African Health Products Regulatory Authority (SAHPRA) approved thePfizer-BioNTechvaccine (BNT162b2) for section 21 Emergency Use Authorisation.[35]

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 Beta variant (lineage B.1.351).[36]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.[37]

On 5 May 2021, a letter summarizing results from the Qatar National Study Group for COVID-19 Vaccination showed 75% effectiveness against infection, with zero cases of severe disease.[38]

Oxford–AstraZeneca

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On 6 February 2021,The Financial Timesreported that provisional trial data from a study undertaken bySouth Africa'sUniversity of the Witwatersrandin conjunction withOxford Universitydemonstrated reduced efficacy of theOxford–AstraZeneca COVID-19 vaccine(AZD1222) against the Beta variant. The study found that in a sample size of 2,000 theAZD1222vaccine afforded only "minimal protection" in all but the most severe cases ofCOVID-19.[39]

On 7 February 2021, theSouth Africangovernment suspended the planned deployment of around 1 million doses of the vaccine whilst they examined the data and awaited advice on how to proceed.[40]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 theJanssen COVID-19 vaccine.[41][42]

In July 2021, following increased incidence of Beta in France, the United Kingdom - a major user of the AstraZeneca vaccine - placed additional restrictions on people travelling to the UK from France. However, the incidence in France is in its Indian Ocean territory ofLa Réunion,[43]as pointed out by French politician and doctorVeronique Trillet-Lenoir.[44]

Sinopharm BIBP

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OtherAfricancountries have begun the roll out theSinopharm BIBP vaccine,withMorocco,Egypt,The SeychellesandZimbabwestarting the mass rollout.[45]So far, the vaccine has proven resistant to the Beta variant, as demonstrated in Zimbabwe.[46]On 2 February 2021, a preprint paper announced that neutralisation activity was reduced by 1.6 fold for the Beta variant.[47]

Moderna

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In February,Modernareported that the current vaccine (mRNA-1273) produced only one sixth of the antibodies in response to theSouth Africanvariant compared with the original virus. They have even launched a trial of a new vaccine to tackle the Beta variant.[48]

Sputnik V

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The South African Health Products Regulatory Authority (SAHPRA) has confirmed that it has received documentation for the vaccine developed by theGamaleya Institute in Russia.[49]

Sputnik V(Gam-COVID-Vac) is one of threeCovid vaccinesworldwide with an efficacy higher than 90% in symptomatic cases. It was found to be slightly less effective however it worked better than its rivals.[1]A three fold reduction in VNA was found against the beta variant.[2][3]A small study of 12 samples published in the nature communications journal showed that the neutralising antibody response was about 6.1 times less against the beta variant.[50]

CoronaVac

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CoronaVacis yet to be approved for use by the South African Health Products Authority (SAHPRA).[51]So far,Sinovachas offered to supplySouth Africawith 5 million doses of the vaccine.[52]

Covaxin

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Covaxin has been found to be effective against the beta variant although with a three fold reduction in neutralization.

CoviVac

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TheCoviVacvaccine Information has not been delivered to the South African government yet.[53]

EpiVacCorona

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TheEpiVacCoronavaccine Information has not been delivered to theSouth Africangovernment yet.[54]

ZF2001

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TheZF2001vaccine Information is in the process of being delivered to theSouth Africangovernment.[55]

Novavax

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A study on theNVX-CoV2373Novavax vaccine showed 60% efficacy (for HIV-negative participants) inSouth Africa,compared to 90% efficacy inBritain.[56]

ImmunityBio

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TheBioVacInstitute, a state-backedSouth Africanvaccine company, plans to use a deal it won to manufacturecoronavirus vaccines.The contract withAmericanbased ImmunityBio Inc is currently conducting phase 1 vaccine trials with theirhAd5 vaccinein the United States and South Africa.[57]

ImmunityBio andBioVacplan to distribute the vaccines throughoutSouth Africaand Africa.[58][59]

Epidemiology

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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.[60][61]The South African health department also indicated that the variant may be driving the second wave of theCOVID-19 pandemicin the country, as the variant spreads faster than other earlier variants of the virus.[9][60]

Statistics

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History

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A genomics team led by theKwaZulu-Natal Research Innovation and Sequencing Platform(KRISP) at theUniversity of KwaZulu-Nataldiscovered the new variant.[62]It was uncovered bywhole genome sequencing.Several genomic sequences from this lineage were submitted to theGISAIDsequence database.[63][better source needed]

On 23 December 2020, UK health ministerMatt Hancockannounced that two people who had travelled fromSouth Africato theUKwere infected with the Beta variant (501.V2 variant).[23][64]On 28 December, the variant had been detected in two people inSwitzerland[65]and in one inFinland.[66]On 29 December, the strain had been detected in a visitor from South Africa toJapan,[67]and in one overseas traveller toQueensland,Australia.[68]On 30 December the variant was detected inZambia.[69]On 31 December, it was also detected inFrance,in a passenger returning from South Africa.[70]On 2 January 2021, the first case of this variant was detected inSouth Korea.[71]Austriareported their first case of this variant, along with four cases of theAlpha varianton 4 January.[72]TheRepublic of Botswanaalso detected their first case on 4 January.[73]ThePeople's Republic of Chinareported the first case of this variant in southernGuangdong provinceon 6 January.[74]

On 8 January 2021, theRepublic of Irelandreported the detection of 3 cases, all linked to travel from South Africa.[75]On the same day a case of reinfection with the new variant by a woman who had had COVID-19 was reported fromBrazil,the first such reinfection reported in the world.[29]Canadareported the first case of this variant inAlbertaon 9 January,[76]andIsraelreported four cases, all of which were imported in people travelling from South Africa.[77]New Zealandreported the first case of this variant on 10 January.[78][79]On 12 January,Germanyreported the detection of the mutation in six people from three different households.[80]The same day, it was reported that the United Kingdom had a total of 29 cases, two of which were previously reported.[81]The following day,Belgiumreported the first case in a person fromWest Flanderswith no travel history,[82]Israel reported four further cases,[83]andTaiwanreported the first case in aSwaziman in his 30s who had tested positive for COVID-19 on 1 January.[84]

On 14 January,Germanydetected a further case[85]and the following day, Canada reported a second case of the mutation which was detected in the Canadian province ofBritish Columbia.[86]A further case was reported in Germany the same day.[87]DenmarkandRéunionreported their first cases on 16 January as Israel discovered a further four cases.[88][89][90]On 17 January, Israel reported another four cases bringing their total number of cases of this variant to 20.[91]Two further cases were reported inThe Netherlandson 18 January bringing the country's total to three.[92]Ghanareported its first case of the variant on 19 January.[93]On 23 January,Panamadetected its first case of the strain in a person from Zimbabwe, who had travelled from South Africa.[94]Also on 23 January,Belgiumreported at least 15 cases of the variant in Ostend,[95]while 6 cases were confirmed in the Comoros.[96]On 26 January, the Republic of Ireland reported the detection of 6 further cases.[97]The United States reported its first cases of the variant on 28 January 2021, in the state ofSouth Carolina.[98]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.[99]Preliminary data reported by Africa CDC on 29 January indicated that the variant had reachedGhana.[100]On 31 January, Israel reported its first case of reinfection with the new variant by a man who returned fromTurkey.[101]

On 1 February 2021, the United KingdomSecretary of State for Health and Social Carereported the random detection of 11 cases of the variant where there was no connection to international travel.[102]The same day, the Canadian province of Ontario reported the first case of the variant in thePeel Region,with a similar absence of travel history and no contact with anyone who had recently been abroad.[103]On 8 February, the Republic of Ireland reported the detection of 2 further cases.[104]

On 8 February 2021,Austriadetected the greatest outbreak of Beta 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 Beta variant by sequencing.[105]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.[106]Tirolean officials stated their intention to relax the lockdown rules in Tirol in keeping with the rest of Austria.[107]

On 22 February, the Israeli Health Ministry stated that the variant had been genetically sequenced in just under 1% of 3,000 community samples.[108]Later on, Israel reported a total of 444 cases of the variant, making it the highest infection rate in the world outside South Africa.[109]On 25 February, the Republic of Ireland reported the detection of 4 further cases.[110]By late February, Turkey had 49 cases of the Beta variant.[111]

On 3 March 2021, thePhilippinesconfirmed its first 6 new cases of the South African variant, with 3 patients fromPasaywith no travel history, and 3 with travel histories fromQatarandUAE.[112]On 5 March 2021,Romaniareported its first two cases of the South African variant, coming from two patients inBucharestandPitești.[113]

On 23 March 2021,Lithuaniaconfirmed its first 2 new cases of the South African strain, 1 inKaunas countyand 1 inVilnius.There are 10 more suspected cases of it. The infected people said, that they didn't travel anywhere.[114]On 26 March there were 3 more cases confirmed, which means that virus is successfully spreading inside.

On 1 April 2021,Malaysiadetected its first cases of South African variant. The health ministry reported two cases believed to originate from the Jalan Lima cluster, involving an employee based at theKuala Lumpur International Airport(KLIA), with other reported cases sparsely detected withinSelangor.[115]As of 1 April, a total of nine cases involving the variant is reported.[116]By 2 May, a total of 48 cases has been detected in least 5 clusters and from contact tracing, of which 20 were found in two clusters inPerakandKelantan.[117]

On 12 April 2021 Turkey had 285 cases in 11 provinces.[118]

Extinction

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In March 2022, the World Health Organization listed theAlpha,Beta andGammavariants as previously circulating citing lack of any detected cases in the prior weeks and months.[119]

See also

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Notes

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  1. ^Other names include:[3][4]
    –20H/501Y.V2(formerly 20C/501Y.V2)
    –501Y.V2 variant
    –South African COVID-19 variant

References

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