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SARS-CoV-2 Alpha variant

December 18, 2023

"B117" redirects here. For other uses, see B117 (disambiguation).

The Alpha variant (B.1.1.7) was[2][3] a SARS-CoV-2 variant of concern. It was estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2 (with most estimates occupying the middle to higher end of this range). Scientists more widely took note of this variant in early December 2020, when a phylogenetic tree showing viral sequences from Kent, United Kingdom looked unusual.[4] The variant began to spread quickly by mid-December, around the same time as infections surged.

SARS-CoV-2 Variant
Alpha
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom.
General details
WHO DesignationAlpha
LineageB1.1.1.7
First detectedKent, England
Date reportedNovember 2020; 3 years ago (2020-11)
StatusVariant of concern
Symptoms
  • None
  • Chills
  • Loss of appetite
  • Headaches
  • Muscle aches
Cases map
Total number of B.1.1.7 sequences by country as of 25 March 2021[1]
Legend:
  10,000+ confirmed sequences
  5,000–9,999 confirmed sequences
  1,000–4,999 confirmed sequences
  500–999 confirmed sequences
  100–499 confirmed sequences
  2–99 confirmed sequences
  1 confirmed sequence
  None or no data available
Major variants

This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant was also notable for having more mutations than normally seen.[5]

By January 2021, more than half of all genomic sequencing of SARS-CoV-2 was carried out in the UK.[6] This had given rise to questions as to how many other important variants were circulating around the world undetected.[7][8]

On 2 February 2021, Public Health England reported that they had detected "[a] limited number of B.1.1.7 VOC-202012/01 genomes with E484K mutations",[9] which they dubbed Variant of Concern 202102/02 (VOC-202102/02).[10] One of the mutations (N501Y) is also present in Beta variant and Gamma variant.

On 31 May 2021, the World Health Organization announced that the Variant of Concern would be labelled "Alpha" for use in public communications.[11][12]

Classification edit

Names edit

The variant is known by several names. Outside the UK it is sometimes referred to as the UK variant or British variant or English variant,[13] despite the existence of other, less common, variants first identified in UK, such as Eta variant (lineage B.1.525). Within the UK, it is commonly referred to as the Kent variant after Kent, where the variant was found.[14][15][16]

In scientific use, the variant had originally been named the first Variant Under Investigation in December 2020 (VUI – 202012/01) by Public Health England (PHE),[17][a] but was reclassified to a Variant of Concern (Variant of Concern 202012/01, abbreviated VOC-202012/01) by Meera Chand and her colleagues in a report published by PHE on 21 December 2020.[b] In a report written on behalf of COVID-19 Genomics UK (COG-UK) Consortium, Andrew Rambaut and his co-authors, using the Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin) tool, dubbed it lineage B.1.1.7,[19] while Nextstrain dubbed the variant 20I/501Y.V1.[20]

The name VOC-202102/02 refers to the variant with the E484K mutation (see below).[10]

Genetic profile edit

  •  
    Amino acid mutations of SARS-CoV-2 Alpha variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.[21]
Defining mutations in VOC-202012/01
(change of amino acid only)
Gene Nucleotide Amino acid
ORF1ab C3267T T1001I
C5388A A1708D
T6954C I2230T
11288–11296 deletion SGF 3675–3677 deletion
Spike 21765–21770 deletion HV 69–70 deletion
21991–21993 deletion Y144 deletion
A23063T N501Y
C23271A A570D
C23604A P681H
C23709T T716I
T24506G S982A
G24914C D1118H
ORF8 C27972T Q27stop
G28048T R52I
A28111G Y73C
N 28280 GAT→CTA D3L
C28977T S235F
Source: Chand et al., table 1 (p. 5)

Mutations in SARS-CoV-2 are common: over 4,000 mutations have been detected in its spike protein alone, according to the COVID-19 Genomics UK (COG-UK) Consortium.[22]

VOC-202012/01 is defined by 23 mutations: 14 non-synonymous mutations, 3 deletions, and 6 synonymous mutations[23] (i.e., there are 17 mutations that change proteins and six that do not[5]).

Symptoms and signs edit

Imperial College London investigated over a million people in England while the Alpha variant was dominant and discovered a wide range of further symptoms linked to Covid. "Chills, loss of appetite, headache and muscle aches" were most common in infected people, as well as classic symptoms. [24]

Diagnosis edit

Several rapid antigen tests for SARS-CoV-2 are in widespread use globally for COVID-19 diagnostics. They are believed to be useful in stopping the chain of transmission of the virus by providing the means to rapidly identify large numbers of cases as part of a mass-testing program. Following the emergence of VOC-202012/01, there was initially concern that rapid tests might not detect it, but Public Health England determined that rapid tests evaluated and used in the United Kingdom detected the variant.[25]

Prevention edit

See also: Oxford–AstraZeneca COVID-19 vaccine § Effectiveness, Pfizer–BioNTech COVID-19 vaccine § Effectiveness, Moderna COVID-19 vaccine § Effectiveness, Novavax COVID-19 vaccine § Efficacy, Sputnik V COVID-19 vaccine § Variants, CoronaVac § Variants, Covaxin § Variants, and Abdala (vaccine) § Efficacy

By late 2020, several COVID-19 vaccines were being deployed or under development.

However, as further mutations occur, concerns were raised as to whether vaccine development would need to be altered. SARS-CoV-2 does not mutate as quickly as, for example, influenza viruses, and the new vaccines that had proved effective by the end of 2020 are types that can be adjusted if necessary.[26] As of the end of 2020, German, British, and American health authorities and experts believe that existing vaccines will be as effective against VOC-202012/01 as against previous variants.[27][28]

On 18 December, NERVTAG determined "that there are currently insufficient data to draw any conclusion on… [a]ntigenic escape".[29]

As of 20 December 2020, Public Health England confirmed there is "no evidence" to suggest that the new variant would be resistant to the Pfizer–BioNTech vaccine currently being used in the UK's vaccination programme, and that people should still be protected.[30]

E484K mutation edit

On 2 February 2021, Public Health England reported that they had detected "[a] limited number of B.1.1.7 VOC-202012/01 genomes with E484K mutations",[9] which is also present in the Beta and Gamma variants;[14] a mutation which may reduce vaccine effectiveness.[14] On 9 February 2021, it became known that some 76 cases with the E484K mutation had been detected, principally in Bristol, but with a genomically distinct group in Liverpool also carrying the mutation.[31] A week later a Research and analysis report from PHE gave a total of 77 confirmed and probable cases involving the E484K mutation across the UK, in two variants, VUI-202102/01 and VOC-202102/02, the latter described as 'B.1.1.7 with E484K'.[10]

On 5 March 2021, it was reported that a B.1.1.7 lineage with the E484K mutation has been detected in two US patients (in Oregon and New York states). Researchers think that the E484K mutation in the Oregon variant has arisen independently.[32][33]

Characteristics edit

Transmissibility edit

The transmissibility of the Alpha variant (lineage B.1.1.7) had generally been found to be substantially higher than that of pre-existing SARS-CoV-2 variants. The variant was discovered by a team of scientists at COG-UK whose initial results found transmissibility was 70% (50-100%) higher.[16][34] A study by the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene & Tropical Medicine reported that the variant was 43 to 90% (range of 95% credible intervals, 38 to 130%) more transmissible than pre-existing variants in the United Kingdom, depending on the method used to assess increases in transmissibility, and measured similar increases in the transmissibility of lineage B.1.1.7 in Denmark, Switzerland, and the United States.[35] Furthermore, a simple model to account for the rapid rise of lineage B.1.1.7 in several countries and the world found that the variant is 50% more transmissible than the local wild type in these three countries and across the world as whole.[36] Another study concluded that it was 75% (70%–80%) more transmissible in the UK between October and November 2020.[37] A later study suggested that these earlier estimates overestimated the transmissibility of the variant and that the transmissibility increase was on the lower ends of these ranges.[38][39]

The Dutch Ministry of Health, Welfare and Sport calculated, based on genome sequencing of positive cases, each week the transmissibility rate of the variant compared to the local wildtype, and found it to fluctuate between 28%-47% higher during the first six weeks of 2021.[40] The Danish Statens Serum Institut in comparison calculated it to be 55% (48%–62%) more transmissible in Denmark based upon the observed development of its relative frequency from 4 January to 12 February 2021.[41] The Institute of Social and Preventive Medicine (ISPM) under University of Bern, calculated the transmissibility of lineage B.1.1.7 based on the weekly development of its observed fraction of all Covid-19 positives during the entire pandemic, and found for 95% confidence intervals under the assumption of a wildtype reproduction number Rw≈1 and an exponentially generation time of 5.2 days, that transmissibility was: 52% (45%–60%) higher when compared to the wildtype in Denmark and 51% (42%-60%) higher when compared to the wildtype in Switzerland.[42]

On 18 December 2020—early on in the risk assessment of the variant—the UK scientific advisory body New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) concluded that they had moderate confidence that VOC-202012/01 was substantially more transmissible than other variants, but that there were insufficient data to reach any conclusion on underlying mechanism of increased transmissibility (e.g. increased viral load, tissue distribution of virus replication, serial interval etc.), the age distribution of cases, or disease severity.[29] Data seen by NERVTAG indicated that the relative reproduction number ("multiplicative advantage") was determined to be 1.74—i.e., the variant is 74% more transmissible—assuming a 6.5-day generational interval. It was demonstrated that the variant grew fast exponentially with respect to the other variants.[43][44][45] The variant out-competed the ancestral variant by a factor of   every two weeks. Another group came to similar conclusions, generating a replicative advantage, independent of "protective measures", of 2.24 per generation of 6.73 days, out-competing the ancestral variant by   every two weeks.[46] Similarly, in Ireland, the variant—as indicated by the missing S gene[c] detection (S-gene target failure [SGTF]), which historically was rare—went from 16.3% to 46.3% of cases in two weeks. This demonstrates, based on the statistics of 116 positive samples, that the variant had a relative higher growth by a factor of  , when compared to the average growth for all other variants by the end of this two week period.[48] The variant became the dominant variant in London, East of England and the South East from low levels in one to two months. A surge of SARS-CoV-2 infections around the start of the new year is seen[by whom?] as being the result of the elevated transmissibility of the variant, while the other variants were in decline.[49][50][51]

One of the most important changes in lineage B.1.1.7 seems to be N501Y,[22] a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[52] This is because of its position inside the spike protein's receptor-binding domain (RBD)—more specifically inside the receptor-binding motif (RBM),[53] a part of the RBD[54]—which binds human ACE2.[55] Mutations in the RBD can change antibody recognition and ACE2 binding specificity[55] and lead to the virus becoming more infectious;.[22] Chand et al. concluded that "[i]t is highly likely that N501Y affects the receptor-binding affinity of the spike protein, and it is possible that this mutation alone or in combination with the deletion at 69/70 in the N-terminal domain (NTD) is enhancing the transmissibility of the virus".[56] In early 2021 a peer-reviewed paper found that the mentioned HV 69–70 deletion in vitro "appeared to have two-fold higher infectivity over a single round of infection compared to [wild-type SARS-CoV-2]" in lentiviral SARS-CoV-2 pseudoviruses.[57]

Using In Silico approach, Shahhosseini et al. demonstrated that the Y501 mutation in lineage B.1.1.7 forms a shorter H-bond (length of 2.94 Å) than its counterpart in the wild type (WT) variant residue N501, indicating that in lineage B.1.1.7 the RBD and hACE2 have a stable interaction. Furthermore, the Y501 mutation in lineage B.1.1.7 contributes more negatively to Binding Free Energy (BFE) (-7.18 kcal/mol) than its counterpart in the WT variant residue N501 (-2.92 kcal/mol). As a result of combining BFE and molecular interaction results, the N501Y mutation in RBD strengthens binding affinity of SARS-CoV-2 RBD to hACE2.[58]

In a detailed affinity and kinetic analysis of the interaction between the Spike RBD and ACE2, the N501Y mutation was found to significantly enhance the binding affinity between the RBD and ACE2 by approximately 10-fold, resulting from a 1.8-fold increase in the association rate constant (kon) and a 7-fold decrease in the dissociation rate constant (koff).[59]

Virulence edit

Matched cohort studies of the Alpha variant (lineage B.1.1.7) found higher mortality rate than earlier circulating variants overall,[60][61] but not in hospitalised patients.[62] An ecological study found no difference in mortality overall.[63]

Initially, NERVTAG said on 18 December 2020 that there were insufficient data to reach a conclusion regarding disease severity. At prime minister Boris Johnson's briefing the following day, officials said that there was "no evidence" as of that date that the variant caused higher mortality or was affected differently by vaccines and treatments;[64] Vivek Murthy agreed with this.[65] Susan Hopkins, the joint medical adviser for the NHS Test and Trace and Public Health England (PHE), declared in mid-December 2020: "There is currently no evidence that this strain causes more severe illness, although it is being detected in a wide geography, especially where there are increased cases being detected."[22] Around a month later, however—on 22 January 2021—Johnson said that "there is some evidence that the new variant [VOC-202012/01]… may be associated with a higher degree of mortality", though Sir Patrick Vallance, the government's Chief Scientific Advisor, stressed that there is not yet enough evidence to be fully certain of this.[66]

In a paper analysing twelve different studies on lineage B.1.1.7 death rate relative to other lineages, it was found to have a higher death rate (71% according to LSHTM, 70% according to University of Exeter, 65% according to Public Health England, and 36% according to Imperial College London), and NERVTAG concluded: "Based on these analyses, it is likely that infection with VOC B.1.1.7 is associated with an increased risk of hospitalisation and death compared to infection with non-VOC viruses".[67] Results of the death studies were associated with some high uncertainty and confidence intervals, because of a limited sample size related to the fact that UK only analysed the VOC status for 8% of all COVID-19 deaths.[68]

A UK case-control study for 54,906 participants, testing positive for SARS-CoV-2 between 1 October 2020 and 29 January 2021 in the community setting (not including vulnerable persons from care centres and other public institutions), reported that patients infected with the Alpha variant (VOC 202012/1) had a hazard ratio for death within 28 days of testing of 1.64 (95% confidence interval 1.32-2.04), as compared with matched patients positive for other variants of SARS-CoV-2.[69] Also in the UK, a survival analysis of 1,146,534 participants testing positive for SARS-CoV-2 between 1 November 2020 and 14 February 2021, including individuals in the community and in care and nursing homes, found a hazard ratio of 1.61 (95% confidence interval 1.42–1.82) for death within 28 days of testing among individuals infected with lineage B.1.1.7; no significant differences in the increased hazard of death associated with lineage B.1.1.7 were found among individuals differing in age, sex, ethnicity, deprivation level, or place of residence.[61] Both studies adjusted for varying COVID-19 mortality by geographical region and over time, correcting for potential biases due to differences in testing rates or differences in the availability of hospital services over time and space.[citation needed]

A Danish study found people infected by lineage B.1.1.7 to be 64% (32%–104%) more likely to get admitted to hospitals compared with people infected by another lineage.[70]

Genetic sequencing of VOC-202012/01 has shown a Q27stop mutation which "truncates the ORF8 protein or renders it inactive".[19] An earlier study of SARS-CoV-2 variants which deleted the ORF8 gene noted that they "have been associated to milder symptoms and better disease outcome".[71] The study also noted that "SARS-CoV-2 ORF8 is an immunoglobulin (Ig)–like protein that modulates pathogenesis", that "SARS-CoV-2 ORF8 mediates major histocompatibility complex I (MHC-I) degradation", and that "SARS-CoV-2 ORF8 suppresses type I interferon (IFN)–mediated antiviral response".[71]

Referring to amino-acid position 501 inside the spike protein, Chand et al. concluded that "it is possible that variants at this position affect the efficacy of neutralisation of virus",[56] but noted that "[t]here is currently no neutralisation data on N501Y available from polyclonal sera from natural infection".[56] The HV 69–70 deletion has, however, been discovered "in viruses that eluded the immune response in some immunocompromised patients",[72] and has also been found "in association with other RBD changes".[56]

Epidemiology edit

 
Test determined growth curves on a logarithmic scale, for development of the Alpha variant (lineage B.1.1.7) share among all coronavirus positive samples in Denmark, the Netherlands, the United Kingdom, Portugal, Switzerland, and Ireland.[78] The slopes noted in brackets, are the relative exponential growth rate per day (e.g. 7.6% per day for Denmark).
 
Test determined growth curves on a logarithmic scale, for development of the Alpha variant (lineage B.1.1.7) share among all coronavirus positive samples in the United Kingdom, countries in the UK, and regions of England.[81] The slopes noted in brackets, are the relative exponential growth rate per day (e.g. 8.6% per day for the UK).

Cases of the Alpha variant (lineage B.1.1.7) were estimated to be under-reported by most countries as the most commonly used tests do not distinguish between this variant and other SARS-CoV-2 variants, and as many SARS-CoV-2 infections are not detected at all. RNA sequencing is required for detection of this variant,[82] although RT-PCR test for specific variants[d] can be used as a proxy test for Alpha — or as a supplementing first-screening test before conducting the whole-genome sequencing.[83][75]

As of 23 March, the Alpha variant had been detected in 125 out of 241 sovereign states and dependencies (or 104 out of 194 WHO member countries),[e] of which some had reported existence of community transmission while others so far only found travel related cases.[87] As of 16 March, it had become the dominant COVID-19 variant for 21 countries: United Kingdom (week 52), Ireland (week 2), Bulgaria (week 4), Slovakia (week 5), Israel (week 5), Luxembourg (week 5), Portugal (week 6), Denmark (week 7), Netherlands (week 7), Norway (week 7), Italy (week 7), Belgium (week 7), France (week 8), Austria (week 8), Switzerland (week 8), Liechtenstein (week 9), Germany (week 9), Sweden (week 9), Spain (week 9), Malta (week 10) and Poland (week 11). The emergence and the fast spreading of the new variant has been detected in Lebanon and a relationship noted between SARS-CoV-2 transmission intensity and the frequency of the new variant during the first twelve days of January.[88] Since February, Alpha has become the dominant variant in Lebanon.[89]

As of February 2021, none of the countries from South America, Central America, Africa, Middle East (except Israel), Asia and Oceania had reported data for the detected share of the Alpha variant among their COVID-19 positives; rendering it unknown whether or not Alpha could be dominant for their COVID-19 pandemic.

Spread in UK edit

The first case was likely in mid-September 2020 in London or Kent, United Kingdom.[90] The variant was sequenced in September.[91] As of 13 December 2020, 1,108 cases with this variant had been identified in the UK in nearly 60 different local authorities. These cases were predominantly in the south east of England. The variant has also been identified in Wales and Scotland.[92] By November, around a quarter of cases in the COVID-19 pandemic in London were being caused by the new variant, and by December, that was a third.[93] In mid-December, it was estimated that almost 60 percent of cases in London involved Alpha.[94] By 25 January 2021, the number of confirmed and probable UK cases had grown to 28,122.[95]

Spread in Europe edit

The variant became dominant for:

In Bulgaria, genome sequencing found the variant to be dominant with 52.1% in week 4, followed by 73.4% in week 9.[97]

 
Distribution of the SARS-CoV-2 virus variants after entering Germany

Also in Slovakia, a RT-PCR Multiplex DX test capable of detecting the 2 deletions specific for lineage B.1.1.7 (ΔH69/ΔV70 and ΔY144),[98] first found the variant nationwide in 74% of cases on 3 February (week 5), followed by 72% of cases on 15 February (week 7), and it then grew to 90% of cases on 3 March (week 9).[99] The same test found earlier on 8 January prevalence of the variant at a rate of 36% in the Michalovce District and 29% in Nitra.[100]

In Israel, the variant was first time detected by genome sequencing 23 December 2020.[101] Leumit Health Care Services however analysed with the proxy test RT-PCR (SGTF) and found the variant at a rate of 3‑4% on 15 December.[102] The national Ministry of Health estimated based on genome sequencing, that the prevalence of the variant became dominant (70%) on 6 February[103] followed by 90% on 16 February.[104]

In Luxembourg, a weekly genome sequencing revealed that the variant grew from 0.3% (week 51) to be dominant with a share of 53.0% in week 5, although results might not be fully representative due to the fact that no correction occurred from potential targeting bias from contact tracing, airport travellers and local outbreaks. Genome sequencing of a population representative randomized test pool - with no target bias - was conducted since week 6, and it confirmed the dominant status of the variant at a rate of 54.1% (week 6) growing to 62.8% (week 9), while the competing Beta variant (lineage B.1.351) was found to be at 18.5% in week 9.[105]

In Denmark the variant grew from 0.3% (week 46 of 2020) to become dominant with 65.9% (week 7 of 2021), and it grew further to 92.7% (week 10); with the regional prevalence ranging from 87.3% in the North Jutland Region to 96.1% in the Central Denmark Region.[106] The observed growth of the relative variant share, was in full accordance with the earlier modelled forecast,[41] that had predicted dominance (over 50%) around mid-February and a prevalence of around 80% of the total circulating variants by early March.[107] In comparison, the genome sequencing only found the competing Beta variant in 0.4% of the positive cases (9 times out of 2315 tests) in week 10.[108][109]

In the Netherlands, a randomly conducted genome sequencing found that the variant grew from 1.3% of cases in week 49 to a dominant share of 61.3% in week 7, followed by 82.0% in week 9; while the competing Beta variant in comparison was found to be at 3.0% in week 9.[74] In Amsterdam, the Alpha variant (lineage B.1.1.7) grew from 5.2% (week 52) to 54.5% (week 6).[110]

In Norway, the variant was found by genome sequencing to grow from 5.7% (week 1) into dominance by a 58.4% (week 7), followed by 65.0% (week 8).[111] Another large survey comprising results of both genome sequencing and PCR proxy tests, with a sample seize of more than 1000 tests per week (since week 4), at the same time found that the variant grew from 2.0% (week 48) into dominance by 60.0% (week 7), followed by 72.7% in week 10 - while only 2.2% of cases in comparison were found to be of the Beta variant.[112] The variant regionally had its highest share in the county of Oslo and Viken,[113] growing from 18% to 90% of analysed samples in Oslo from 20 January to 23 February (although with the data-corrected estimate a bit lower at 50-70% on 23 February); while growing from 21% to 80% of analysed samples in Viken from 25 January to 23 February (although with the data-corrected estimate a bit lower at 50% on 23 February).[114] For the period 15 February to 14 March, the combined survey of genome sequencing and PCR proxy tests, also found the Alpha variant was at a dominant rate over 50% for 8 out of 11 regions, with its highest rate (82%) found for Oslo; while the region Nordland was different from all other regions by having only 6% cases of Alpha along with a dominant 88% of cases represented by the Beta variant.[112]

In Portugal, the variant represented according to a national genome sequencing survey: 16.0% of the Covid-19 infections during 10–19 January (week 2),[115] followed by a dominant 58.2% in week 6.[116] A national RT-PCR proxy test based on SGTF and SGTL observations, found the variant at a rate of 33.5% in week 4, but observed afterwards a decelerating pace for the weekly rise of the variant share (reason unknown), and according to this study it only became dominant by 50.5% (91.8% of 55.0% SGTFL) in week 8, followed by 64.3% (91.8% of 70% SGTFL) in week 10.[75]

In Italy, the Alpha variant accounted for 17.8% of cases nationwide on 4–5 February (week 5),[117] followed by 54.0% on 18 February (week 7). The regional prevalence for week 7 ranged from 0% in Aosta Valley (although only one sample was tested) to 93.3% in Molise. In week 7, the competing Gamma variant had a prevalence of 4.3% (ranging between 0%-36.2% regionally) and the South African variant a prevalence of 0.4% (ranging between 0%-2.9% regionally).[118]

In Switzerland, a nationwide weekly genome sequencing survey found that the Alpha variant grew from 0.05% (week 51) to a dominant 58.2% of cases in week 8, followed by 71.1% in week 9.[76] This was in full accordance with a model from 9 February that had forecast dominance around mid-February.[119] In comparison, the competing Beta variant was only found nationwide in 1.0% of the positive cases in week 9.[76]

In Belgium, genome sequencing of samples selected randomly after excluding all samples from active targeted testing related to local outbreaks or travels (creating a statistical representative national sample with a seize equal to 4.4% of all COVID-19 positive tests), found that the Alpha variant share grew from 7.1% in week 1 to a dominant 51.5% in week 7, followed by 79.3% in week 10.[120] The variant was first time detected by targeted genome sequencing in week 49, but due to a small sample seize (not being random, and less than 100 tests per week) then no reliable variant share data could be determined before week 1.[121] The proxy test for the variant (RT-PCR SGTF) was also conducted for a sample seize equal to 25.8% of all COVID-19 positive tests, and found a dominant 54.8% SGTF rate for week 10. In comparison, the competing Beta variant was found to be at 3.6% and the Gamma variant had a prevalence of 1.8% in week 10.[120]

In France, scientists accurately forecast the Alpha variant (VOC-202012/01) would likely become dominant nationwide around week 8–11 of 2021.[122] A nationwide survey of randomly selected positive COVID-19 samples first analysed by a RT-PCR screening test and subsequently confirmed by genome sequencing, revealed that the variant grew from a share of 3.3% (388/11916) on 7–8 January (week 1)[123] to 13.3% (475/3561) on 27 January (week 4),[85] followed by 44.3% (273/615) on 16 February (week 7).[85] In week 8, the variant was found to have a dominant share of 56.4% (758/1345) according to the interpretable results of a weekly genome sequencing survey comprising 0.9% of all COVID-19 positive tests, or 59.5% according to a variant-specific RT-PCR survey testing 54% of all the COVID-19 positive tests.[124] In week 10, the variant was found to have a share of 71.9% according to a variant-specific RT-PCR survey testing 56.9% of all the COVID-19 positive tests. The spread of the variant differed regionally for the 96 departments located in Metropolitan France for week 10, with 91 departments over 50% and 5 departments with 30%-50% (of which the Moselle department in particular was notable due to finding a high 38.3% rate of the competing Beta variant, that - despite having declined from a dominant 54.4% value in week 8 - still was significantly above the 5.0% national average for this specific variant).[125]

In Austria, Agentur für Gesundheit und Ernährungssicherheit (AGES) collected data from N501Y RT-PCR specific tests combined with subsequent genome sequencing analysis, and found that the variant grew from 7.2% (week 1) to a dominant 61.3% (week 8), followed by 61.2% in week 9 and 48.3% in week 10. If all N501Y positive tests had been analysed further by genome sequencing, then these listed shares could have been even higher, for example they could have been as mcuh as: 2.4% higher for week 1, 23.0% higher for week 7, 4.0% higher for week 8, 6.8% higher for week 9 and 25.4% higher for week 10. The competing Beta variant was only found nationwide in 0.3% of the positive cases in week 10, and for the region Tyrol - where it had been most prevalent - its share declined from 24.5% in week 4 to just 1.9% in week 10. Regionally Alpha was found to be dominant with over 50% for 7 out of 9 regions, with the only two exceptions being Tyrol and Vorarlberg.[126]

In Germany, the largest and probably most representative national survey published by the Robert Koch Institute (entitled RKI-Testzahlerfassung), determined the share of circulating COVID-19 variants for the latest week by analysing 53,272 COVID-19 positive samples either by genome sequencing or RT-PCR proxy tests, with data collected on a voluntary basis from 84 laboratories from the university / research / clinical / outpatient sector - spread evenly across the nation. The survey did not utilize data weights or data selection criteria to ensure existence of geographical representativity, but might still be regarded as somewhat representative for the national average due to its big sample seize. According to the RKI-Testzahlerfassung survey, the variant grew from a share of 2.0% (week 2) to a dominant share of 54.5% (week 9), followed by 63.5% in week 10. In comparison, the competing Beta variant was only found nationwide in 0.9% of the positive cases in week 10.[127]

In Malta, the variant was first time detected by genome sequencing on 30 December 2020,[128] and represented 8% of the positive cases in week 7.[129] A new RT-PCR variant specific test was introduced for the surveillance,[130] where the first results reported on 10 March revealed the variant now represented 61% of cases nationwide.[131]

In Sweden, the national authorities initially expected the variant would become dominant around week 12–14 under the assumption of 50% increased transmissibility compared to the original virus.[132] In average, the variant share was found growing from 10.8% (week 4) to 36.9% (week 7) across five of its southern regions (Skåne, Västra Götaland, Västmanland, Gävleborg and Örebro).[133] For week 7, the share of the variant was for the first time also calculated to 30.4% as the overall average for 19 out of 21 Swedish regions (ranging from 3.3% in Blekinge to 45% in Gävleborg). For week 9, the share of the variant was calculated to a dominant 56.4% as the overall average for the 19 regions (ranging from 16% in Kronoberg to 72% in Gävleborg). For week 10, the share of the variant was calculated to have increased further to 71.3% as the overall average for the 19 regions (ranging from 40% in Kronoberg to 84% in Jönköping). Although no geographical weights were applied to ensure geographical representativity for the calculated average for the 19 regions, the overall sample seize of 12,417 variant tests represented 43.1% of all COVID-19 positive PCR-tests for week 10, inferring that the result of the survey might be close to represent the actual true average for the nation as a whole.[86]

In the microstate Liechtenstein, the first case of Alpha was detected on 19 December 2020. During the entire pandemic, 67 VOC-N501Y PCR-positive cases were detected comprising 58 cases of Alpha, 1 of Beta (detected 1 February) and 8 un-identified N501Y cases (from 10 Dec. to 22 Feb.), as of 18 March 2021. The weekly average of each days calculated 7-day rolling average for the share of all detected VOC-N501Y cases (which is a good proxy for Alpha in Liechtenstein), was found to be 10.9% in week 5, followed by a dominant 52.2% in week 9 (where 8 out of 15 tests were found to be Alpha); and grew further to 73.4% in week 10 (where 6 out of 9 tests were found to be Alpha).[134]

In Spain, the variant share was estimated nationwide to be 5%-10% of cases on 29 January,[135] followed by 20%-25% of cases on 18 February[136][137] and 25%-30% of cases on 22 February,[138] and estimated to be dominant with over 50% as of 3 March (week 9).[139] As of week 10, the prevalence of the variant ranged from 18.3% to 97.0% for the 17 regions, with all but two regions having a dominant rate above 50%:[140]

In Poland, a national survey among infected teachers led to experts estimating that the variant share was between 5% and 10% nationwide as of 11 February,[141] while ECDC reported it to be 9% as of 15 February.[142] According to Health minister Adam Niedzielski, the variant was found at a rate of 5% in the first studies from the second half of January, and then it increased by ten percentage points every ten days, until it became dominant nationwide by a 52% rate on 16 March (week 11).[143][144] Regionally, the variant had already exceeded 70% for Warmian-Masurian and Pomeranian on 22–23 February (week 8),[145] and even reached 90% for the Greater Poland Voivodeship on 17 March (week 11).[146]

In Finland, no statistical representative national survey had been conducted as of February 2021, as the national genome sequencing mainly targeted further analysis of COVID-19 positive samples from travellers and local outbreak clusters.[147] Helsinky University Hospital (HUS), operating in the Helsinki and Uusimaa Hospital District, found the variant in 10% of all samples collected randomly during a few days ahead of 14 February in the capitol region (also known as the Helsinky constituency and Uusimaa constituency). For the capitol region, the variant was modelled to become dominant (over 50%) in the second half of March (week 11-13).[148]

In Iceland, the national authorities implemented a strict 3 test and quarantine regime for all persons entering the country from abroad, that so far successfully managed to prevent new infectious VOCs from gaining a foothold in the country. As of 4 March, a total of 90 travellers had tested positive for the Alpha variant at Iceland's borders and the 20 additional domestic cases were all closely connected to the border cases, with no cases related to community transmission.[149]

Spread in North America edit

In the United States, the variant first appeared late November 2020,[150] grew from 1.2% in late January and became predominant around the end of March.[151][152]

In Canada, the variant first appeared in Ontario late December 2020.[153] By 13 February, it had spread to all ten provinces.[154] Testing and confirmation of the Alpha variant (lineage B.1.1.7) in COVID-19-positive samples has been inconsistent across the country.[155] On 3 February, the province of Alberta was the first to screen all COVID-19 positive samples for variants of concern.[155][156] As of 23 March, the Alpha variant had been detected in 5812 cases, and was most prevalent in the province of Alberta.[157] In Ontario, a combined RT-PCR (N501Y) and genome sequencing study found that all VOCs represented 4.4% of all COVID-19 positives on 20 January (week 3), and that Alpha comprised 99% of all those VOCs.[158] Public Health Ontario laboratories found the variant in close to 7% of all COVID-19 positives in week 5, representing 97% (309/319) of all detected VOCs.[159] Alpha became the dominant variant on or around 16 March; 53% of all positive cases were VOCs, and it was presumed 97% of VOCs were Alpha.[160] In Quebec, where the variant was also widespread, it was expected to become dominant by late March or in April.[161]

The relatively low sensitivity of the projected dominance dates to the current percentage of the variant is due to its fast relative exponential growth. Recently, Delta appears to have overtaken Alpha in North America as it has in the UK.

Development edit

Development of the Alpha variant (lineage B.1.1.7)
(share of analysed SARS-CoV-2–positive tests in a given week)
Country Test 2020 Week 42 Week 43 Week 44 Week 45 Week 46 Week 47 Week 48 Week 49 Week 50 Week 51 Week 52 Week 53 2021 Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10
United Kingdom Seq.[77] 0.05% 0.35% 1.0% 2.7% 6.3% 10.2% 10.2% 13.9% 32.9% 45.7% 51.3% 70.6% 74.1% 78.6% 86.0% 89.1% – – – – – –
England SGTF[162]*Seq.%[163]

Seq.[96]
SGTF rawdata[f]
SGTF model[f]

0.07%

(0.02%)
(N/A)
(N/A)

0.4%

(0.5%)
(N/A)
(N/A)

0.9%

(1.2%)
(N/A)
(N/A)

2.9%

(1.5%)
(N/A)
(N/A)

5.5%

(5.3%)
(N/A)
(N/A)

9.1%

(7.8%)
(15.2%)
(m:13.3%)

18.0%

(11.4%)
(24.3%)
(m:15.9%)

32.2%

(22.1%)
(36.8%)
(m:22.0%)

51.8%

(38.1%)
(49.3%)
(m:32.1%)

63.7%

(61.8%)
(60.7%)
(m:57.2%)

72.4%

(62.1%)
(72.1%)
(m:68.9%)

77.9%

(78.4%)
(75.0%)
(m:74.0%)

82.1%

(76.7%)
(80.7%)
(m:78.3%)

87.5%

(79.7%)
(83.3%)
(m:82.1%)

90.6%

(–)
(88.2%)
(m:86.0%)

93.8%

(–)
(87.7%)
(m:89.3%)

95.7%

(–)
(93.4%)
(m:92.5%)

97.4%

(–)
(95.3%)
(m:94.5%)

98.1%

(–)
(97.0%)
(m:95.4%)

98.6%

(–)
(95.6%)
(m:95.5%)

98.7%

(–)
(94.2%)
(m:95.2%)

–

(–)
(96.1%)
(m:94.1%)

Northern Ireland SGTF rawdata[f]
SGTF model[f] 		N/A N/A N/A N/A N/A 17.9%
(m:14.0%) 		7.4%
(m:14.9%) 		37.5%
(m:16.3%) 		23.0%
(m:18.5%) 		50.0%
(m:36.1%) 		25.0%
(m:42.1%) 		58.8%
(m:44.7%) 		45.2%
(m:52.7%) 		71.4%
(m:67.0%) 		78.2%
(m:74.0%) 		72.4%
(m:81.4%) 		95.7%
(m:86.5%) 		88.9%
(m:90.5%) 		92.2%
(m:92.4%) 		100.0%
(m:93.0%) 		86.2%
(m:92.6%) 		100.0%
(m:91.1%)
Scotland SGTF rawdata[f]
SGTF model[f] 		N/A N/A N/A N/A N/A 9.5%
(m:5.8%) 		9.7%
(m:6.7%) 		10.4%
(m:7.7%) 		11.7%
(m:10.2%) 		51.4%
(m:26.2%) 		40.0%
(m:39.5%) 		35.8%
(m:43.9%) 		64.1%
(m:49.8%) 		67.2%
(m:64.2%) 		63.3%
(m:65.0%) 		69.2%
(m:70.0%) 		70.6%
(m:77.3%) 		93.9%
(m:84.7%) 		82.0%
(m:90.0%) 		100.0%
(m:93.7%) 		93.0%
(m:95.8%) 		100.0%
(m:96.9%)
Wales SGTF rawdata[f]
SGTF model[f] 		N/A N/A N/A N/A N/A 27.9%
(m:18.1%) 		8.3%
(m:16.0%) 		10.7%
(m:13.3%) 		26.3%
(m:12.1%) 		13.4%
(m:15.0%) 		15.9%
(m:14.7%) 		19.8%
(m:20.4%) 		54.4%
(m:34.8%) 		61.5%
(m:59.6%) 		69.0%
(m:65.0%) 		68.1%
(m:68.7%) 		77.0%
(m:73.4%) 		71.8%
(m:76.6%) 		75.8%
(m:78.5%) 		87.9%
(m:78.9%) 		80.0%
(m:77.2%) 		69.9%
(m:73.3%)
Ireland SGTF rawdata[48] – – – 1.9%
(few data) 		0.0%
(few data) 		0.0%
(few data) 		6.1%
(few data) 		2.2%
(few data) 		1.6%
(few data) 		7.5% 16.3% 26.2% 46.3% 57.7% 69.5% 75.0% 90.1% 88.6% 90.8% – – –
Bulgaria Seq.[97] – – – – – – – – – – – – – – – 52.1% – 70.8% – – 73.4% –
Israel SGTF w.51+1
Seq. after w.1 		– – – – – – – – – 3–4%
(Dec.15)[102] 		– – 10–20%
(Jan.5)[102] 		10–20%
(Jan.11)[166] 		30–40%
(Jan.19)[167] 		40–50%
(Jan.25)[168] 		~70%
(Feb.2)[103] 		~80%
(Feb.9)[169] 		~90%
(Feb.16)[104] 		– – –
Slovakia PCR (SGTF+ΔY144) [99] – – – – – – – – – – – – – – – – ~74%
(Feb.3) 		– ~72%
(Feb.15) 		– ~90%
(Mar.3) 		–
Luxembourg Seq.[105] – – – – – – – – – 0.3% 0.9% 4.2% 8.7% 15.5% 16.9% 36.2% 53.0% 54.1% 53.8% 63.7% 62.8% –
Denmark Seq.[106] – – – – 0.3% 0.2% 0.4% 0.4% 0.4% 0.8% 1.8% 1.9% 3.5% 7.0% 13.1% 19.6% 29.6% 47.0% 65.9% 75.3% 85.1% 92.7%
Netherlands Seq.[74] – – – – – – – 1.3% 0.8% 0.5% 2.1% 4.4% 9.6% 15.9% 22.7% 24.7% 31.0.% 40.3% 61.3% 75.2% 82.0% –
Norway PCR proxy and Seq.[112]
Seq.[170][111] 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		0.0%
(–) 		2.0%
(–) 		0.0%
(0.0%) 		4.9%
(0.0%) 		8.9%
(7.2%) 		6.0%
(2.9%) 		14.9%
(1.3%) 		18.9%
(5.7%) 		19.5%
(11.6%) 		15.2%
(9.3%) 		19.8%
(20.1%) 		34.1%
(30.3%) 		43.6%
(40.8%) 		60.0%
(58.4%) 		71.8%
(65.0%) 		76.7%
(–) 		72.7%
(–)
Italy Seq.%[117][118] – – – – – – – – – – – – – – – – 17.8% – 54.0% – – –
France PCR proxy
Seq.
SGTF*Seq.% 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(3.3%)[123] 		–
(–)
(–) 		–
(–)
(–) 		–
(–)
(13.3%)[85] 		–
(–)
(–) 		36.1%[171]
(–)
(–) 		49.3%[172]
(45.8%)[172]
(44.3%)[85] 		59.5%[124]
(56.4%)[124]
(–) 		65.8%[85]
(69.0%)[125]
(–) 		71.9%[125]
(–)
(–)
Switzerland Seq.[76] – – – – – – – – – 0.05% 0.4% 0.8% 2.6% 4.9% 9.2% 16.5% 26.0% 32.4% 47.0% 58.2% 71.1% –
Austria PCR(N501Y)*Seq.%[126]
Seq.B117+unseq.N501Y[126] 		– – – – – – – – – – – – 7.2%[g]
(9.6%) 		17.4%[g]
(23.8%) 		14.7%[g]
(19.6%) 		22.5%[g]
(28.6%) 		28.7%[g]
(37.2%) 		24.0%[g]
(45.4%) 		35.1%[g]
(58.1%) 		61.3%[g]
(65.3%) 		61.2%[g]
(68.0%) 		48.3%[g]
(73.7%)
Belgium Seq.[121][120]
SGTF[121][120] 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		0.0%
(<5%) 		0.0%
(<5%) 		0.0%
(<5%) 		13.6%
(<5%) 		0.0%
(<5%) 		7.1%
(7.2%) 		7.7%
(6.9%) 		13.4%
(16.6%) 		23.3%
(19.5%) 		39.4%
(22.4%) 		43.2%
(27.9%) 		51.5%
(34.4%) 		57.6%
(45.8%) 		66.5%
(46.3%) 		79.3%
(54.8%)
Portugal SGTFL*Seq.%[75] – – – – – – – 1.7% 0.8% 1.2% 1.7% 2.9% 6.8% 12.3% 22.7% 33.5% 39.2% 40.9% 45.7% 50.5% 56.0% 64.3%
Sweden Seq. all N501Y+A570D pos. tests[86] – – – – – – – – – – – – – – – 10.8%
(av. for 5 out of 21 regions)[h]		 15.1%
(av. for 5 out of 21 regions)[i]		 27.3%
(av. for 5 out of 21 regions)[j]		 30.4%
(av. for 19 out of 21 regions)[k]		 41.5%
(av. for 19 out of 21 regions)[l]		 56.4%
(av. for 17 out of 21 regions)[m]		 71.3%
(av. for 18 out of 21 regions)[n]
Germany PCR proxy and Seq.[127]
Seq.[127] 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(–) 		–
(2.6%) 		2.0%
(8.8%) 		3.6%
(4.9%) 		4.7%
(10.7%) 		7.2%
(17.7%) 		17.6%
(20.8%) 		25.9%
(33.2%) 		40.0%
(42.9%) 		54.5%
(48.3%) 		63.5%
(–)
Liechtenstein PCR proxy: N501Y[134] – – – – – – – – – – – – – – – – 10.9% 28.5% 32.8% 47.0% 52.2% 73.4%
Spain Estimated based on PCR proxy[140] – – – – – – – – – – – – – – – 5-10%
(Jan.29)[135] 		– – 20-25%
(Feb.18)[137] 		25-30%
(Feb.22)[138] 		>50%
(Mar.3)[139] 		–
United States SGTF*Seq.%[174] – – – – – – – – – 0.05% 0.2% 0.4% 0.5% 1.0% 1.9% 3.0% 4.7% 7.6% 12.4% 19.3% 28.8% 37.4%
California SGTF*Seq.%[174] – – – – – – – – – 0.3% 0.3% 0.7% 1.1% 1.3% 2.0% 1.9% 4.2% 5.9% 13.1% 16.6% 18.8% 28.0%
Florida SGTF*Seq.%[174] – – – – – – – – – 0.2% 0.5% 0.9% 1.0% 2.3% 4.6% 8.1% 10.7% 14.5% 21.0% 28.3% 39.8% 47.0%
Other countries without weekly/periodic data, but with a variant share above 5%: 00 Malta (61%),[131] and Poland (52%).[144]

The following additional countries did not report variant shares, but are likely to have a significant share present due to their finding of more than 50 cases confirmed by whole genome sequencing per 13 March 2021:[175]

The GISAID database of all sequenced COVID-19 genomes, calculates for each country for the past four weeks an average "Relative Variant Genome Frequency" for submitted samples. Those observed frequencies are however subject to sampling and reporting biases, and do not represent exact variant share prevalence due to absence of statistical representativity.[175]

Countries reporting a first case edit

December 2020 edit

Cases of the variant began to be reported globally during December, being reported in Denmark,[64][176] Belgium,[177] the Netherlands, Australia[64][176] and Italy.[178] Shortly after, several other countries confirmed their first cases, the first of whom were found in Iceland and Gibraltar,[179][180] then Singapore, Israel and Northern Ireland on 23 December,[181][182][183] Germany and Switzerland on 24 December,[184][185] and the Republic of Ireland and Japan confirmed on 25 December.[186][187]

The first cases in Canada, France, Lebanon, Spain and Sweden were reported on 26 December.[188][189][190][191] Jordan, Norway, and Portugal reported their first case on 27 December,[192][193] Finland and South Korea reported their first cases on 28 December,[194][195] and Chile, India, Pakistan and the United Arab Emirates reported their first cases on 29 December.[196][197][198][199] The first case of new variant in Malta and Taiwan are reported on 30 December.[128][200] China and Brazil reported their first cases of the new variant on 31 December.[201][202] The United Kingdom and Denmark are sequencing their SARS-CoV-2 cases at considerably higher rates than most others,[203] and it was considered likely that additional countries would detect the variant later.[204]

The United States reported a case in Colorado with no travel history on 29 December, the sample was taken on 24 December.[205] On 6 January 2021, the US Centers for Disease Control and Prevention announced that it had found at least 52 confirmed cases in California, Florida, Colorado, Georgia, and New York.[206] In the following days, more cases of the variant were reported in other states, leading former CDC director Tom Frieden to express his concerns that the U.S. will soon face "close to a worst-case scenario".[207]

January 2021 edit

Turkey detected its first cases in 15 people from England on 1 January 2021.[208] It was reported on 1 January that Denmark had found a total of 86 cases of the variant, equalling an overall frequency of less than 1% of the sequenced cases in the period from its first detection in the country in mid-November to the end of December;[209][210] this had increased to 1.6% of sequenced tests in the period from mid-November to week two of 2021, with 7% of sequenced tests in this week alone being of Alpha variant (lineage B.1.1.7).[211] Luxembourg and Vietnam reported their first case of this variant on 2 January 2021.[212][213]

On 3 January 2021, Greece and Jamaica detected their first four cases of this variant[214][215] and Cyprus announced that it had detected Alpha (VOC 202012/01) in 12 samples.[216] At the same time, New Zealand and Thailand reported their first cases of this variant, where the former reported six cases made up of five from the United Kingdom and one from South Africa,[217] and the latter reported the cases from a family of four who had arrived from Kent.[218] Georgia reported its first case[219] and Austria reported their first four cases of this variant, along with one case of Beta variant, on 4 January.[220]

On 5 January, Iran,[221] Oman,[222] and Slovakia reported their first cases of VOC-202012/01.[223] On 8 January, Romania reported its first case of the variant, an adult woman from Giurgiu County who declared not having left the country recently.[224] On 9 January, Peru confirmed its first case of the variant.[225] Mexico and Russia reported their first case of this variant on 10 January,[226] then Malaysia and Latvia on 11 January.[227][228]

On 12 January, Ecuador confirmed its first case of this variant.[229] The Philippines and Hungary both detected the presence of the variant on 13 January.[230][231] The Gambia recorded first cases of the variant on 14 January with it being the first confirmation of the variant's presence in Africa.[232] On 15 January, the Dominican Republic confirmed its first case of the new variant[233] and Argentina confirmed its first case of the variant on 16 January.[234] Czech Republic and Morocco reported their first cases on 18 January[235][236] while Ghana and Kuwait confirmed their first cases on 19 January.[237][238] Nigeria confirmed its first case on 25 January.[239] On 28 January, Senegal detected its first case of the variant.[240]

In early January, an outbreak linked to a primary school led to the detection of at least 30 cases of the new variant in the Bergschenhoek area of the Netherlands, signifying local transmission.[241]

On 16 January, the Los Angeles County Department of Public Health confirmed the variant was detected in L.A. County, with public health officials believing that it is spreading in the community.[242]

On 24 January, a person travelling from Africa to Faroe Islands tested positive upon arrival to the islands, and went directly into quarantine.[243]

On 28 January, North Macedonia confirmed the variant was detected in a 46-year-old man, who had already recovered.[244]

February 2021 edit

On 1 February, Lithuania has confirmed the first cases of the new lineage.[citation needed] On 4 February, health authorities in Uruguay announced the first case of the variant in the country. The case was detected in a person who entered the country on 20 December 2020 and has been in quarantine ever since.[245] On 10 February, the Health Ministry of Croatia confirmed that out of 61 sequenced samples since 20 January, the variant was detected in 3 samples: a male 50 year old and 3.5 year old from Zagreb, and a male 34-year-old from Brod-Posavina County.[246] On 12 February, the variant was detected from four areas in Sri Lanka,[247] and the Canadian province of Newfoundland and Labrador confirmed an outbreak of the variant.[248]

March 2021 edit

On 2 March, Indonesia reports its first cases of the variant in two migrant workers returning from Saudi Arabia.[249] On the same day, Tunisia[250] reported their first cases of the variant. The presence of the variant in Ivory Coast was confirmed on 25 March.[251]

N501Y mutation elsewhere edit

The N501Y mutation arose independently multiple times in different locations:

  • In April 2020, it was seen for the first time in a few isolated sequences in Brazil.[252]
  • In June 2020, the mutation appeared in an Australian lineage.[252]
  • In July 2020, (according to Dr Julian Tang, University of Leicester) N501Y appeared in a lineage circulating in United States.[252][citation needed]
  • In September 2020, it was found in a lineage in Wales, that evolved independently and was different from lineage B.1.1.7.[52]
  • In September 2020,[1] the much more transmissible and widespread lineage B.1.1.7 (501Y.V1) was detected for the first time in Kent (England).[19]
  • In October 2020, another highly transmissible variant of concern termed lineage B.1.351 (501Y.V2, Beta variant) was first time detected by genome sequencing in Nelson Mendela Bay (South Africa).[253] Phylogeographic analysis suggests this lineage emerged already in July or August 2020.[254]
  • In December 2020,[255] another highly transmissible variant termed lineage P.1 (501Y.V3, Gamma variant) was detected in Manaus (Brazil).[256]

Statistics edit

Table edit

Graphics edit

Confirmed cases by countries edit

  • Note: The graphs presented here are only viewable by computers and some phones. If you cannot view it on your cell phone, switch to desktop mode from your browser.
  • Data provided by various sources, such as; governmental, press or officials are updated every week since their last publication.

History edit

Detection edit

 
False-colour transmission electron micrograph of the Alpha variant. The variant's increased transmissibility is believed to be due to changes in structure of the spike proteins, shown here in green.

The Alpha variant (lineage B.1.1.7) was first detected in early December 2020 by analysing genome data with knowledge that the rates of infection in Kent were not falling despite national restrictions.[5][260]

The two earliest genomes that belong to lineage B.1.1.7 were collected on 20 September 2020 in Kent and another on 21 September 2020 in Greater London.[19] These sequences were submitted to the GISAID sequence database (sequence accessions EPI_ISL_601443 and EPI_ISL_581117, respectively).[261]

Backwards tracing using genetic evidence suggests lineage B.1.1.7 emerged in September 2020 and then circulated at very low levels in the population until mid-November. The increase in cases linked to the variant first became apparent in late November when Public Health England (PHE) was investigating why infection rates in Kent were not falling despite national restrictions. PHE then discovered a cluster linked to this variant spreading rapidly into London and Essex.[30]

Also important was the nature of the RT-PCR test used predominantly in the UK, Thermo Fisher Scientific's TaqPath COVID-19. The test matches RNA in three locations, and stopped working for the spike gene due to the HV 69–70 deletion—a deletion of the amino acids histidine and valine in positions 69 and 70, respectively[262]—in the spike protein of lineage B.1.1.7. This made preliminary identification easier because it could be better suspected which cases were with lineage B.1.1.7 through genome sequencing.[263]

It has been suggested that the variant may have originated in a chronically infected immunocompromised person, giving the virus a long time to replicate and evolve.[264][5][265][266]

Control edit

In the presence of a more transmissible variant, stronger physical distancing and lockdown measures were opted for to avoid overwhelming the population due to its tendency to grow exponentially.[267]

All countries of the United Kingdom were affected by domestic travel restrictions in reaction to the increased spread of the virus—at least partly attributed to Alpha—effective from 20 December 2020.[268][269] During December 2020, an increasing number of countries around the world either announced temporary bans on, or were considering banning, passenger travel from the UK, and in several cases from other countries such as the Netherlands and Denmark. Some countries banned flights; others allowed only their nationals to enter, subject to a negative SARS-CoV-2 test.[270] A WHO spokesperson said that, "[a]cross Europe, where transmission is intense and widespread, countries need to redouble their control and prevention approaches". Most bans by EU countries were for 48 hours, pending an integrated political crisis response meeting of EU representatives on 21 December to evaluate the threat from the new variant and coordinate a joint response.[271][272]

Many countries around the world imposed restrictions on passenger travel from the United Kingdom; neighbouring France also restricted manned goods vehicles (imposing a total ban before devising a testing protocol and permitting their passage once more).[273] Some also applied restrictions on travel from other countries.[274][275][276][277] As of 21 December 2020, at least 42 countries had restricted flights from the UK,[270] and Japan was restricting entry of all foreign nationals after cases of the new variant were detected in the country.[278]

The usefulness of travel bans has been contested as limited in cases where the variant has likely already arrived, especially if the estimated growth rate per week of the virus is higher locally.[279][280]

Extinction edit

In October 2021, Dr Jenny Harries, chief executive of the UK Health and Security Agency stated that previous circulating variants such as Alpha had 'disappeared' and replaced by the Delta variant.[281] In March 2022, the World Health Organization listed the Alpha, Beta and Gamma variants as previously circulating citing lack of any detected cases in the prior weeks and months.[282]

See also edit

Notes edit

  1. ^ Written as VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) by GISAID[283] and the ECDC.[284]
  2. ^ The difference between the two is explained by PHE:

    SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological, or pathogenic properties, are raised for formal investigation. At this point they are designated Variant Under Investigation (VUI) with a year, month, and number. Following a risk assessment with the relevant expert committee, they may be designated Variant of Concern (VOC).[18]
  3. ^ a b SARS-CoV-2's S gene encodes its spike protein.[47]
  4. ^ An example of this is the delta (Δ)–PCR test, which in connection to SARS-CoV-2, has been used to detect the HV 69–70 deletion in variants with this mutation[83] through what has been named "spike-gene target failure" (SGTF) or "spike-gene drop out"[75] for the spike (S) gene[c] in a subset of RT-PCR assays (e.g., TaqPath COVID-19 RT-PCR assay, ThermoFisher).[84] Though existing in a few other variants of SARS-CoV-2,[75] the HV 69–70 deletion in the spike protein is present in the vast majority of B.1.1.7 genomes, which enables the delta-PCR test to be used as a proxy test for the lineage—or as a supplementing first-screening test before conducting the whole-genome sequencing.[83][75]
    Another example of a RT-PCR test intended to detect specific variants is the one detecting all genomes with the N501Y mutation (e.g., Alpha, Gamma variant, and Beta variant), which is now also being used as a first-step screening tool ahead of genome sequencing by several laboratories/countries (e.g. by some parts of France).[85]
    A third and fourth RT-PCR test intended for detecting specific variants pre-screen the samples for variants respectively with the N501Y+A570D mutations (Alpha) and N501Y without the A570D mutation (Beta, Gamma, and other N501Y variants).[86]
  5. ^ 104 WHO members had reported a detection of the Alpha variant (lineage B.1.1.7), as of 23 March 2021: Albania, Angola, Argentina, Australia, Austria, Azerbaijan, Bahrain, Bangladesh, Barbados, Belarus, Belgium, Belize, Bosnia and Herzegovina, Brazil, Brunei Darussalam, Bulgaria, Cabo Verde, Cambodia, Canada, Chile, China, Costa Rica, Croatia, Cyprus, Czech Republic, Democratic Republic of the Congo, Denmark, Dominican Republic, Ecuador, Estonia, Finland, France, Gambia, Georgia, Germany, Ghana, Greece, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Israel, Italy, Jamaica, Japan, Jordan, Kenya, Kuwait, Latvia, Lebanon, Libya, Lithuania, Luxembourg, Malaysia, Malta, Mauritania, Mauritius, Mexico, Monaco, Montenegro, Morocco, Nepal, Netherlands, New Zealand, Nigeria, North Macedonia, Norway, Oman, Pakistan, Peru, Philippines, Poland, Portugal, Republic of Korea (South Korea), Republic of Moldova, Romania, Russia, Rwanda, Saint Lucia, Saudi Arabia, Senegal, Serbia, Singapore, Slovakia, Slovenia, South Africa, Spain, Sri Lanka, Sweden, Switzerland, Thailand, Trinidad and Tobago, Tunisia, Turkey, Ukraine, United Arab Emirates, United Kingdom, United States, Uruguay, Uzbekistan, Vietnam.[87]

    90 WHO members had not reported any detection of the Alpha variant (lineage B.1.1.7), as of 23 March 2021: Afghanistan, Algeria, Andorra, Antigua and Barbuda, Armenia, Bahamas, Benin, Bhutan, Bolivia, Botswana, Burkina Faso, Burundi, Cameroon, Central African Republic, Chad, Colombia, Comoros, Congo, Cook Islands, Côte d'Ivoire, Cuba, Democratic People's Republic of Korea (North Korea), Djibouti, Dominica, Egypt, El Salvador, Equatorial Guinea, Eritrea, Ethiopia, Fiji, Gabon, Grenada, Guatemala, Guinea-Bissau, Guyana, Haiti, Honduras, Guinea, Kazakhstan, Kiribati, Kyrgyzstan, Lao People's Democratic Republic, Lesotho, Liberia, Madagascar, Malawi, Maldives, Mali, Marshall Islands, Micronesia, Mongolia, Mozambique, Myanmar, Namibia, Nauru, Nicaragua, Niger, Niue, Palau, Panama, Papua New Guinea, Paraguay, Qatar, Saint Kitts and Nevis, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Seychelles, Sierra Leone, Solomon Islands, Somalia, South Sudan, Sudan, Suriname, Swaziland, Syrian Arab Republic, Tajikistan, Timor-Leste, Togo, Tonga, Turkmenistan, Tuvalu, Uganda, United Republic of Tanzania, Vanuatu, Venezuela, Yemen, Zambia, Zimbabwe.[87]
  6. ^ a b c d e f g h The weekly UK infection survey lists for each country in Great Britain a set of raw data and average-smoothed modelled data from SGTF analysed PCR tests collected from private households (excl. tests from hospitals, care centres and public institutions). Raw data as well as model data for Wales, Northern Ireland and Scotland must be treated with caution due to a small number of collected samples, resulting in great data uncertainty.[164][165]
    • All PCR tests were analysed for 3 genes present in the coronavirus: N protein, S protein and ORF1ab (see Table 6A in the Infection Survey). Each PCR test can have any one, any two or all three genes detected. Coronavirus positives are those where one or more of these genes is detected in the swab (other than tests that are only positive on the S-gene which is not considered a reliable indicator of the virus if found on its own). The new B.1.1.7 variant of COVID-19 has genetic changes in the S gene, that results in the S-gene no longer being detected in the current test, meaning that it will only be positive on the ORF1ab and the N gene. The survey uses the terms "New UK variant compatible" for ORF1ab + N protein gene positives, "not compatible with new UK variant" for ORF1ab + N protein + S protein gene positive, and "virus too low to be identifiable" for all other gene patterns (a reasonable definition given that all samples taken from the first phase of the COVID-19 disease where virus exist by identifiable quantity, either will be positive by "ORF1ab+N" or "ORF1ab+N+S"). However, further uncertainty exists given that not all "New UK variant compatible" SGTF cases (positive on ORF1ab and N-genes, but not the S-gene) will be the new UK variant - due to some other competing variants also delivering this same test pattern; and prior to mid-November 2020 the data should not be read as being an indicator of the variant at all.[164][165]
    • The weekly B.1.1.7 variant share raw data is calculated from Table 6A, by dividing the "ORF1ab+N" percentage with the percentage sum of "ORF1ab+N" and "ORF1ab+N+S". Table 6C utilized the raw data from table 6A as input for calculation of some modelled (average-smoothed and weighted) daily estimated figures for the respective percentage of the population being coronavirus positive by either the "New UK variant compatible virus", or a "Not compatible with new UK variant virus" or a "virus too low to be identifiable", with data from earlier dates in 2020 also being available when downloading the published earlier editions of the Infection Survey. The modelled weekly average value for the Alpha variant, noted in this table as the value (m: %), is calculated as the average for the listed seven days in each week of "New UK variant compatible percentage" divided by the sum of "New UK variant compatible percentage" and "Not compatible with new UK variant percentage".[164][165]
  7. ^ a b c d e f g h i j In Austria, the listed B.1.1.7 variant shares represent the percentage of all positive COVID-19 tests being confirmed to be B.1.1.7 by genome sequencing. However, many N501Y positive RT-PCR tests were not variant determined further by genome sequencing, and likely would have returned a B.1.1.7 positive result for the vast majority of such tests if the genome sequencing analysis had been done. If all N501Y positive tests had been analysed further by genome sequencing, then the listed weekly B.1.1.7 shares could have been uptil: 9.6% for week 1 (2.4% higher), 23.8% for week 2 (6.4% higher), 19.6% for week 3 (4.9% higher), 28.6% for week 4 (6.1% higher), 37.2% for week 5 (8.5% higher), 45.4% for week 6 (21.4% higher), 58.1% for week 7 (23.0% higher), 65.3% for week 8 (4.0% higher), 68.0% for week 9 (6.8% higher) and 73.7% for week 10 (25.4% higher).[126]
  8. ^ In Sweden, a study comprising 11% of all SARS-CoV-2–positive PCR samples nationwide for week 4 found the B.1.1.7 share to be 10.8% (243/2244). Samples were, however, only collected from five southern regions (Skåne, Västra Götaland, Västmanland, Gävleborg and Örebro), which were not considered to be statistically representative for the demography and geography of Sweden as a whole. The national authorities plan to expand the weekly study to cover more regions for the following weeks in February 2021.[173][133]
  9. ^ In Sweden, a study comprising 16% of all SARS-CoV-2–positive PCR samples nationwide for week 5 found the B.1.1.7 share to be 15.1% (488/3224). Samples were, however, only collected from five southern regions (Skåne, Västra Götaland, Västmanland, Gävleborg and Örebro), which were not considered to be statistically representative for the demography and geography of Sweden as a whole. The national authorities also calculated a two-week average (week 5+6) for 19 out of 21 regions, and plan to expand the weekly study to cover more regions for the following weeks in February 2021.[133]
  10. ^ In Sweden, a study comprising 18% of all SARS-CoV-2–positive PCR samples nationwide for week 6 found the B.1.1.7 share to be 27.3% (1021/3742). Samples were, however, only collected from five southern regions (Skåne, Västra Götaland, Västmanland, Gävleborg and Örebro), which were not considered to be statistically representative for the demography and geography of Sweden as a whole. The national authorities also calculated a two-week average (week 5+6) for 19 out of 21 regions, and plan to expand the weekly study to cover more regions for the following weeks in February 2021.[133]
  11. ^ In Sweden, a study comprising 47.8% of all SARS-CoV-2–positive PCR samples nationwide for week 7, collected samples from 19 out of 21 regions (all except Gotland and Västerbotten), and found the B.1.1.7 share to be 30.4% (3316/10910) as a simple overall average (with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize/correct each regions share of the overall sample).[86]
  12. ^ In Sweden, a study comprising 42.2% of all SARS-CoV-2–positive PCR samples nationwide for week 8, collected samples from 19 out of 21 regions (all except Gotland and Västerbotten), and found the B.1.1.7 share to be 41.5% (4643/11191) as a simple overall average (with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize/correct each regions share of the overall sample).[86]
  13. ^ In Sweden, a study comprising 37.8% of all SARS-CoV-2–positive PCR samples nationwide for week 9, collected samples from 17 out of 21 regions (all except Gotland, Västerbotten, Norrbotten and Östergötland), and found the B.1.1.7 share to be 56.4% (5939/10528) as a simple overall average (with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize/correct each regions share of the overall sample).[86]
  14. ^ In Sweden, a study comprising 43.1% of all SARS-CoV-2–positive PCR samples nationwide for week 10, collected samples from 18 out of 21 regions (all except Gotland, Västerbotten and Östergötland), and found the B.1.1.7 share to be 71.3% (8850/12417) as a simple overall average (with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize/correct each regions share of the overall sample).[86]

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December 18, 2023
sars, alpha, variant, b117, redirects, here, other, uses, b117, disambiguation, alpha, variant, sars, variant, concern, estimated, more, transmissible, than, wild, type, sars, with, most, estimates, occupying, middle, higher, this, range, scientists, more, wid. B117 redirects here For other uses see B117 disambiguation The Alpha variant B 1 1 7 was 2 3 a SARS CoV 2 variant of concern It was estimated to be 40 80 more transmissible than the wild type SARS CoV 2 with most estimates occupying the middle to higher end of this range Scientists more widely took note of this variant in early December 2020 when a phylogenetic tree showing viral sequences from Kent United Kingdom looked unusual 4 The variant began to spread quickly by mid December around the same time as infections surged SARS CoV 2 VariantAlphaScientifically accurate atomic model of the external structure of SARS CoV 2 Each ball is an atom General detailsWHO DesignationAlphaLineageB1 1 1 7First detectedKent EnglandDate reportedNovember 2020 3 years ago 2020 11 StatusVariant of concernSymptomsNone Chills Loss of appetite Headaches Muscle achesCases mapTotal number of B 1 1 7 sequences by country as of 25 March 2021 1 Legend 10 000 confirmed sequences 5 000 9 999 confirmed sequences 1 000 4 999 confirmed sequences 500 999 confirmed sequences 100 499 confirmed sequences 2 99 confirmed sequences 1 confirmed sequence None or no data availableMajor variantsAlpha B 1 1 7 Beta B 1 351 Gamma P 1 Delta B 1 617 2 Omicron B 1 1 529 BA 1 B 1 1 529 1 BA 2 B 1 1 529 2 BA 3 B 1 1 529 3 BA 4 B 1 1 529 4 BA 5 B 1 1 529 5 vteThis increase is thought to be at least partly because of one or more mutations in the virus spike protein The variant was also notable for having more mutations than normally seen 5 By January 2021 more than half of all genomic sequencing of SARS CoV 2 was carried out in the UK 6 This had given rise to questions as to how many other important variants were circulating around the world undetected 7 8 On 2 February 2021 Public Health England reported that they had detected a limited number of B 1 1 7 VOC 202012 01 genomes with E484K mutations 9 which they dubbed Variant of Concern 202102 02 VOC 202102 02 10 One of the mutations N501Y is also present in Beta variant and Gamma variant On 31 May 2021 the World Health Organization announced that the Variant of Concern would be labelled Alpha for use in public communications 11 12 Contents 1 Classification 1 1 Names 1 2 Genetic profile 2 Symptoms and signs 3 Diagnosis 4 Prevention 4 1 E484K mutation 5 Characteristics 5 1 Transmissibility 5 2 Virulence 6 Epidemiology 6 1 Spread in UK 6 2 Spread in Europe 6 3 Spread in North America 6 4 Development 6 5 Countries reporting a first case 6 5 1 December 2020 6 5 2 January 2021 6 5 3 February 2021 6 5 4 March 2021 6 6 N501Y mutation elsewhere 7 Statistics 7 1 Table 7 2 Graphics 7 2 1 Confirmed cases by countries 8 History 8 1 Detection 8 2 Control 8 3 Extinction 9 See also 10 Notes 11 References 12 External linksClassification editNames edit The variant is known by several names Outside the UK it is sometimes referred to as the UK variant or British variant or English variant 13 despite the existence of other less common variants first identified in UK such as Eta variant lineage B 1 525 Within the UK it is commonly referred to as the Kent variant after Kent where the variant was found 14 15 16 In scientific use the variant had originally been named the first Variant Under Investigation in December 2020 VUI 202012 01 by Public Health England PHE 17 a but was reclassified to a Variant of Concern Variant of Concern 202012 01 abbreviated VOC 202012 01 by Meera Chand and her colleagues in a report published by PHE on 21 December 2020 b In a report written on behalf of COVID 19 Genomics UK COG UK Consortium Andrew Rambaut and his co authors using the Phylogenetic Assignment of Named Global Outbreak Lineages pangolin tool dubbed it lineage B 1 1 7 19 while Nextstrain dubbed the variant 20I 501Y V1 20 The name VOC 202102 02 refers to the variant with the E484K mutation see below 10 Genetic profile edit nbsp Amino acid mutations of SARS CoV 2 Alpha variant plotted on a genome map of SARS CoV 2 with a focus on Spike 21 Defining mutations in VOC 202012 01 change of amino acid only Gene Nucleotide Amino acidORF1ab C3267T T1001IC5388A A1708DT6954C I2230T11288 11296 deletion SGF 3675 3677 deletionSpike 21765 21770 deletion HV 69 70 deletion21991 21993 deletion Y144 deletionA23063T N501YC23271A A570DC23604A P681HC23709T T716IT24506G S982AG24914C D1118HORF8 C27972T Q27stopG28048T R52IA28111G Y73CN 28280 GAT CTA D3LC28977T S235FSource Chand et al table 1 p 5 Mutations in SARS CoV 2 are common over 4 000 mutations have been detected in its spike protein alone according to the COVID 19 Genomics UK COG UK Consortium 22 VOC 202012 01 is defined by 23 mutations 14 non synonymous mutations 3 deletions and 6 synonymous mutations 23 i e there are 17 mutations that change proteins and six that do not 5 Symptoms and signs editImperial College London investigated over a million people in England while the Alpha variant was dominant and discovered a wide range of further symptoms linked to Covid Chills loss of appetite headache and muscle aches were most common in infected people as well as classic symptoms 24 Diagnosis editSeveral rapid antigen tests for SARS CoV 2 are in widespread use globally for COVID 19 diagnostics They are believed to be useful in stopping the chain of transmission of the virus by providing the means to rapidly identify large numbers of cases as part of a mass testing program Following the emergence of VOC 202012 01 there was initially concern that rapid tests might not detect it but Public Health England determined that rapid tests evaluated and used in the United Kingdom detected the variant 25 Prevention editSee also Oxford AstraZeneca COVID 19 vaccine Effectiveness Pfizer BioNTech COVID 19 vaccine Effectiveness Moderna COVID 19 vaccine Effectiveness Novavax COVID 19 vaccine Efficacy Sputnik V COVID 19 vaccine Variants CoronaVac Variants Covaxin Variants and Abdala vaccine Efficacy By late 2020 several COVID 19 vaccines were being deployed or under development However as further mutations occur concerns were raised as to whether vaccine development would need to be altered SARS CoV 2 does not mutate as quickly as for example influenza viruses and the new vaccines that had proved effective by the end of 2020 are types that can be adjusted if necessary 26 As of the end of 2020 German British and American health authorities and experts believe that existing vaccines will be as effective against VOC 202012 01 as against previous variants 27 28 On 18 December NERVTAG determined that there are currently insufficient data to draw any conclusion on a ntigenic escape 29 As of 20 December 2020 update Public Health England confirmed there is no evidence to suggest that the new variant would be resistant to the Pfizer BioNTech vaccine currently being used in the UK s vaccination programme and that people should still be protected 30 E484K mutation edit On 2 February 2021 Public Health England reported that they had detected a limited number of B 1 1 7 VOC 202012 01 genomes with E484K mutations 9 which is also present in the Beta and Gamma variants 14 a mutation which may reduce vaccine effectiveness 14 On 9 February 2021 it became known that some 76 cases with the E484K mutation had been detected principally in Bristol but with a genomically distinct group in Liverpool also carrying the mutation 31 A week later a Research and analysis report from PHE gave a total of 77 confirmed and probable cases involving the E484K mutation across the UK in two variants VUI 202102 01 and VOC 202102 02 the latter described as B 1 1 7 with E484K 10 On 5 March 2021 it was reported that a B 1 1 7 lineage with the E484K mutation has been detected in two US patients in Oregon and New York states Researchers think that the E484K mutation in the Oregon variant has arisen independently 32 33 Characteristics editTransmissibility edit The transmissibility of the Alpha variant lineage B 1 1 7 had generally been found to be substantially higher than that of pre existing SARS CoV 2 variants The variant was discovered by a team of scientists at COG UK whose initial results found transmissibility was 70 50 100 higher 16 34 A study by the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene amp Tropical Medicine reported that the variant was 43 to 90 range of 95 credible intervals 38 to 130 more transmissible than pre existing variants in the United Kingdom depending on the method used to assess increases in transmissibility and measured similar increases in the transmissibility of lineage B 1 1 7 in Denmark Switzerland and the United States 35 Furthermore a simple model to account for the rapid rise of lineage B 1 1 7 in several countries and the world found that the variant is 50 more transmissible than the local wild type in these three countries and across the world as whole 36 Another study concluded that it was 75 70 80 more transmissible in the UK between October and November 2020 37 A later study suggested that these earlier estimates overestimated the transmissibility of the variant and that the transmissibility increase was on the lower ends of these ranges 38 39 The Dutch Ministry of Health Welfare and Sport calculated based on genome sequencing of positive cases each week the transmissibility rate of the variant compared to the local wildtype and found it to fluctuate between 28 47 higher during the first six weeks of 2021 40 The Danish Statens Serum Institut in comparison calculated it to be 55 48 62 more transmissible in Denmark based upon the observed development of its relative frequency from 4 January to 12 February 2021 41 The Institute of Social and Preventive Medicine ISPM under University of Bern calculated the transmissibility of lineage B 1 1 7 based on the weekly development of its observed fraction of all Covid 19 positives during the entire pandemic and found for 95 confidence intervals under the assumption of a wildtype reproduction number Rw 1 and an exponentially generation time of 5 2 days that transmissibility was 52 45 60 higher when compared to the wildtype in Denmark and 51 42 60 higher when compared to the wildtype in Switzerland 42 On 18 December 2020 early on in the risk assessment of the variant the UK scientific advisory body New and Emerging Respiratory Virus Threats Advisory Group NERVTAG concluded that they had moderate confidence that VOC 202012 01 was substantially more transmissible than other variants but that there were insufficient data to reach any conclusion on underlying mechanism of increased transmissibility e g increased viral load tissue distribution of virus replication serial interval etc the age distribution of cases or disease severity 29 Data seen by NERVTAG indicated that the relative reproduction number multiplicative advantage was determined to be 1 74 i e the variant is 74 more transmissible assuming a 6 5 day generational interval It was demonstrated that the variant grew fast exponentially with respect to the other variants 43 44 45 The variant out competed the ancestral variant by a factor of 1 74 14 6 5 3 3 displaystyle 1 74 14 6 5 3 3 nbsp every two weeks Another group came to similar conclusions generating a replicative advantage independent of protective measures of 2 24 per generation of 6 73 days out competing the ancestral variant by 2 24 14 6 73 5 4 displaystyle 2 24 14 6 73 5 4 nbsp every two weeks 46 Similarly in Ireland the variant as indicated by the missing S gene c detection S gene target failure SGTF which historically was rare went from 16 3 to 46 3 of cases in two weeks This demonstrates based on the statistics of 116 positive samples that the variant had a relative higher growth by a factor of 46 3 100 16 3 100 46 3 16 3 4 4 displaystyle 46 3 cdot 100 16 3 100 46 3 cdot 16 3 4 4 nbsp when compared to the average growth for all other variants by the end of this two week period 48 The variant became the dominant variant in London East of England and the South East from low levels in one to two months A surge of SARS CoV 2 infections around the start of the new year is seen by whom as being the result of the elevated transmissibility of the variant while the other variants were in decline 49 50 51 One of the most important changes in lineage B 1 1 7 seems to be N501Y 22 a change from asparagine N to tyrosine Y in amino acid position 501 52 This is because of its position inside the spike protein s receptor binding domain RBD more specifically inside the receptor binding motif RBM 53 a part of the RBD 54 which binds human ACE2 55 Mutations in the RBD can change antibody recognition and ACE2 binding specificity 55 and lead to the virus becoming more infectious 22 Chand et al concluded that i t is highly likely that N501Y affects the receptor binding affinity of the spike protein and it is possible that this mutation alone or in combination with the deletion at 69 70 in the N terminal domain NTD is enhancing the transmissibility of the virus 56 In early 2021 a peer reviewed paper found that the mentioned HV 69 70 deletion in vitro appeared to have two fold higher infectivity over a single round of infection compared to wild type SARS CoV 2 in lentiviral SARS CoV 2 pseudoviruses 57 Using In Silico approach Shahhosseini et al demonstrated that the Y501 mutation in lineage B 1 1 7 forms a shorter H bond length of 2 94 A than its counterpart in the wild type WT variant residue N501 indicating that in lineage B 1 1 7 the RBD and hACE2 have a stable interaction Furthermore the Y501 mutation in lineage B 1 1 7 contributes more negatively to Binding Free Energy BFE 7 18 kcal mol than its counterpart in the WT variant residue N501 2 92 kcal mol As a result of combining BFE and molecular interaction results the N501Y mutation in RBD strengthens binding affinity of SARS CoV 2 RBD to hACE2 58 In a detailed affinity and kinetic analysis of the interaction between the Spike RBD and ACE2 the N501Y mutation was found to significantly enhance the binding affinity between the RBD and ACE2 by approximately 10 fold resulting from a 1 8 fold increase in the association rate constant kon and a 7 fold decrease in the dissociation rate constant koff 59 Virulence edit Matched cohort studies of the Alpha variant lineage B 1 1 7 found higher mortality rate than earlier circulating variants overall 60 61 but not in hospitalised patients 62 An ecological study found no difference in mortality overall 63 Initially NERVTAG said on 18 December 2020 that there were insufficient data to reach a conclusion regarding disease severity At prime minister Boris Johnson s briefing the following day officials said that there was no evidence as of that date that the variant caused higher mortality or was affected differently by vaccines and treatments 64 Vivek Murthy agreed with this 65 Susan Hopkins the joint medical adviser for the NHS Test and Trace and Public Health England PHE declared in mid December 2020 There is currently no evidence that this strain causes more severe illness although it is being detected in a wide geography especially where there are increased cases being detected 22 Around a month later however on 22 January 2021 Johnson said that there is some evidence that the new variant VOC 202012 01 may be associated with a higher degree of mortality though Sir Patrick Vallance the government s Chief Scientific Advisor stressed that there is not yet enough evidence to be fully certain of this 66 In a paper analysing twelve different studies on lineage B 1 1 7 death rate relative to other lineages it was found to have a higher death rate 71 according to LSHTM 70 according to University of Exeter 65 according to Public Health England and 36 according to Imperial College London and NERVTAG concluded Based on these analyses it is likely that infection with VOC B 1 1 7 is associated with an increased risk of hospitalisation and death compared to infection with non VOC viruses 67 Results of the death studies were associated with some high uncertainty and confidence intervals because of a limited sample size related to the fact that UK only analysed the VOC status for 8 of all COVID 19 deaths 68 A UK case control study for 54 906 participants testing positive for SARS CoV 2 between 1 October 2020 and 29 January 2021 in the community setting not including vulnerable persons from care centres and other public institutions reported that patients infected with the Alpha variant VOC 202012 1 had a hazard ratio for death within 28 days of testing of 1 64 95 confidence interval 1 32 2 04 as compared with matched patients positive for other variants of SARS CoV 2 69 Also in the UK a survival analysis of 1 146 534 participants testing positive for SARS CoV 2 between 1 November 2020 and 14 February 2021 including individuals in the community and in care and nursing homes found a hazard ratio of 1 61 95 confidence interval 1 42 1 82 for death within 28 days of testing among individuals infected with lineage B 1 1 7 no significant differences in the increased hazard of death associated with lineage B 1 1 7 were found among individuals differing in age sex ethnicity deprivation level or place of residence 61 Both studies adjusted for varying COVID 19 mortality by geographical region and over time correcting for potential biases due to differences in testing rates or differences in the availability of hospital services over time and space citation needed A Danish study found people infected by lineage B 1 1 7 to be 64 32 104 more likely to get admitted to hospitals compared with people infected by another lineage 70 Genetic sequencing of VOC 202012 01 has shown a Q27stop mutation which truncates the ORF8 protein or renders it inactive 19 An earlier study of SARS CoV 2 variants which deleted the ORF8 gene noted that they have been associated to milder symptoms and better disease outcome 71 The study also noted that SARS CoV 2 ORF8 is an immunoglobulin Ig like protein that modulates pathogenesis that SARS CoV 2 ORF8 mediates major histocompatibility complex I MHC I degradation and that SARS CoV 2 ORF8 suppresses type I interferon IFN mediated antiviral response 71 Referring to amino acid position 501 inside the spike protein Chand et al concluded that it is possible that variants at this position affect the efficacy of neutralisation of virus 56 but noted that t here is currently no neutralisation data on N501Y available from polyclonal sera from natural infection 56 The HV 69 70 deletion has however been discovered in viruses that eluded the immune response in some immunocompromised patients 72 and has also been found in association with other RBD changes 56 Epidemiology edit nbsp Test determined growth curves on a logarithmic scale for development of the Alpha variant lineage B 1 1 7 share among all coronavirus positive samples in Denmark the Netherlands the United Kingdom Portugal Switzerland and Ireland 78 The slopes noted in brackets are the relative exponential growth rate per day e g 7 6 per day for Denmark nbsp Test determined growth curves on a logarithmic scale for development of the Alpha variant lineage B 1 1 7 share among all coronavirus positive samples in the United Kingdom countries in the UK and regions of England 81 The slopes noted in brackets are the relative exponential growth rate per day e g 8 6 per day for the UK Cases of the Alpha variant lineage B 1 1 7 were estimated to be under reported by most countries as the most commonly used tests do not distinguish between this variant and other SARS CoV 2 variants and as many SARS CoV 2 infections are not detected at all RNA sequencing is required for detection of this variant 82 although RT PCR test for specific variants d can be used as a proxy test for Alpha or as a supplementing first screening test before conducting the whole genome sequencing 83 75 As of 23 March the Alpha variant had been detected in 125 out of 241 sovereign states and dependencies or 104 out of 194 WHO member countries e of which some had reported existence of community transmission while others so far only found travel related cases 87 As of 16 March it had become the dominant COVID 19 variant for 21 countries United Kingdom week 52 Ireland week 2 Bulgaria week 4 Slovakia week 5 Israel week 5 Luxembourg week 5 Portugal week 6 Denmark week 7 Netherlands week 7 Norway week 7 Italy week 7 Belgium week 7 France week 8 Austria week 8 Switzerland week 8 Liechtenstein week 9 Germany week 9 Sweden week 9 Spain week 9 Malta week 10 and Poland week 11 The emergence and the fast spreading of the new variant has been detected in Lebanon and a relationship noted between SARS CoV 2 transmission intensity and the frequency of the new variant during the first twelve days of January 88 Since February Alpha has become the dominant variant in Lebanon 89 As of February 2021 none of the countries from South America Central America Africa Middle East except Israel Asia and Oceania had reported data for the detected share of the Alpha variant among their COVID 19 positives rendering it unknown whether or not Alpha could be dominant for their COVID 19 pandemic Spread in UK edit The first case was likely in mid September 2020 in London or Kent United Kingdom 90 The variant was sequenced in September 91 As of 13 December 2020 1 108 cases with this variant had been identified in the UK in nearly 60 different local authorities These cases were predominantly in the south east of England The variant has also been identified in Wales and Scotland 92 By November around a quarter of cases in the COVID 19 pandemic in London were being caused by the new variant and by December that was a third 93 In mid December it was estimated that almost 60 percent of cases in London involved Alpha 94 By 25 January 2021 the number of confirmed and probable UK cases had grown to 28 122 95 Spread in Europe edit The variant became dominant for South East England in week 48 the last week of November 2020 43 England in week 51 of 2020 96 United Kingdom in week 52 of 2020 77 Scotland and Northern Ireland in week 1 of 2021 79 Wales in week 2 of 2021 79 Ireland in week 2 of 2021 48 In Bulgaria genome sequencing found the variant to be dominant with 52 1 in week 4 followed by 73 4 in week 9 97 nbsp Distribution of the SARS CoV 2 virus variants after entering GermanyAlso in Slovakia a RT PCR Multiplex DX test capable of detecting the 2 deletions specific for lineage B 1 1 7 DH69 DV70 and DY144 98 first found the variant nationwide in 74 of cases on 3 February week 5 followed by 72 of cases on 15 February week 7 and it then grew to 90 of cases on 3 March week 9 99 The same test found earlier on 8 January prevalence of the variant at a rate of 36 in the Michalovce District and 29 in Nitra 100 In Israel the variant was first time detected by genome sequencing 23 December 2020 101 Leumit Health Care Services however analysed with the proxy test RT PCR SGTF and found the variant at a rate of 3 4 on 15 December 102 The national Ministry of Health estimated based on genome sequencing that the prevalence of the variant became dominant 70 on 6 February 103 followed by 90 on 16 February 104 In Luxembourg a weekly genome sequencing revealed that the variant grew from 0 3 week 51 to be dominant with a share of 53 0 in week 5 although results might not be fully representative due to the fact that no correction occurred from potential targeting bias from contact tracing airport travellers and local outbreaks Genome sequencing of a population representative randomized test pool with no target bias was conducted since week 6 and it confirmed the dominant status of the variant at a rate of 54 1 week 6 growing to 62 8 week 9 while the competing Beta variant lineage B 1 351 was found to be at 18 5 in week 9 105 In Denmark the variant grew from 0 3 week 46 of 2020 to become dominant with 65 9 week 7 of 2021 and it grew further to 92 7 week 10 with the regional prevalence ranging from 87 3 in the North Jutland Region to 96 1 in the Central Denmark Region 106 The observed growth of the relative variant share was in full accordance with the earlier modelled forecast 41 that had predicted dominance over 50 around mid February and a prevalence of around 80 of the total circulating variants by early March 107 In comparison the genome sequencing only found the competing Beta variant in 0 4 of the positive cases 9 times out of 2315 tests in week 10 108 109 In the Netherlands a randomly conducted genome sequencing found that the variant grew from 1 3 of cases in week 49 to a dominant share of 61 3 in week 7 followed by 82 0 in week 9 while the competing Beta variant in comparison was found to be at 3 0 in week 9 74 In Amsterdam the Alpha variant lineage B 1 1 7 grew from 5 2 week 52 to 54 5 week 6 110 In Norway the variant was found by genome sequencing to grow from 5 7 week 1 into dominance by a 58 4 week 7 followed by 65 0 week 8 111 Another large survey comprising results of both genome sequencing and PCR proxy tests with a sample seize of more than 1000 tests per week since week 4 at the same time found that the variant grew from 2 0 week 48 into dominance by 60 0 week 7 followed by 72 7 in week 10 while only 2 2 of cases in comparison were found to be of the Beta variant 112 The variant regionally had its highest share in the county of Oslo and Viken 113 growing from 18 to 90 of analysed samples in Oslo from 20 January to 23 February although with the data corrected estimate a bit lower at 50 70 on 23 February while growing from 21 to 80 of analysed samples in Viken from 25 January to 23 February although with the data corrected estimate a bit lower at 50 on 23 February 114 For the period 15 February to 14 March the combined survey of genome sequencing and PCR proxy tests also found the Alpha variant was at a dominant rate over 50 for 8 out of 11 regions with its highest rate 82 found for Oslo while the region Nordland was different from all other regions by having only 6 cases of Alpha along with a dominant 88 of cases represented by the Beta variant 112 In Portugal the variant represented according to a national genome sequencing survey 16 0 of the Covid 19 infections during 10 19 January week 2 115 followed by a dominant 58 2 in week 6 116 A national RT PCR proxy test based on SGTF and SGTL observations found the variant at a rate of 33 5 in week 4 but observed afterwards a decelerating pace for the weekly rise of the variant share reason unknown and according to this study it only became dominant by 50 5 91 8 of 55 0 SGTFL in week 8 followed by 64 3 91 8 of 70 SGTFL in week 10 75 In Italy the Alpha variant accounted for 17 8 of cases nationwide on 4 5 February week 5 117 followed by 54 0 on 18 February week 7 The regional prevalence for week 7 ranged from 0 in Aosta Valley although only one sample was tested to 93 3 in Molise In week 7 the competing Gamma variant had a prevalence of 4 3 ranging between 0 36 2 regionally and the South African variant a prevalence of 0 4 ranging between 0 2 9 regionally 118 In Switzerland a nationwide weekly genome sequencing survey found that the Alpha variant grew from 0 05 week 51 to a dominant 58 2 of cases in week 8 followed by 71 1 in week 9 76 This was in full accordance with a model from 9 February that had forecast dominance around mid February 119 In comparison the competing Beta variant was only found nationwide in 1 0 of the positive cases in week 9 76 In Belgium genome sequencing of samples selected randomly after excluding all samples from active targeted testing related to local outbreaks or travels creating a statistical representative national sample with a seize equal to 4 4 of all COVID 19 positive tests found that the Alpha variant share grew from 7 1 in week 1 to a dominant 51 5 in week 7 followed by 79 3 in week 10 120 The variant was first time detected by targeted genome sequencing in week 49 but due to a small sample seize not being random and less than 100 tests per week then no reliable variant share data could be determined before week 1 121 The proxy test for the variant RT PCR SGTF was also conducted for a sample seize equal to 25 8 of all COVID 19 positive tests and found a dominant 54 8 SGTF rate for week 10 In comparison the competing Beta variant was found to be at 3 6 and the Gamma variant had a prevalence of 1 8 in week 10 120 In France scientists accurately forecast the Alpha variant VOC 202012 01 would likely become dominant nationwide around week 8 11 of 2021 122 A nationwide survey of randomly selected positive COVID 19 samples first analysed by a RT PCR screening test and subsequently confirmed by genome sequencing revealed that the variant grew from a share of 3 3 388 11916 on 7 8 January week 1 123 to 13 3 475 3561 on 27 January week 4 85 followed by 44 3 273 615 on 16 February week 7 85 In week 8 the variant was found to have a dominant share of 56 4 758 1345 according to the interpretable results of a weekly genome sequencing survey comprising 0 9 of all COVID 19 positive tests or 59 5 according to a variant specific RT PCR survey testing 54 of all the COVID 19 positive tests 124 In week 10 the variant was found to have a share of 71 9 according to a variant specific RT PCR survey testing 56 9 of all the COVID 19 positive tests The spread of the variant differed regionally for the 96 departments located in Metropolitan France for week 10 with 91 departments over 50 and 5 departments with 30 50 of which the Moselle department in particular was notable due to finding a high 38 3 rate of the competing Beta variant that despite having declined from a dominant 54 4 value in week 8 still was significantly above the 5 0 national average for this specific variant 125 In Austria Agentur fur Gesundheit und Ernahrungssicherheit AGES collected data from N501Y RT PCR specific tests combined with subsequent genome sequencing analysis and found that the variant grew from 7 2 week 1 to a dominant 61 3 week 8 followed by 61 2 in week 9 and 48 3 in week 10 If all N501Y positive tests had been analysed further by genome sequencing then these listed shares could have been even higher for example they could have been as mcuh as 2 4 higher for week 1 23 0 higher for week 7 4 0 higher for week 8 6 8 higher for week 9 and 25 4 higher for week 10 The competing Beta variant was only found nationwide in 0 3 of the positive cases in week 10 and for the region Tyrol where it had been most prevalent its share declined from 24 5 in week 4 to just 1 9 in week 10 Regionally Alpha was found to be dominant with over 50 for 7 out of 9 regions with the only two exceptions being Tyrol and Vorarlberg 126 In Germany the largest and probably most representative national survey published by the Robert Koch Institute entitled RKI Testzahlerfassung determined the share of circulating COVID 19 variants for the latest week by analysing 53 272 COVID 19 positive samples either by genome sequencing or RT PCR proxy tests with data collected on a voluntary basis from 84 laboratories from the university research clinical outpatient sector spread evenly across the nation The survey did not utilize data weights or data selection criteria to ensure existence of geographical representativity but might still be regarded as somewhat representative for the national average due to its big sample seize According to the RKI Testzahlerfassung survey the variant grew from a share of 2 0 week 2 to a dominant share of 54 5 week 9 followed by 63 5 in week 10 In comparison the competing Beta variant was only found nationwide in 0 9 of the positive cases in week 10 127 In Malta the variant was first time detected by genome sequencing on 30 December 2020 128 and represented 8 of the positive cases in week 7 129 A new RT PCR variant specific test was introduced for the surveillance 130 where the first results reported on 10 March revealed the variant now represented 61 of cases nationwide 131 In Sweden the national authorities initially expected the variant would become dominant around week 12 14 under the assumption of 50 increased transmissibility compared to the original virus 132 In average the variant share was found growing from 10 8 week 4 to 36 9 week 7 across five of its southern regions Skane Vastra Gotaland Vastmanland Gavleborg and Orebro 133 For week 7 the share of the variant was for the first time also calculated to 30 4 as the overall average for 19 out of 21 Swedish regions ranging from 3 3 in Blekinge to 45 in Gavleborg For week 9 the share of the variant was calculated to a dominant 56 4 as the overall average for the 19 regions ranging from 16 in Kronoberg to 72 in Gavleborg For week 10 the share of the variant was calculated to have increased further to 71 3 as the overall average for the 19 regions ranging from 40 in Kronoberg to 84 in Jonkoping Although no geographical weights were applied to ensure geographical representativity for the calculated average for the 19 regions the overall sample seize of 12 417 variant tests represented 43 1 of all COVID 19 positive PCR tests for week 10 inferring that the result of the survey might be close to represent the actual true average for the nation as a whole 86 In the microstate Liechtenstein the first case of Alpha was detected on 19 December 2020 During the entire pandemic 67 VOC N501Y PCR positive cases were detected comprising 58 cases of Alpha 1 of Beta detected 1 February and 8 un identified N501Y cases from 10 Dec to 22 Feb as of 18 March 2021 The weekly average of each days calculated 7 day rolling average for the share of all detected VOC N501Y cases which is a good proxy for Alpha in Liechtenstein was found to be 10 9 in week 5 followed by a dominant 52 2 in week 9 where 8 out of 15 tests were found to be Alpha and grew further to 73 4 in week 10 where 6 out of 9 tests were found to be Alpha 134 In Spain the variant share was estimated nationwide to be 5 10 of cases on 29 January 135 followed by 20 25 of cases on 18 February 136 137 and 25 30 of cases on 22 February 138 and estimated to be dominant with over 50 as of 3 March week 9 139 As of week 10 the prevalence of the variant ranged from 18 3 to 97 0 for the 17 regions with all but two regions having a dominant rate above 50 140 No data reported by Extremadura 18 3 for week 10 in Aragon 27 0 for week 7 in Canary Islands 51 3 for week 8 in Castile and Leon 52 2 for week 10 in Valencia 52 8 for week 10 in Castilla La Mancha 53 3 for week 4 in Galicia 59 5 for week 9 in La Rioja 59 7 for week 10 in Madrid 61 6 for week 11 in Andalusia 76 1 for week 10 in Balearic Islands 76 7 for week 10 in Murcia 77 4 for week 10 in Basque Country 77 8 for week 10 in Navarre 83 1 for week 10 in Cantabria 84 6 for week 9 in Catalonia 97 0 for week 10 in Asturias In Poland a national survey among infected teachers led to experts estimating that the variant share was between 5 and 10 nationwide as of 11 February 141 while ECDC reported it to be 9 as of 15 February 142 According to Health minister Adam Niedzielski the variant was found at a rate of 5 in the first studies from the second half of January and then it increased by ten percentage points every ten days until it became dominant nationwide by a 52 rate on 16 March week 11 143 144 Regionally the variant had already exceeded 70 for Warmian Masurian and Pomeranian on 22 23 February week 8 145 and even reached 90 for the Greater Poland Voivodeship on 17 March week 11 146 In Finland no statistical representative national survey had been conducted as of February 2021 as the national genome sequencing mainly targeted further analysis of COVID 19 positive samples from travellers and local outbreak clusters 147 Helsinky University Hospital HUS operating in the Helsinki and Uusimaa Hospital District found the variant in 10 of all samples collected randomly during a few days ahead of 14 February in the capitol region also known as the Helsinky constituency and Uusimaa constituency For the capitol region the variant was modelled to become dominant over 50 in the second half of March week 11 13 148 In Iceland the national authorities implemented a strict 3 test and quarantine regime for all persons entering the country from abroad that so far successfully managed to prevent new infectious VOCs from gaining a foothold in the country As of 4 March a total of 90 travellers had tested positive for the Alpha variant at Iceland s borders and the 20 additional domestic cases were all closely connected to the border cases with no cases related to community transmission 149 Spread in North America edit In the United States the variant first appeared late November 2020 150 grew from 1 2 in late January and became predominant around the end of March 151 152 In Canada the variant first appeared in Ontario late December 2020 153 By 13 February it had spread to all ten provinces 154 Testing and confirmation of the Alpha variant lineage B 1 1 7 in COVID 19 positive samples has been inconsistent across the country 155 On 3 February the province of Alberta was the first to screen all COVID 19 positive samples for variants of concern 155 156 As of 23 March the Alpha variant had been detected in 5812 cases and was most prevalent in the province of Alberta 157 In Ontario a combined RT PCR N501Y and genome sequencing study found that all VOCs represented 4 4 of all COVID 19 positives on 20 January week 3 and that Alpha comprised 99 of all those VOCs 158 Public Health Ontario laboratories found the variant in close to 7 of all COVID 19 positives in week 5 representing 97 309 319 of all detected VOCs 159 Alpha became the dominant variant on or around 16 March 53 of all positive cases were VOCs and it was presumed 97 of VOCs were Alpha 160 In Quebec where the variant was also widespread it was expected to become dominant by late March or in April 161 The relatively low sensitivity of the projected dominance dates to the current percentage of the variant is due to its fast relative exponential growth Recently Delta appears to have overtaken Alpha in North America as it has in the UK Development edit Development of the Alpha variant lineage B 1 1 7 share of analysed SARS CoV 2 positive tests in a given week Country Test 2020 Week 42 Week 43 Week 44 Week 45 Week 46 Week 47 Week 48 Week 49 Week 50 Week 51 Week 52 Week 53 2021 Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10United Kingdom Seq 77 0 05 0 35 1 0 2 7 6 3 10 2 10 2 13 9 32 9 45 7 51 3 70 6 74 1 78 6 86 0 89 1 England SGTF 162 Seq 163 Seq 96 SGTF rawdata f SGTF model f 0 07 0 02 N A N A 0 4 0 5 N A N A 0 9 1 2 N A N A 2 9 1 5 N A N A 5 5 5 3 N A N A 9 1 7 8 15 2 m 13 3 18 0 11 4 24 3 m 15 9 32 2 22 1 36 8 m 22 0 51 8 38 1 49 3 m 32 1 63 7 61 8 60 7 m 57 2 72 4 62 1 72 1 m 68 9 77 9 78 4 75 0 m 74 0 82 1 76 7 80 7 m 78 3 87 5 79 7 83 3 m 82 1 90 6 88 2 m 86 0 93 8 87 7 m 89 3 95 7 93 4 m 92 5 97 4 95 3 m 94 5 98 1 97 0 m 95 4 98 6 95 6 m 95 5 98 7 94 2 m 95 2 96 1 m 94 1 Northern Ireland SGTF rawdata f SGTF model f N A N A N A N A N A 17 9 m 14 0 7 4 m 14 9 37 5 m 16 3 23 0 m 18 5 50 0 m 36 1 25 0 m 42 1 58 8 m 44 7 45 2 m 52 7 71 4 m 67 0 78 2 m 74 0 72 4 m 81 4 95 7 m 86 5 88 9 m 90 5 92 2 m 92 4 100 0 m 93 0 86 2 m 92 6 100 0 m 91 1 Scotland SGTF rawdata f SGTF model f N A N A N A N A N A 9 5 m 5 8 9 7 m 6 7 10 4 m 7 7 11 7 m 10 2 51 4 m 26 2 40 0 m 39 5 35 8 m 43 9 64 1 m 49 8 67 2 m 64 2 63 3 m 65 0 69 2 m 70 0 70 6 m 77 3 93 9 m 84 7 82 0 m 90 0 100 0 m 93 7 93 0 m 95 8 100 0 m 96 9 Wales SGTF rawdata f SGTF model f N A N A N A N A N A 27 9 m 18 1 8 3 m 16 0 10 7 m 13 3 26 3 m 12 1 13 4 m 15 0 15 9 m 14 7 19 8 m 20 4 54 4 m 34 8 61 5 m 59 6 69 0 m 65 0 68 1 m 68 7 77 0 m 73 4 71 8 m 76 6 75 8 m 78 5 87 9 m 78 9 80 0 m 77 2 69 9 m 73 3 Ireland SGTF rawdata 48 1 9 few data 0 0 few data 0 0 few data 6 1 few data 2 2 few data 1 6 few data 7 5 16 3 26 2 46 3 57 7 69 5 75 0 90 1 88 6 90 8 Bulgaria Seq 97 52 1 70 8 73 4 Israel SGTF w 51 1Seq after w 1 3 4 Dec 15 102 10 20 Jan 5 102 10 20 Jan 11 166 30 40 Jan 19 167 40 50 Jan 25 168 70 Feb 2 103 80 Feb 9 169 90 Feb 16 104 Slovakia PCR SGTF DY144 99 74 Feb 3 72 Feb 15 90 Mar 3 Luxembourg Seq 105 0 3 0 9 4 2 8 7 15 5 16 9 36 2 53 0 54 1 53 8 63 7 62 8 Denmark Seq 106 0 3 0 2 0 4 0 4 0 4 0 8 1 8 1 9 3 5 7 0 13 1 19 6 29 6 47 0 65 9 75 3 85 1 92 7 Netherlands Seq 74 1 3 0 8 0 5 2 1 4 4 9 6 15 9 22 7 24 7 31 0 40 3 61 3 75 2 82 0 Norway PCR proxy and Seq 112 Seq 170 111 0 0 2 0 0 0 0 0 4 9 0 0 8 9 7 2 6 0 2 9 14 9 1 3 18 9 5 7 19 5 11 6 15 2 9 3 19 8 20 1 34 1 30 3 43 6 40 8 60 0 58 4 71 8 65 0 76 7 72 7 Italy Seq 117 118 17 8 54 0 France PCR proxySeq SGTF Seq 3 3 123 13 3 85 36 1 171 49 3 172 45 8 172 44 3 85 59 5 124 56 4 124 65 8 85 69 0 125 71 9 125 Switzerland Seq 76 0 05 0 4 0 8 2 6 4 9 9 2 16 5 26 0 32 4 47 0 58 2 71 1 Austria PCR N501Y Seq 126 Seq B117 unseq N501Y 126 7 2 g 9 6 17 4 g 23 8 14 7 g 19 6 22 5 g 28 6 28 7 g 37 2 24 0 g 45 4 35 1 g 58 1 61 3 g 65 3 61 2 g 68 0 48 3 g 73 7 Belgium Seq 121 120 SGTF 121 120 0 0 lt 5 0 0 lt 5 0 0 lt 5 13 6 lt 5 0 0 lt 5 7 1 7 2 7 7 6 9 13 4 16 6 23 3 19 5 39 4 22 4 43 2 27 9 51 5 34 4 57 6 45 8 66 5 46 3 79 3 54 8 Portugal SGTFL Seq 75 1 7 0 8 1 2 1 7 2 9 6 8 12 3 22 7 33 5 39 2 40 9 45 7 50 5 56 0 64 3 Sweden Seq all N501Y A570D pos tests 86 10 8 av for 5 out of 21 regions h 15 1 av for 5 out of 21 regions i 27 3 av for 5 out of 21 regions j 30 4 av for 19 out of 21 regions k 41 5 av for 19 out of 21 regions l 56 4 av for 17 out of 21 regions m 71 3 av for 18 out of 21 regions n Germany PCR proxy and Seq 127 Seq 127 2 6 2 0 8 8 3 6 4 9 4 7 10 7 7 2 17 7 17 6 20 8 25 9 33 2 40 0 42 9 54 5 48 3 63 5 Liechtenstein PCR proxy N501Y 134 10 9 28 5 32 8 47 0 52 2 73 4 Spain Estimated based on PCR proxy 140 5 10 Jan 29 135 20 25 Feb 18 137 25 30 Feb 22 138 gt 50 Mar 3 139 United States SGTF Seq 174 0 05 0 2 0 4 0 5 1 0 1 9 3 0 4 7 7 6 12 4 19 3 28 8 37 4 California SGTF Seq 174 0 3 0 3 0 7 1 1 1 3 2 0 1 9 4 2 5 9 13 1 16 6 18 8 28 0 Florida SGTF Seq 174 0 2 0 5 0 9 1 0 2 3 4 6 8 1 10 7 14 5 21 0 28 3 39 8 47 0 Other countries without weekly periodic data but with a variant share above 5 0 0 Malta 61 131 and Poland 52 144 The following additional countries did not report variant shares but are likely to have a significant share present due to their finding of more than 50 cases confirmed by whole genome sequencing per 13 March 2021 175 Turkey 486 cases Finland 268 cases Australia 140 cases Chile 124 cases Croatia 121 cases Nigeria 113 cases South Korea 90 cases Slovenia 87 cases Latvia 83 cases India 81 cases Romania 76 cases Ghana 67 cases Singapore 66 cases New Zealand 63 cases North Macedonia 53 cases Brazil 53 cases Taiwan 32 cases The GISAID database of all sequenced COVID 19 genomes calculates for each country for the past four weeks an average Relative Variant Genome Frequency for submitted samples Those observed frequencies are however subject to sampling and reporting biases and do not represent exact variant share prevalence due to absence of statistical representativity 175 Countries reporting a first case edit December 2020 edit Cases of the variant began to be reported globally during December being reported in Denmark 64 176 Belgium 177 the Netherlands Australia 64 176 and Italy 178 Shortly after several other countries confirmed their first cases the first of whom were found in Iceland and Gibraltar 179 180 then Singapore Israel and Northern Ireland on 23 December 181 182 183 Germany and Switzerland on 24 December 184 185 and the Republic of Ireland and Japan confirmed on 25 December 186 187 The first cases in Canada France Lebanon Spain and Sweden were reported on 26 December 188 189 190 191 Jordan Norway and Portugal reported their first case on 27 December 192 193 Finland and South Korea reported their first cases on 28 December 194 195 and Chile India Pakistan and the United Arab Emirates reported their first cases on 29 December 196 197 198 199 The first case of new variant in Malta and Taiwan are reported on 30 December 128 200 China and Brazil reported their first cases of the new variant on 31 December 201 202 The United Kingdom and Denmark are sequencing their SARS CoV 2 cases at considerably higher rates than most others 203 and it was considered likely that additional countries would detect the variant later 204 The United States reported a case in Colorado with no travel history on 29 December the sample was taken on 24 December 205 On 6 January 2021 the US Centers for Disease Control and Prevention announced that it had found at least 52 confirmed cases in California Florida Colorado Georgia and New York 206 In the following days more cases of the variant were reported in other states leading former CDC director Tom Frieden to express his concerns that the U S will soon face close to a worst case scenario 207 January 2021 edit Turkey detected its first cases in 15 people from England on 1 January 2021 208 It was reported on 1 January that Denmark had found a total of 86 cases of the variant equalling an overall frequency of less than 1 of the sequenced cases in the period from its first detection in the country in mid November to the end of December 209 210 this had increased to 1 6 of sequenced tests in the period from mid November to week two of 2021 with 7 of sequenced tests in this week alone being of Alpha variant lineage B 1 1 7 211 Luxembourg and Vietnam reported their first case of this variant on 2 January 2021 212 213 On 3 January 2021 Greece and Jamaica detected their first four cases of this variant 214 215 and Cyprus announced that it had detected Alpha VOC 202012 01 in 12 samples 216 At the same time New Zealand and Thailand reported their first cases of this variant where the former reported six cases made up of five from the United Kingdom and one from South Africa 217 and the latter reported the cases from a family of four who had arrived from Kent 218 Georgia reported its first case 219 and Austria reported their first four cases of this variant along with one case of Beta variant on 4 January 220 On 5 January Iran 221 Oman 222 and Slovakia reported their first cases of VOC 202012 01 223 On 8 January Romania reported its first case of the variant an adult woman from Giurgiu County who declared not having left the country recently 224 On 9 January Peru confirmed its first case of the variant 225 Mexico and Russia reported their first case of this variant on 10 January 226 then Malaysia and Latvia on 11 January 227 228 On 12 January Ecuador confirmed its first case of this variant 229 The Philippines and Hungary both detected the presence of the variant on 13 January 230 231 The Gambia recorded first cases of the variant on 14 January with it being the first confirmation of the variant s presence in Africa 232 On 15 January the Dominican Republic confirmed its first case of the new variant 233 and Argentina confirmed its first case of the variant on 16 January 234 Czech Republic and Morocco reported their first cases on 18 January 235 236 while Ghana and Kuwait confirmed their first cases on 19 January 237 238 Nigeria confirmed its first case on 25 January 239 On 28 January Senegal detected its first case of the variant 240 In early January an outbreak linked to a primary school led to the detection of at least 30 cases of the new variant in the Bergschenhoek area of the Netherlands signifying local transmission 241 On 16 January the Los Angeles County Department of Public Health confirmed the variant was detected in L A County with public health officials believing that it is spreading in the community 242 On 24 January a person travelling from Africa to Faroe Islands tested positive upon arrival to the islands and went directly into quarantine 243 On 28 January North Macedonia confirmed the variant was detected in a 46 year old man who had already recovered 244 February 2021 edit On 1 February Lithuania has confirmed the first cases of the new lineage citation needed On 4 February health authorities in Uruguay announced the first case of the variant in the country The case was detected in a person who entered the country on 20 December 2020 and has been in quarantine ever since 245 On 10 February the Health Ministry of Croatia confirmed that out of 61 sequenced samples since 20 January the variant was detected in 3 samples a male 50 year old and 3 5 year old from Zagreb and a male 34 year old from Brod Posavina County 246 On 12 February the variant was detected from four areas in Sri Lanka 247 and the Canadian province of Newfoundland and Labrador confirmed an outbreak of the variant 248 March 2021 edit On 2 March Indonesia reports its first cases of the variant in two migrant workers returning from Saudi Arabia 249 On the same day Tunisia 250 reported their first cases of the variant The presence of the variant in Ivory Coast was confirmed on 25 March 251 N501Y mutation elsewhere edit The N501Y mutation arose independently multiple times in different locations In April 2020 it was seen for the first time in a few isolated sequences in Brazil 252 In June 2020 the mutation appeared in an Australian lineage 252 In July 2020 according to Dr Julian Tang University of Leicester N501Y appeared in a lineage circulating in United States 252 citation needed In September 2020 it was found in a lineage in Wales that evolved independently and was different from lineage B 1 1 7 52 In September 2020 1 the much more transmissible and widespread lineage B 1 1 7 501Y V1 was detected for the first time in Kent England 19 In October 2020 another highly transmissible variant of concern termed lineage B 1 351 501Y V2 Beta variant was first time detected by genome sequencing in Nelson Mendela Bay South Africa 253 Phylogeographic analysis suggests this lineage emerged already in July or August 2020 254 In December 2020 255 another highly transmissible variant termed lineage P 1 501Y V3 Gamma variant was detected in Manaus Brazil 256 Statistics editTable edit Cases by country Country Confirmed cases GISAID 257 as of 13 August 2021 Last Case Reported nbsp United Kingdom 268 386 27 June 2021 nbsp Canada 228 525 258 6 July 2021 nbsp USA 212 465 29 June 2021 nbsp Germany 102 642 28 June 2021 nbsp Denmark 62 570 29 June 2021 nbsp Sweden 58 838 21 June 2021 nbsp France 32 782 28 June 2021 nbsp Netherlands 28 773 25 June 2021 nbsp Japan 32 899 1 July 2021 nbsp Italy 25 420 30 June 2021 nbsp Switzerland 21 726 26 June 2021 nbsp Spain 22 258 5 July 2021 nbsp Belgium 20 724 1 July 2021 nbsp Poland 14 804 21 June 2021 nbsp Ireland 15 798 23 June 2021 nbsp Lithuania 9 334 11 June 2021 nbsp Israel 7 988 24 June 2021 nbsp Norway 8 526 23 June 2021 nbsp Slovenia 8 366 20 June 2021 nbsp Finland 7 953 259 25 May 2021 nbsp Greece 5 481 7 June 2021 nbsp Portugal 5 015 23 June 2021 nbsp Slovakia 4 480 19 June 2021 nbsp Luxembourg 4 898 25 May 2021 nbsp Croatia 4 350 11 June 2021 nbsp Austria 3 836 20 June 2021 nbsp Czech Republic 4 299 24 June 2021 nbsp India 3 361 1 June 2021 nbsp Latvia 3 135 28 May 2021 nbsp Estonia 2 993 8 May 2021 nbsp Bulgaria 3 056 17 May 2021 nbsp Mexico 1 705 24 June 2021 nbsp Thailand 726 20 June 2021 nbsp Romania 767 15 June 2021 nbsp Philippines 1 001 30 March 2021 nbsp Turkey 637 25 May 2021 nbsp South Korea 735 8 June 2021 nbsp Aruba 551 16 June 2021 nbsp Brazil 584 1 June 2021 nbsp Australia 506 4 July 2021 nbsp Kenya 559 3 June 2021 nbsp Cambodia 470 26 June 2021 nbsp Sint Maarten 384 24 June 2021 nbsp Russia 361 12 June 2021 nbsp Curacao 318 19 May 2021 nbsp Sri Lanka 386 25 June 2021 nbsp Ghana 347 24 April 2021 nbsp North Macedonia 258 22 April 2021 nbsp Qatar 231 23 May 2021 nbsp Singapore 190 17 June 2021 nbsp Pakistan 179 28 May 2021 nbsp Bonaire 183 15 June 2021 nbsp Kazakhstan 162 27 April 2021 nbsp New Zealand 152 14 June 2021 nbsp Malta 148 11 June 2021 nbsp Chile 162 12 June 2021 nbsp Nigeria 140 19 March 2021 nbsp South Africa 165 17 June 2021 nbsp Gibraltar 131 8 March 2021 nbsp Argentina 139 7 May 2021 nbsp Ecuador 167 17 June 2021 nbsp China 102 7 June 2021 nbsp Canary Islands 110 10 March 2021 nbsp Morocco 106 22 April 2021 nbsp Costa Rica 129 24 May 2021 nbsp Bangladesh 93 8 June 2021 nbsp Colombia 99 25 May 2021 nbsp Jordan 90 4 May 2021 nbsp Bosnia and Herzegovina 68 21 June 2021 nbsp Iraq 48 9 March 2021 nbsp Guadeloupe 87 8 June 2021 nbsp Reunion 80 8 June 2021 nbsp Angola 79 23 April 2021 nbsp Gambia 72 25 March 2021 nbsp Indonesia 63 28 June 2021 nbsp Ukraine 70 18 March 2021 nbsp Iran 52 8 May 2021 nbsp Bahrain 54 14 June 2021 nbsp French Guiana 59 22 May 2021 nbsp Guam 39 11 May 2021 nbsp Gabon 44 5 May 2021 nbsp Guinea Bissau 31 5 February 2021 nbsp Taiwan 50 29 May 2021 nbsp Djibouti 62 31 March 2021 nbsp Hungary 29 26 February 2021 nbsp Albania 28 11 March 2021 nbsp Palestine 22 9 April 2021 nbsp Vietnam 25 6 May 2021 nbsp Georgia 66 6 April 2021 nbsp Serbia 45 11 March 2021 nbsp Kuwait 21 5 June 2021 nbsp Martinique 154 25 May 2021 nbsp Togo 21 25 February 2021 nbsp United Arab Emirates 19 29 December 2020 nbsp Barbados 26 21 May 2021 nbsp Iceland 20 5 January 2021 nbsp Saint Lucia 28 29 April 2021 nbsp Senegal 35 30 April 2021 nbsp Uganda 17 15 June 2021 nbsp Lebanon 767 3 May 2021 nbsp Cote d Ivoire 15 9 March 2021 nbsp Jamaica 152 12 February 2021 nbsp Suriname 15 14 May 2021 nbsp Armenia 7 18 March 2021 nbsp Cameroon 11 17 April 2021 nbsp Egypt 7 17 May 2021 nbsp Guinea 25 30 March 2021 nbsp Malaysia 31 4 June 2021 nbsp Nepal 11 2 June 2021 nbsp Cyprus 10 27 January 2021 nbsp Wallis and Futuna 10 19 April 2021 nbsp Trinidad and Tobago 9 4 May 2021 nbsp Democratic Republic of the Congo 16 28 March 2021 nbsp Dominican Republic 16 14 April 2021 nbsp Peru 17 7 April 2021 nbsp Liechtenstein 14 16 May 2021 nbsp Montenegro 7 21 January 2021 nbsp Rwanda 6 21 May 2021 nbsp Antigua and Barbuda 12 6 May 2021 nbsp Cayman Islands 10 15 May 2021 nbsp Turks and Caicos Islands 5 22 March 2021 nbsp Dominica 16 1 April 2021 nbsp Paraguay 4 8 April 2021 nbsp Puerto Rico 4 11 June 2021 nbsp Azerbaijan 3 7 February 2021 nbsp Belarus 3 24 February 2021 nbsp Burkina Faso 3 3 February 2021 nbsp Ethiopia 3 4 February 2021 nbsp Kosovo 22 6 January 2021 nbsp Malta 148 10 June 2021 nbsp Moldova 16 3 March 2021 nbsp Monaco 3 17 April 2021 nbsp Republic of the Congo 29 5 March 2021 nbsp Tunisia 6 8 March 2021 nbsp Anguilla 2 23 March 2021 nbsp Bermuda 2 5 January 2021 nbsp Central African Republic 2 17 March 2021 nbsp Faroe Islands 2 4 May 2021 nbsp Grenada 3 8 April 2021 nbsp Malawi 2 8 March 2021 nbsp Mayotte 2 21 May 2021 nbsp Montserrat 2 5 February 2021 nbsp Myanmar 2 28 May 2021 nbsp Somalia 6 5 March 2021 nbsp Zambia 2 11 February 2021 nbsp Belize 1 20 January 2021 nbsp British Virgin Islands 1 19 April 2021 nbsp Equatorial Guinea 1 9 February 2021 nbsp Guatemala 17 7 April 2021 nbsp Haiti 1 19 May 2021 nbsp Honduras 1 23 April 2021 nbsp Mauritius 1 10 January 2021 nbsp Mozambique 1 21 April 2021 nbsp Northern Mariana Islands 1 29 April 2021 nbsp Oman 30 22 December 2020 nbsp Saudi Arabia 4 15 April 2021 nbsp Niger 1 9 January 2021 nbsp Libya 1 5 June 2021 nbsp South Sudan 1 3 April 2021 nbsp Burundi 1 27 May 2021 nbsp Chad 1 nbsp Uzbekistan 2 25 June 2021 nbsp Cabo Verde 4 3 February 2021 nbsp Benin 15 3 March 2021 nbsp Namibia 3 March 2021 nbsp Maldives 4 29 March 2021 nbsp Venezuela 3 7 May 2021 World 167 countries Total 1 248 973 Total as of 13 August 2021Graphics edit Confirmed cases by countries edit Note The graphs presented here are only viewable by computers and some phones If you cannot view it on your cell phone switch to desktop mode from your browser Data provided by various sources such as governmental press or officials are updated every week since their last publication Graphs are unavailable due to technical issues There is more info on Phabricator and on MediaWiki wiki gt 100 000 casesGraphs are unavailable due to technical issues There is more info on Phabricator and on MediaWiki wiki gt 10 000 casesGraphs are unavailable due to technical issues There is more info on Phabricator and on MediaWiki wiki gt 1 000 casesGraphs are unavailable due to technical issues There is more info on Phabricator and on MediaWiki wiki gt 100 casesHistory editDetection edit nbsp False colour transmission electron micrograph of the Alpha variant The variant s increased transmissibility is believed to be due to changes in structure of the spike proteins shown here in green The Alpha variant lineage B 1 1 7 was first detected in early December 2020 by analysing genome data with knowledge that the rates of infection in Kent were not falling despite national restrictions 5 260 The two earliest genomes that belong to lineage B 1 1 7 were collected on 20 September 2020 in Kent and another on 21 September 2020 in Greater London 19 These sequences were submitted to the GISAID sequence database sequence accessions EPI ISL 601443 and EPI ISL 581117 respectively 261 Backwards tracing using genetic evidence suggests lineage B 1 1 7 emerged in September 2020 and then circulated at very low levels in the population until mid November The increase in cases linked to the variant first became apparent in late November when Public Health England PHE was investigating why infection rates in Kent were not falling despite national restrictions PHE then discovered a cluster linked to this variant spreading rapidly into London and Essex 30 Also important was the nature of the RT PCR test used predominantly in the UK Thermo Fisher Scientific s TaqPath COVID 19 The test matches RNA in three locations and stopped working for the spike gene due to the HV 69 70 deletion a deletion of the amino acids histidine and valine in positions 69 and 70 respectively 262 in the spike protein of lineage B 1 1 7 This made preliminary identification easier because it could be better suspected which cases were with lineage B 1 1 7 through genome sequencing 263 It has been suggested that the variant may have originated in a chronically infected immunocompromised person giving the virus a long time to replicate and evolve 264 5 265 266 Control edit In the presence of a more transmissible variant stronger physical distancing and lockdown measures were opted for to avoid overwhelming the population due to its tendency to grow exponentially 267 All countries of the United Kingdom were affected by domestic travel restrictions in reaction to the increased spread of the virus at least partly attributed to Alpha effective from 20 December 2020 268 269 During December 2020 an increasing number of countries around the world either announced temporary bans on or were considering banning passenger travel from the UK and in several cases from other countries such as the Netherlands and Denmark Some countries banned flights others allowed only their nationals to enter subject to a negative SARS CoV 2 test 270 A WHO spokesperson said that a cross Europe where transmission is intense and widespread countries need to redouble their control and prevention approaches Most bans by EU countries were for 48 hours pending an integrated political crisis response meeting of EU representatives on 21 December to evaluate the threat from the new variant and coordinate a joint response 271 272 Many countries around the world imposed restrictions on passenger travel from the United Kingdom neighbouring France also restricted manned goods vehicles imposing a total ban before devising a testing protocol and permitting their passage once more 273 Some also applied restrictions on travel from other countries 274 275 276 277 As of 21 December 2020 update at least 42 countries had restricted flights from the UK 270 and Japan was restricting entry of all foreign nationals after cases of the new variant were detected in the country 278 The usefulness of travel bans has been contested as limited in cases where the variant has likely already arrived especially if the estimated growth rate per week of the virus is higher locally 279 280 Extinction edit In October 2021 Dr Jenny Harries chief executive of the UK Health and Security Agency stated that previous circulating variants such as Alpha had disappeared and replaced by the Delta variant 281 In March 2022 the World Health Organization listed the Alpha Beta and Gamma variants as previously circulating citing lack of any detected cases in the prior weeks and months 282 See also edit nbsp COVID 19 portal nbsp Medicine portal nbsp Viruses portalVariants of SARS CoV 2 Beta Gamma Delta Epsilon Zeta Eta Theta Iota Kappa Lambda Mu OmicronNotes edit Written as VUI 202012 01 Variant Under Investigation year 2020 month 12 variant 01 by GISAID 283 and the ECDC 284 The difference between the two is explained by PHE SARS CoV 2 variants if considered to have concerning epidemiological immunological or pathogenic properties are raised for formal investigation At this point they are designated Variant Under Investigation VUI with a year month and number Following a risk assessment with the relevant expert committee they may be designated Variant of Concern VOC 18 a b SARS CoV 2 s S gene encodes its spike protein 47 An example of this is the delta D PCR test which in connection to SARS CoV 2 has been used to detect the HV 69 70 deletion in variants with this mutation 83 through what has been named spike gene target failure SGTF or spike gene drop out 75 for the spike S gene c in a subset of RT PCR assays e g TaqPath COVID 19 RT PCR assay ThermoFisher 84 Though existing in a few other variants of SARS CoV 2 75 the HV 69 70 deletion in the spike protein is present in the vast majority of B 1 1 7 genomes which enables the delta PCR test to be used as a proxy test for the lineage or as a supplementing first screening test before conducting the whole genome sequencing 83 75 Another example of a RT PCR test intended to detect specific variants is the one detecting all genomes with the N501Y mutation e g Alpha Gamma variant and Beta variant which is now also being used as a first step screening tool ahead of genome sequencing by several laboratories countries e g by some parts of France 85 A third and fourth RT PCR test intended for detecting specific variants pre screen the samples for variants respectively with the N501Y A570D mutations Alpha and N501Y without the A570D mutation Beta Gamma and other N501Y variants 86 104 WHO members had reported a detection of the Alpha variant lineage B 1 1 7 as of 23 March 2021 Albania Angola Argentina Australia Austria Azerbaijan Bahrain Bangladesh Barbados Belarus Belgium Belize Bosnia and Herzegovina Brazil Brunei Darussalam Bulgaria Cabo Verde Cambodia Canada Chile China Costa Rica Croatia Cyprus Czech Republic Democratic Republic of the Congo Denmark Dominican Republic Ecuador Estonia Finland France Gambia Georgia Germany Ghana Greece Hungary Iceland India Indonesia Iran Iraq Ireland Israel Italy Jamaica Japan Jordan Kenya Kuwait Latvia Lebanon Libya Lithuania Luxembourg Malaysia Malta Mauritania Mauritius Mexico Monaco Montenegro Morocco Nepal Netherlands New Zealand Nigeria North Macedonia Norway Oman Pakistan Peru Philippines Poland Portugal Republic of Korea South Korea Republic of Moldova Romania Russia Rwanda Saint Lucia Saudi Arabia Senegal Serbia Singapore Slovakia Slovenia South Africa Spain Sri Lanka Sweden Switzerland Thailand Trinidad and Tobago Tunisia Turkey Ukraine United Arab Emirates United Kingdom United States Uruguay Uzbekistan Vietnam 87 90 WHO members had not reported any detection of the Alpha variant lineage B 1 1 7 as of 23 March 2021 Afghanistan Algeria Andorra Antigua and Barbuda Armenia Bahamas Benin Bhutan Bolivia Botswana Burkina Faso Burundi Cameroon Central African Republic Chad Colombia Comoros Congo Cook Islands Cote d Ivoire Cuba Democratic People s Republic of Korea North Korea Djibouti Dominica Egypt El Salvador Equatorial Guinea Eritrea Ethiopia Fiji Gabon Grenada Guatemala Guinea Bissau Guyana Haiti Honduras Guinea Kazakhstan Kiribati Kyrgyzstan Lao People s Democratic Republic Lesotho Liberia Madagascar Malawi Maldives Mali Marshall Islands Micronesia Mongolia Mozambique Myanmar Namibia Nauru Nicaragua Niger Niue Palau Panama Papua New Guinea Paraguay Qatar Saint Kitts and Nevis Saint Vincent and the Grenadines Samoa San Marino Sao Tome and Principe Seychelles Sierra Leone Solomon Islands Somalia South Sudan Sudan Suriname Swaziland Syrian Arab Republic Tajikistan Timor Leste Togo Tonga Turkmenistan Tuvalu Uganda United Republic of Tanzania Vanuatu Venezuela Yemen Zambia Zimbabwe 87 a b c d e f g h The weekly UK infection survey lists for each country in Great Britain a set of raw data and average smoothed modelled data from SGTF analysed PCR tests collected from private households excl tests from hospitals care centres and public institutions Raw data as well as model data for Wales Northern Ireland and Scotland must be treated with caution due to a small number of collected samples resulting in great data uncertainty 164 165 All PCR tests were analysed for 3 genes present in the coronavirus N protein S protein and ORF1ab see Table 6A in the Infection Survey Each PCR test can have any one any two or all three genes detected Coronavirus positives are those where one or more of these genes is detected in the swab other than tests that are only positive on the S gene which is not considered a reliable indicator of the virus if found on its own The new B 1 1 7 variant of COVID 19 has genetic changes in the S gene that results in the S gene no longer being detected in the current test meaning that it will only be positive on the ORF1ab and the N gene The survey uses the terms New UK variant compatible for ORF1ab N protein gene positives not compatible with new UK variant for ORF1ab N protein S protein gene positive and virus too low to be identifiable for all other gene patterns a reasonable definition given that all samples taken from the first phase of the COVID 19 disease where virus exist by identifiable quantity either will be positive by ORF1ab N or ORF1ab N S However further uncertainty exists given that not all New UK variant compatible SGTF cases positive on ORF1ab and N genes but not the S gene will be the new UK variant due to some other competing variants also delivering this same test pattern and prior to mid November 2020 the data should not be read as being an indicator of the variant at all 164 165 The weekly B 1 1 7 variant share raw data is calculated from Table 6A by dividing the ORF1ab N percentage with the percentage sum of ORF1ab N and ORF1ab N S Table 6C utilized the raw data from table 6A as input for calculation of some modelled average smoothed and weighted daily estimated figures for the respective percentage of the population being coronavirus positive by either the New UK variant compatible virus or a Not compatible with new UK variant virus or a virus too low to be identifiable with data from earlier dates in 2020 also being available when downloading the published earlier editions of the Infection Survey The modelled weekly average value for the Alpha variant noted in this table as the value m is calculated as the average for the listed seven days in each week of New UK variant compatible percentage divided by the sum of New UK variant compatible percentage and Not compatible with new UK variant percentage 164 165 a b c d e f g h i j In Austria the listed B 1 1 7 variant shares represent the percentage of all positive COVID 19 tests being confirmed to be B 1 1 7 by genome sequencing However many N501Y positive RT PCR tests were not variant determined further by genome sequencing and likely would have returned a B 1 1 7 positive result for the vast majority of such tests if the genome sequencing analysis had been done If all N501Y positive tests had been analysed further by genome sequencing then the listed weekly B 1 1 7 shares could have been uptil 9 6 for week 1 2 4 higher 23 8 for week 2 6 4 higher 19 6 for week 3 4 9 higher 28 6 for week 4 6 1 higher 37 2 for week 5 8 5 higher 45 4 for week 6 21 4 higher 58 1 for week 7 23 0 higher 65 3 for week 8 4 0 higher 68 0 for week 9 6 8 higher and 73 7 for week 10 25 4 higher 126 In Sweden a study comprising 11 of all SARS CoV 2 positive PCR samples nationwide for week 4 found the B 1 1 7 share to be 10 8 243 2244 Samples were however only collected from five southern regions Skane Vastra Gotaland Vastmanland Gavleborg and Orebro which were not considered to be statistically representative for the demography and geography of Sweden as a whole The national authorities plan to expand the weekly study to cover more regions for the following weeks in February 2021 173 133 In Sweden a study comprising 16 of all SARS CoV 2 positive PCR samples nationwide for week 5 found the B 1 1 7 share to be 15 1 488 3224 Samples were however only collected from five southern regions Skane Vastra Gotaland Vastmanland Gavleborg and Orebro which were not considered to be statistically representative for the demography and geography of Sweden as a whole The national authorities also calculated a two week average week 5 6 for 19 out of 21 regions and plan to expand the weekly study to cover more regions for the following weeks in February 2021 133 In Sweden a study comprising 18 of all SARS CoV 2 positive PCR samples nationwide for week 6 found the B 1 1 7 share to be 27 3 1021 3742 Samples were however only collected from five southern regions Skane Vastra Gotaland Vastmanland Gavleborg and Orebro which were not considered to be statistically representative for the demography and geography of Sweden as a whole The national authorities also calculated a two week average week 5 6 for 19 out of 21 regions and plan to expand the weekly study to cover more regions for the following weeks in February 2021 133 In Sweden a study comprising 47 8 of all SARS CoV 2 positive PCR samples nationwide for week 7 collected samples from 19 out of 21 regions all except Gotland and Vasterbotten and found the B 1 1 7 share to be 30 4 3316 10910 as a simple overall average with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize correct each regions share of the overall sample 86 In Sweden a study comprising 42 2 of all SARS CoV 2 positive PCR samples nationwide for week 8 collected samples from 19 out of 21 regions all except Gotland and Vasterbotten and found the B 1 1 7 share to be 41 5 4643 11191 as a simple overall average with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize correct each regions share of the overall sample 86 In Sweden a study comprising 37 8 of all SARS CoV 2 positive PCR samples nationwide for week 9 collected samples from 17 out of 21 regions all except Gotland Vasterbotten Norrbotten and Ostergotland and found the B 1 1 7 share to be 56 4 5939 10528 as a simple overall average with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize correct each regions share of the overall sample 86 In Sweden a study comprising 43 1 of all SARS CoV 2 positive PCR samples nationwide for week 10 collected samples from 18 out of 21 regions all except Gotland Vasterbotten and Ostergotland and found the B 1 1 7 share to be 71 3 8850 12417 as a simple overall average with a potential geographically skewed misrepresentation in the calculation as no data weights were used to normalize correct each regions share of the overall sample 86 References edit a b B 1 1 7 report cov lineages org Retrieved 29 January 2021 Tracking SARS CoV 2 variants www who int Retrieved 17 August 2022 Variants of concern CDGN Retrieved 17 August 2022 Kupferschmidt Kai Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear www science org Science Retrieved 24 February 2023 a b c d Peacock Sharon 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February 2021 NERVTAG paper on COVID 19 variant of concern B 1 1 7 NERVTAG update note on B 1 1 7 severity 2021 02 11 PDF www gov uk Peston Robert 22 January 2021 New Covid 19 strain may be more lethal Robert Peston learns ITV News Retrieved 24 January 2021 Challen Robert Brooks Pollock Ellen Read Jonathan M Dyson Louise Tsaneva Atanasova Krasimira Danon Leon 9 March 2021 Risk of mortality in patients infected with SARS CoV 2 variant of concern 202012 1 matched cohort study BMJ 372 n579 doi 10 1136 bmj n579 PMC 7941603 PMID 33687922 Statens Serum Institut 24 February 2021 B 1 1 7 kan fore til flere indlaeggelser B 1 1 7 might lead to more hospital admissions in Danish Retrieved 25 February 2021 a b Zinzula Luca 2020 Lost in deletion The enigmatic ORF8 protein of SARS CoV 2 Biochemical and Biophysical Research Communications 538 116 24 doi 10 1016 j bbrc 2020 10 045 PMC 7577707 PMID 33685621 Kupferschmidt Kai 20 December 2020 Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear Science doi 10 1126 science abg2626 S2CID 234564870 See also COG UK 20 December 2020 p 4 69 70del has been identified in variants associated with immune escape in immunocompromised patients Genomic overview of SARS CoV 2 in Denmark 30 January 2021 Retrieved 1 February 2021 a b c National Institute for Public Health and the Environment RIVM Ministry of Health Welfare and Sport 23 March 2021 Variants of the coronavirus SARS CoV 2 www rivm nl Retrieved 23 March 2021 a b c d e f g Borges Vitor et al 19 January 2021 Tracking SARS CoV 2 VOC 202012 01 lineage B 1 1 7 dissemination in Portugal insights from nationwide RT PCR Spike gene drop out data Update information including data from weeks 3 10 2021 Posted after the article on 16 March 2021 Footnote of the previous updates explain that 91 8 of total SGTF SGTL 90 of SGTF and 100 of SGTL was confirmed by genome sequence to be the B 1 1 7 variant The B 1 1 7 shares were calculated as 91 8 of the total SGTF SGTL share for each week Retrieved 16 March 2021 a b c d Swiss National COVID 19 Science Task Force Genomic Characterisation Retrieved 15 March 2021 a href Template Cite web html title Template Cite web cite web a CS1 maint numeric names authors list link a b c d SARS CoV 2 Variants of Concern in Switzerland IBZ Shiny January 2021 Archived from the original on 17 February 2021 Retrieved 18 February 2021 Data sources Denmark 73 The Netherlands 74 Portugal 75 Switzerland 76 The United Kingdom 77 Ireland 48 a b c Coronavirus COVID 19 Infection Survey UK 29 January 2021 10 Positive tests that are compatible with the new UK variant www ons gov uk 29 January 2021 Retrieved 1 February 2021 nbsp This article incorporates text published under the British Open Government Licence v3 0 Walker A Sarah Vihta Karina Doris Gethings Owen Pritchard Emma Jones Joel House Thomas Bell Iain Bell John I Newton John N Farrar Jeremy Diamond Ian Studley Ruth Rourke Emma Hay Jodie Hopkins Susan Crook Derrick Peto Tim Matthews Philippa C Eyre David W Stoesser Nicole Pouwels Koen B 15 January 2021 Increased infections but not viral burden with a new SARS CoV 2 variant medRxiv 10 1101 2021 01 13 21249721 Data sources UK national 2021 01 21 77 South East England 2020 12 31 43 UK countries 2021 01 29 79 England regions 2021 01 15 80 Risk related to spread of new SARSCoV 2 variants of concern in the EU EEA PDF www ecdc europa eu 29 December 2020 Retrieved 1 February 2021 a b c Statens Serum Institut 4 February 2021 Delta PCR testen The delta PCR test in Danish Retrieved 11 February 2021 Antonin Bal Gregory Destras Alexandre Gaymard Karl Stefic Julien Marlet et al COVID Diagnosis HCL Study Group 21 January 2021 Two step strategy for the identification of SARS CoV 2 variant of concern 202012 01 and other variants with spike deletion H69 V70 France August to December 2020 Eurosurveillance 26 3 doi 10 2807 1560 7917 ES 2021 26 3 2100008 PMC 7848679 PMID 33478625 a b c d e f Sante Publique France 11 March 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54 delle infezioni dovute a variante inglese il 4 3 a quella brasiliana e lo 0 4 a quella sudafricana CS N 14 2021 In Italy 54 of infections due to the English variant 4 3 to the Brazilian one and 0 4 to the South African one in Italian Retrieved 5 March 2021 Wissenschaftliches update 09 februar 2021 Scientific update of 9 February 2021 in German Swiss National COVID 19 Task Force 9 February 2021 Retrieved 17 February 2021 a b c d Sciensano 19 March 2021 Covid 19 Wekelijks Epidemiologisch Bulletin 19 Maart 2021 Covid 19 Weekly Epidemiological Bulletin 19 March 2021 PDF Moleculaire surveillance van SARS CoV 2 p 20 22 in Dutch Retrieved 19 March 2021 a b c Sciensano 19 February 2021 Covid 19 Wekelijks Epidemiologisch Bulletin 19 Februari 2021 Covid 19 Weekly Epidemiological Bulletin February 19 2021 PDF Moleculaire surveillance van SARS CoV 2 p 21 24 in Dutch Retrieved 25 February 2021 Estimated date of dominance of VOC 202012 01 strain in France and projected scenarios PDF 16 January 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