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SARS-CoV-2 Gamma variant

Source: Wikipedia, the free encyclopedia.

Total number of P.1 sequences by country as of 21 April 2021[1]
Legend:
  1,000+ confirmed sequences
  500–999 confirmed sequences
  100–499 confirmed sequences
  2–99 confirmed sequences
  1 confirmed sequence
  None or no data available

Gamma variant, also known as lineage P.1,[a] is one of the variants of SARS-CoV-2, the virus that causes COVID-19.[6] This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T.[5][7] This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier.[5][8] It was subsequently declared to be in circulation in Brazil.[5] Under the simplified naming scheme proposed by the World Health Organization, P.1 has been labeled Gamma variant, and is currently considered a variant of concern.[9]

Gamma caused widespread infection in early 2021 in the city of Manaus, the capital of Amazonas, although the city had already experienced widespread infection in May 2020,[10] with a study[11] indicating high seroprevalence of antibodies for SARS-CoV-2.[12] A research article published in Science Journal indicate that P.1 infected people have a greater chance of transmissibility and death than B.1.1.28 infected ones.[13]

The Gamma variant comprises the two distinct subvariants 28-AM-1 and 28-AM-2, which both carry the K417T, E484K, N501Y mutations, and which both developed independently of each other within the same Brazilian Amazonas region.[14]

Gamma is notably different from the Zeta variant (lineage P.2) which is also circulating strongly in Brazil. In particular, Zeta only carries the E484K mutation and has neither of the other two mutations of concern, N501Y and K417T.[14][7]

Classification

Initial reports claimed that both P.1 and P.2 were two separate and different descendants of the Brazilian lineage B.1.1.248.[15][16] However, B.1.1.248 later lost its status as a distinct lineage and was reclassified to B.1.1.28.[17] P.1 has also been called B.1.1.28.1,[18] while P.2 has been B.1.1.28.2 or VUI-202101/01.[19] Since only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation of B.1.1.28.1 to P.1 and B.1.1.28.2 to P.2.[5][20]

Following its detection, genome data for four samples of the new variant were shared to GISAID having been assigned the ID range: EPI_ISL_792680 to EPI_ISL_792683.[21]

Mutations

Defining mutations in Gamma variant
Gene Amino acid
ORF1ab synT733C
synC2749T
S1188L
K1795Q
del11288-11296 (3675-3677 SGF)
synC12778T
synC13860T
E5665D
Spike L18F
T20N
P26S
D138Y
R190S
K417T
E484K
N501Y
H 655Y
T1027I
ORF8 E92K
ins28269-28273
N P80R
Source: Faria et al. (2021), Figure 1.B

Variants of SARS-CoV-2 As well as having eight mutations (four of these synonymous genetic mutations) in its open reading frames (ORF1a and ORF1b) – one of which is a set of deletions – Gamma has 10 defining mutations in its spike protein, including N501Y and E484K. It also has two mutations – one an insertion – in its ORF8 region and one in its N region.[5][23]

Descendant and sublineages

Coronavirus lineage B.1.1.28 has originated four known lineages classified as variant of interest (VOI) or variant of concern (VOC): lineages P.1, P.2, P.3 and P.4.

Lineage P.2 (B.1.1.28.2, Zeta variant), first detected in October 2020 in the state of Rio de Janeiro, Brazil, only shares one mutation of concern with P.1, which is the E484K.[24] The other P.2 mutations are without concern and rarely found for other variants. The five P.2-specific mutations are: E484K in S-gene, A119S in N-gene, 5’UTR C100U, plus L3468V and synC11824U in ORF1ab-gene. Other mutations commonly found in P.2 are: 3’UTR C29754U, F120F (synC28253U) in ORF8, M234I in the N-gene, plus L3930F and synA12964G in ORF1ab.[25]

Lineage P.3 (Theta variant) was first identified in the Philippines on 18 February 2021 when two mutations of concern were detected in Central Visayas.[26]

The remaining B.1.1.28 derivative virus is lineage P.4. Although researchers have not identified its precise origin, it was first sequenced in Itirapina, Brazil, and was already circulating in various municipalities in the state of São Paulo of the same country. It carries a mutation of concern in the spike protein called L452R which is also present in lineage B.1.617 (Delta and Kappa variants) detected in India, Epsilon variant (lineages B.1.427 and B.1.429) from California, United States.[27][28] The branch of this lineage is P.4.1 (VUI-NP13L)—suspected to have arisen in Goiás, Brazil, around June–July 2020— also rapidly spread to the southeast of the country, where for example Taquara had its first genome sequence, and to the northeast of the nation. It was detected internationally, with reported cases in Japan, Netherlands and England. The P.4.1 has V1176F and D614G mutations in spike protein.[29]

Prevention

Circulation

Development of the Gamma variant
(share of analyzed SARS-CoV-2–positive tests in a given week)
Country Region Sector Test Week 12[30] Week 13 Week 14[31] Week 15 Week 16 Week 17
 Peru Lima Lima Metropolitana 39.70%
Lima Este 63.20%
Lima Norte 50.00%
Lima Sur 41.90%
Central Lima 25.00%
Cajamarca Unknown 75.00%
Cuzco Unknown 70.00%
Madre de Dios Unknown 52.50%
Ucayali Unknown 47.60%
Piura Unknown 25.00%
La Libertad Unknown 25.00%
Ayacucho Unknown 20.00%
Loreto Unknown 08.10% 08.10%
Ancash Unknown 02.50%

Statistics

Cases by country (PANGO)
Country Confirmed cases Suspected cases First detection References
 Canada 19,643 0 7 February 2021 [32][33][34][35]
 Brazil 10,556 0 14 January 2021 [36][5][32]
 Italy 838 0 25 January 2021 [37][38][39][32]
 Germany 276 0 22 January 2021 [40][32]
 Japan 96 0 6 January 2021 [41][42][32]
 Denmark 40 0 3 March 2021 [43][44][32]
 South Korea 3 0 18 January 2021 [45]
 Faroe Islands 1 0 18 January 2021 [46][32]
 Finland 2 0 18 February 2021 [47]
 Ireland 25 0 19 February 2021 [48][49][50][51][52][32]
 United States 15,786 0 25 January 2021 [53][54][55][32]
 Peru 103 0 4 February 2021 [56][57][58][59][60]
 Netherlands 499 0 29 January 2021 [61][32]
 Colombia 165 0 30 January 2021 [62][63][32]
 Croatia 2 0 18 February 2021 [64]
 Turkey 166 0 3 February 2021 [65][66][32][67]
 France 219 0 4 February 2021 [32][68]
 Argentina 230 0 8 February 2021 [69][32]
 Portugal 148 0 11 February 2021 [70][71][72][32]
 Belgium 1,333 0 16 February 2021 [32]
 French Guiana 225 0 16 February 2021 [32]
 Spain 635 0 16 February 2021 [32]
  Switzerland 153 0 16 February 2021 [32]
 Mexico 814 0 28 January 2021 [32]
 Sweden 68 0 20 February 2021 [73][32]
 United Kingdom 155 0 28 February 2021 [32][74][75][76][77]
 India 2 0 17 February 2021 [78]
 Australia 5 0 6 March 2021 [32]
 Romania 5 0 8 March 2021 [79][32]
 Sint Maarten 1 0 10 March 2021 [32]
 Philippines 2 0 13 March 2021 [80][81]
 New Zealand 7 0 18 March 2021 [32]
 Slovenia 4 0 21 March 2021 [32]
 Uruguay 112 0 22 March 2021 [82]
 Chile 975 0 24 March 2021 [83][32]
 Paraguay 53 0 25 March 2021 [84][32]
 Aruba 96 0 29 March 2021 [32]
 Luxembourg 43 0 30 March 2021 [32]
 Jordan 5 0 4 April 2021 [32]
 Costa Rica 32 0 11 April 2021 [32]
 Suriname 106 0 11 April 2021 [32]
 Ecuador 27 0 14 April 2021 [32]
 Singapore 8 0 16 April 2021 [32]
 Norway 4 0 24 February 2021 [32]
 Poland 5 0 13 April 2021 [32]
 Thailand 1 0 5 April 2021 [32]
 Guyane 1 0 3 May 2021 [32]
 Bangladesh 1 0 3 May 2021 [32]
 China 2 0 10 May 2021 [32]
 Lithuania 3 0 10 May 2021 [32]
 Curacao 6 0 24 April 2021 [32]
 Malta 22 0 18 April 2021 [32]
 Austria 17 0 15 April 2021 [32]
 Trinidad and Tobago 14 0 23 April 2021 [85][86][87]
 Haiti 46 0 15 May 2021 [32]
 Cayman Islands 1 0 17 June 2021 [32]
 Bolivia 10 0 19 March 2021 [32]
 Czech Republic 9 0 21 April 2021 [32]
 Dominican Republic 4 0 11 March 2021 [32]
 Israel 9 0 11 April 2021 [32]
 Venezuela 17 0 10 February 2021 [32]
 Taiwan 4 0 20 February 2021 [32]
 Hungary 1 0 22 July 2021 [88]
  World
Total: 63 countries
Total: 52,079 Total: 0 Total as of 27 June 2021
Cases by country (Updated as of 9 August 2021) GISAID[89]
Country Confirmed cases Collection date
 USA 23,373 29 June 2021
 Brazil 16,200 13 June 2021
 Canada 8,070 5 July 2021
 Belgium 1,974 1 July 2021
 Mexico 2,278 24 June 2021
 Chile 2,522 13 June 2021
 Spain 957 26 June 2021
 Italy 2,181 29 June 2021
 Netherlands 566 17 June 2021
 Colombia 346 1 June 2021
 Germany 806 22 June 2021
 France 577 23 June 2021
 Trinidad and Tobago 255 15 June 2021
 Argentina 329 12 May 2021
 French Guiana 318 11 June 2021
 United Kingdom 224 23 June 2021
 Portugal 190 23 June 2021
 Uruguay 173 15 April 2021
  Switzerland 187 21 June 2021
 Aruba 121 20 June 2021
 Japan 118 13 June 2021
 Suriname 117 25 May 2021
 Sweden 141 14 June 2021
 Paraguay 54 4 May 2021
 Denmark 63 29 June 2021
 Haiti 47 20 May 2021
 Luxembourg 2 19 April 2021
 Finland 7 23 May 2021
 Bangladesh 1 18 February 2021
 Barbados 3 22 May 2021
 Cayman Islands 1 17 June 2021
 Faroe Islands 1 12 January 2021
 Guam 1 30 April 2021
 Guyana 3 18 January 2021
 Philippines 2 21 February 2021
 Puerto Rico 1 9 June 2021
 Costa Rica 69 29 June 2021
 Ecuador 145 21 July 2021
 Turkey 88 29 June 2021
 Peru 42 14 June 2021
 Dominican Republic 38 10 June 2021
 Malta 32 22 June 2021
 Ireland 29 21 June 2021
 Austria 28 18 June 2021
 Poland 24 14 July 2021
 Czech Republic 20 22 June 2021
 Israel 19 6 July 2021
 Bolivia 17 2 June 2021
 Venezuela 17 26 May 2021
 Curacao 14 24 June 2021
 Romania 12 12 June 2021
 South Korea 10 3 July 2021
 Norway 9 1 July 2021
 Australia 8 25 April 2021
 Singapore 8 11 June 2021
 Slovenia 7 4 June 2021
 New Zealand 7 31 May 2021
 Croatia 6 29 June 2021
 Lithuania 6 30 June 2021
 Jordan 5 28 April 2021
 Taiwan 4 28 January 2021
 India 3 12 May 2021
 Bosnia and Herzegovina 3 5 July 2021
 China 2 17 April 2021
 Pakistan 1 17 May 2021
 Angola 1 22 March 2021
 Latvia 1 1 April 2021
 Thailand 1 5 April 2021
 Russia 1 21 May 2021
 Greece 1 14 May 2021
 Bonaire 1 7 July 2021
World (71 countries) Total: 63,769 Total as of 9 August 2021

History

On 12 January 2021, the Brazil–United Kingdom CADDE Centre confirmed 13 local cases of lineage P.1 in Manaus, Amazonas state, the largest city of the Amazon rain forest.[5] The new lineage was absent in 27 samples collected from March to November 2020 from Manaus, but it was identified for the same city in 42% (n=13/31) of the samples collected 15–23 December 2020, followed by 52.2% (n=35/67) during 15–31 December 2020 and 85.4% (n=41/48) during 1–9 January 2021. Most notably, the P.2 was rapidly outcompeted by P1 going from the second half of December to 1–9 January, where the lineage P.2 share for Manaus decreased from 25.4% to 6.3%.[5][90]

A study of 180 sequenced Brazilian samples collected in the state of Rio de Janeiro during 2020, identified emergence of the novel lineage P.2 of SARS-CoV-2 (originating from B.1.1.28). P.2 was first detected by genome sequencing in October 2020, but it was estimated to have emerged in early July 2020.[25] As of December 2020, although having significantly increased in frequency throughout the state, it was still largely confined to the state capital Rio de Janeiro. In May 2020 the main lineages behind the COVID-19 positives were B.1.1.33 (70%) and B.1.1.28 (20%), whereas by September the main lineages were B.1.1.33 (50%) and B.1.1.28 (40%), with no detected presence of P.2, while during October and November P.2 was the most common lineage with a share close to 50% (according to the Pangolin tool).[91] The study also found the E484K mutation as "widely spread" across all analysed P.2 samples (36 out of 38).[91]

Researchers at the Oswaldo Cruz Foundation published a preprint genomic epidemiology study of 250 collected genomes from different places in Amazonas and found that P.1 infections can produce nearly 10 times more viral load than in other COVID-19-infected persons involving lineages B.1.1.28 and B.1.195. The lineage also showed 2.2 times higher transmissibility with the same ability to infect both adults (18–59 years old) and older persons (60 years old and higher), suggesting P.1 and its sublineages are more successful at infecting younger humans with no gender differential.[92]

The Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) produced another journal article of samples collected in Manaus between November 2020 and January 2021. The study indicated lineage P.1 to be ≈2.0 times (50% CrI, 1.72.4 times) more transmissible and was shown to be capable of evading ≈32% (50% CrI, 2146%) of inherited immunity from previous coronavirus diseases, leading to the possibility of reinfection. These increased statistics also had the same reflection in fatality, in that P.1 infections can be ≈50% (50% CrI, 2090%) more lethal.[93][94][95] As part of ongoing research, the variant's capacity to neutralise antibodies has been evaluated by scientists in a published preprint work demonstrating that 8 CoronaVac-immunised persons had a poor blood plasma response against lineage P.1. Since the study only had a small number of participants, it was not possible to establish any statistical conclusion as a larger number of vaccinated people would need to be studied.[96] Scientists at MIT, Harvard and Cambridge, and hospitals physicians in Boston, corroborated that people fully vaccinated with Pfizer and Moderna vaccines have significantly decreased neutralisation with P.1—in a preprint work.[97]

See also

Notes

  1. ^ Other names include:
    20J/501Y.V3
    Variant of Concern 202101/02 (VOC-202101/02)[2]
    Brazilian variant or Brazil variant[3][4][5]

References

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