SARS-CoV-2 Gamma variant

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File:Lineage P.1 sequences by country as of 21 April 2021.svg
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,[lower-alpha 1] 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), 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 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 diseased people has greater chance of transmissibility and death than B.1.1.28 infected.[13]

Variant Gamma 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

  • SARS-CoV-2 Gamma variant.svg

    Amino acid mutations of SARS-CoV-2 Gamma variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.[22]

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

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See also: CoronaVac § Variants

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]
  World
Total: 62 countries		 Total: 52,078 Total: 0 Total as of 27 June 2021
Cases by country (Updated as of 6 July 2021) GISAID[88]
Country Confirmed cases Last Case Reported
USA 18,307 29 June 2021
Brazil 12,456 13 June 2021
Canada 7,459
Belgium 1,518 1 July 2021
Mexico 1,285 24 June 2021
Chile 1,185 13 June 2021
Spain 786 26 June 2021
Italy 551 29 June 2021
Netherlands 518 17 June 2021
Colombia 316 1 June 2021
Germany 312 22 June 2021
France 280 23 June 2021
Trinidad and Tobago 250 15 June 2021
Argentina 236 12 May 2021
French Guiana 225 11 June 2021
United Kingdom 200 23 June 2021
Portugal 176 23 June 2021
Uruguay 171 15 April 2021
Switzerland 162 21 June 2021
Aruba 116 20 June 2021
Japan 108 13 June 2021
Suriname 108 25 May 2021
Sweden 70 14 June 2021
Paraguay 53 4 May 2021
Denmark 49 29 June 2021
Haiti 47 20 May 2021
Luxembourg 47 21 May 2021
Ecuador 36 18 June 2021
Costa Rica 32 21 May 2021
Ireland 27 27 May 2021
Peru 25 22 February 2021
Austria 24 10 June 2021
Malta 24 21 June 2021
Turkey 23 29 March 2021
Bolivia 17 2 June 2021
Venezuela 17 26 May 2021
Czech Republic 13 9 June 2021
Dominican Republic 12 10 June 2021
Israel 11 16 May 2021
Singapore 8 11 June 2021
Australia 7 25 April 2021
New Zealand 7 31 May 2021
Norway 7 15 June 2021
Poland 7 19 June 2021
Curaçao 6 28 May 2021
Romania 6 25 May 2021
Jordan 5 28 April 2021
Slovenia 4 31 May 2021
Taiwan 4 28 January 2021
Lithuania 3 31 May 2021
South Korea 3 3 April 2021
China 2 17 April 2021
Croatia 2 19 April 2021
Finland 2 23 May 2021
Bangladesh 1 18 February 2021
Barbados 1 22 May 2021
Cayman Islands 1 17 June 2021
Faroe Islands 1 12 January 2021
Guam 1 30 April 2021
Guyana 1 18 January 2021
Philippines 1 21 February 2021
Puerto Rico 1 9 June 2021
World (62 countries) Total: 47,333 Total as of 6 July 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][89]

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).[90] The study also found the E484K mutation as "widely spread" across all analysed P.2 samples (36 out of 38).[90]

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.[91]

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, 1.7–2.4 times) more transmissible and was shown to be capable of evading ≈32% (50% CrI, 21–46%) 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, 20–90%) more lethal.[92][93][94] 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.[95] 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.[96]

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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External links

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