SARS-CoV-2 Gamma variant

Last updated

Total number of P.1 sequences by country as of 21 April 2021
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1,000+ confirmed sequences
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None or no data available 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
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) 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]

Contents

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
GeneAmino 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
ORF8E92K
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)
CountryRegionSectorTestWeek 12 [30] Week 13Week 14 [31] Week 15Week 16Week 17
Flag of Peru.svg  Peru Lima Lima Metropolitana 39.70%
Lima Este 63.20%
Lima Norte 50.00%
Lima Sur 41.90%
Central Lima 25.00%
Cajamarca Unknown75.00%
Cuzco Unknown70.00%
Madre de Dios Unknown52.50%
Ucayali Unknown47.60%
Piura Unknown25.00%
La Libertad Unknown25.00%
Ayacucho Unknown20.00%
Loreto Unknown08.10%08.10%
Ancash Unknown02.50%

Statistics

Cases by country (PANGO)
CountryConfirmed casesSuspected casesFirst detectionReferences
Flag of Canada (Pantone).svg Canada19,64307 February 2021 [32] [33] [34] [35]
Flag of Brazil.svg Brazil10,556014 January 2021 [36] [5] [32]
Flag of Italy.svg Italy838025 January 2021 [37] [38] [39] [32]
Flag of Germany.svg Germany276022 January 2021 [40] [32]
Flag of Japan.svg Japan9606 January 2021 [41] [42] [32]
Flag of Denmark.svg Denmark4003 March 2021 [43] [44] [32]
Flag of South Korea.svg South Korea3018 January 2021 [45]
Flag of the Faroe Islands.svg Faroe Islands1018 January 2021 [46] [32]
Flag of Finland.svg Finland2018 February 2021 [47]
Flag of Ireland.svg Ireland25019 February 2021 [48] [49] [50] [51] [52] [32]
Flag of the United States.svg United States15,786025 January 2021 [53] [54] [55] [32]
Flag of Peru.svg Peru10304 February 2021 [56] [57] [58] [59] [60]
Flag of the Netherlands.svg Netherlands499029 January 2021 [61] [32]
Flag of Colombia.svg Colombia165030 January 2021 [62] [63] [32]
Flag of Croatia.svg Croatia2018 February 2021 [64]
Flag of Turkey.svg Turkey16603 February 2021 [65] [66] [32] [67]
Flag of France.svg France21904 February 2021 [32] [68]
Flag of Argentina.svg Argentina23008 February 2021 [69] [32]
Flag of Portugal.svg Portugal148011 February 2021 [70] [71] [72] [32]
Flag of Belgium (civil).svg Belgium1,333016 February 2021 [32]
Flag of France.svg French Guiana225016 February 2021 [32]
Flag of Spain.svg Spain635016 February 2021 [32]
Flag of Switzerland.svg  Switzerland153016 February 2021 [32]
Flag of Mexico.svg Mexico814028 January 2021 [32]
Flag of Sweden.svg Sweden68020 February 2021 [73] [32]
Flag of the United Kingdom.svg United Kingdom155028 February 2021 [32] [74] [75] [76] [77]
Flag of India.svg India2017 February 2021 [78]
Flag of Australia (converted).svg Australia506 March 2021 [32]
Flag of Romania.svg Romania508 March 2021 [79] [32]
Flag of Sint Maarten.svg Sint Maarten1010 March 2021 [32]
Flag of the Philippines.svg Philippines2013 March 2021 [80] [81]
Flag of New Zealand.svg New Zealand7018 March 2021 [32]
Flag of Slovenia.svg Slovenia4021 March 2021 [32]
Flag of Uruguay.svg Uruguay112022 March 2021 [82]
Flag of Chile.svg Chile975024 March 2021 [83] [32]
Flag of Paraguay.svg Paraguay53025 March 2021 [84] [32]
Flag of Aruba.svg Aruba96029 March 2021 [32]
Flag of Luxembourg.svg Luxembourg43030 March 2021 [32]
Flag of Jordan.svg Jordan504 April 2021 [32]
Flag of Costa Rica.svg Costa Rica32011 April 2021 [32]
Flag of Suriname.svg Suriname106011 April 2021 [32]
Flag of Ecuador.svg Ecuador27014 April 2021 [32]
Flag of Singapore.svg Singapore8016 April 2021 [32]
Flag of Norway.svg Norway4024 February 2021 [32]
Flag of Poland.svg Poland5013 April 2021 [32]
Flag of Thailand.svg Thailand105 April 2021 [32]
Flag of France.svg Guyane103 May 2021 [32]
Flag of Bangladesh.svg Bangladesh103 May 2021 [32]
Flag of the People's Republic of China.svg China2010 May 2021 [32]
Flag of Lithuania.svg Lithuania3010 May 2021 [32]
Flag of Curacao.svg Curacao6024 April 2021 [32]
Flag of Malta.svg Malta22018 April 2021 [32]
Flag of Austria.svg Austria17015 April 2021 [32]
Flag of Trinidad and Tobago.svg Trinidad and Tobago14023 April 2021 [85] [86] [87]
Flag of Haiti.svg Haiti46015 May 2021 [32]
Flag of the Cayman Islands.svg Cayman Islands1017 June 2021 [32]
Bandera de Bolivia (Estado).svg Bolivia10019 March 2021 [32]
Flag of the Czech Republic.svg Czech Republic9021 April 2021 [32]
Flag of the Dominican Republic.svg Dominican Republic4011 March 2021 [32]
Flag of Israel.svg Israel9011 April 2021 [32]
Flag of Venezuela.svg Venezuela17010 February 2021 [32]
Flag of the Republic of China.svg Taiwan4020 February 2021 [32]
Flag of Hungary.svg Hungary1022 July 2021 [88]
 World
Total: 63 countries
Total: 52,079Total: 0Total as of 27 June 2021
Cases by country (Updated as of 9 August 2021) GISAID [89]
CountryConfirmed casesCollection date
Flag of the United States.svg USA23,37329 June 2021
Flag of Brazil.svg Brazil16,20013 June 2021
Flag of Canada (Pantone).svg Canada8,0705 July 2021
Flag of Belgium (civil).svg Belgium1,9741 July 2021
Flag of Mexico.svg Mexico2,27824 June 2021
Flag of Chile.svg Chile2,52213 June 2021
Flag of Spain.svg Spain95726 June 2021
Flag of Italy.svg Italy2,18129 June 2021
Flag of the Netherlands.svg Netherlands56617 June 2021
Flag of Colombia.svg Colombia3461 June 2021
Flag of Germany.svg Germany80622 June 2021
Flag of France.svg France57723 June 2021
Flag of Trinidad and Tobago.svg Trinidad and Tobago25515 June 2021
Flag of Argentina.svg Argentina32912 May 2021
Flag of France.svg French Guiana31811 June 2021
Flag of the United Kingdom.svg United Kingdom22423 June 2021
Flag of Portugal.svg Portugal19023 June 2021
Flag of Uruguay.svg Uruguay17315 April 2021
Flag of Switzerland.svg  Switzerland18721 June 2021
Flag of Aruba.svg Aruba12120 June 2021
Flag of Japan.svg Japan11813 June 2021
Flag of Suriname.svg Suriname11725 May 2021
Flag of Sweden.svg Sweden14114 June 2021
Flag of Paraguay.svg Paraguay544 May 2021
Flag of Denmark.svg Denmark6329 June 2021
Flag of Haiti.svg Haiti4720 May 2021
Flag of Luxembourg.svg Luxembourg219 April 2021
Flag of Finland.svg Finland723 May 2021
Flag of Bangladesh.svg Bangladesh118 February 2021
Flag of Barbados.svg Barbados322 May 2021
Flag of the Cayman Islands.svg Cayman Islands117 June 2021
Flag of the Faroe Islands.svg Faroe Islands112 January 2021
Flag of Guam.svg Guam130 April 2021
Flag of Guyana.svg Guyana318 January 2021
Flag of the Philippines.svg Philippines221 February 2021
Flag of Puerto Rico.svg Puerto Rico19 June 2021
Flag of Costa Rica.svg Costa Rica6929 June 2021
Flag of Ecuador.svg Ecuador14521 July 2021
Flag of Turkey.svg Turkey8829 June 2021
Flag of Peru.svg Peru4214 June 2021
Flag of the Dominican Republic.svg Dominican Republic3810 June 2021
Flag of Malta.svg Malta3222 June 2021
Flag of Ireland.svg Ireland2921 June 2021
Flag of Austria.svg Austria2818 June 2021
Flag of Poland.svg Poland2414 July 2021
Flag of the Czech Republic.svg Czech Republic2022 June 2021
Flag of Israel.svg Israel196 July 2021
Bandera de Bolivia (Estado).svg Bolivia172 June 2021
Flag of Venezuela.svg Venezuela1726 May 2021
Flag of Curacao.svg Curacao1424 June 2021
Flag of Romania.svg Romania1212 June 2021
Flag of South Korea.svg South Korea103 July 2021
Flag of Norway.svg Norway91 July 2021
Flag of Australia (converted).svg Australia825 April 2021
Flag of Singapore.svg Singapore811 June 2021
Flag of Slovenia.svg Slovenia74 June 2021
Flag of New Zealand.svg New Zealand731 May 2021
Flag of Croatia.svg Croatia629 June 2021
Flag of Lithuania.svg Lithuania630 June 2021
Flag of Jordan.svg Jordan528 April 2021
Flag of the Republic of China.svg Taiwan428 January 2021
Flag of India.svg India312 May 2021
Flag of Bosnia and Herzegovina.svg Bosnia and Herzegovina35 July 2021
Flag of the People's Republic of China.svg China217 April 2021
Flag of Pakistan.svg Pakistan117 May 2021
Flag of Angola.svg Angola122 March 2021
Flag of Latvia.svg Latvia11 April 2021
Flag of Thailand.svg Thailand15 April 2021
Flag of Russia.svg Russia121 May 2021
Flag of Greece.svg Greece114 May 2021
Flag of Bonaire.svg Bonaire17 July 2021
World (71 countries)Total: 63,769Total 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]

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SARS-CoV-2 Mu variant Variant of the SARS-CoV-2 virus

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