SARS-CoV-2 Variant

Gamma
General details
WHO Designation	Gamma
Other Names	20J/501Y.V3, Variant of Concern 202101/02 (VOC-202101/02),[1] Brazilian variant or Brazil variant'[2][3][4]
Lineage	P.1
First detected	Tokyo, Japan
Date reported	6 January 2021; 3 years ago (2021-01-06)
Status	Variant of concern
Cases map
Major variants
Alpha (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)
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The Gamma variant (P.1)^[a] was^[6][7] one of the variants of SARS-CoV-2, the virus that causes COVID-19.^[8] This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T.^[4][9] It 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.^[4][10] It was subsequently declared to be in circulation in Brazil.^[4] Under the simplified naming scheme proposed by the World Health Organization, P.1 was labeled Gamma variant, and was considered a variant of concern until March 2022, when it was largely displaced by the delta and omicron variants.^[11]

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,^[12] with a study^[13] indicating high seroprevalence of antibodies for SARS-CoV-2.^[14] 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.^[15]

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.^[16]

Gamma is notably different from the Zeta variant (lineage P.2) which also circulated strongly in Brazil. In particular, Zeta only carries the E484K mutation and has neither of the other two mutations of concern, N501Y and K417T.^[16][9]

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.^[17][18] However, B.1.1.248 later lost its status as a distinct lineage and was reclassified to B.1.1.28.^[19] P.1 has also been called B.1.1.28.1,^[20] while P.2 has been B.1.1.28.2 or VUI-202101/01.^[21] 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.^[4][22]

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.^[23]

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 gene and one in its N gene.^[4][24]

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.^[26] 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.^[27]

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.^[28]

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.^[29][30] 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.^[31]

Prevention

Statistics

Zdroj:https://en.wikipedia.org?pojem=SARS-CoV-2_Gamma_variant
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Cases by country

Country	Confirmed cases (PANGO)	Confirmed cases (GISAID)[32] as of 3 November 2023	First detection	References
United States	15,786	23,373	25 January 2021	[33][34][35][36]
Canada	19,643	8,070	7 February 2021	[36][37][38][39]
Brazil	10,556	16,200	14 January 2021	[40][4][36]
Chile	975	2,522	24 March 2021	[41][36]
Mexico	814	2,278	28 January 2021	[36]
Italy	838	2,181	25 January 2021	[42][43][44][36]
Belgium	1,333	1,974	16 February 2021	[36]
Spain	635	957	16 February 2021	[36]
Luxembourg	43	928	30 March 2021	[36]
Germany	276	806	22 January 2021	[45][36]
France	219	577	4 February 2021	[36][46]
Netherlands	499	566	29 January 2021	[47][36]
Colombia	165	346	30 January 2021	[48][49][36]
Argentina	230	329	8 February 2021	[50][36]
French Guiana	225	318	16 February 2021	[36]
Trinidad and Tobago	14	255	23 April 2021	[51][52][53]
United Kingdom	155	224	28 February 2021	[36][54][55][56][1]
Portugal	148	190	11 February 2021	[57][58][59][36]
Switzerland	153	187	16 February 2021	[36]
Uruguay	112	173	22 March 2021	[60]
Turkey	166	88	3 February 2021	[61][62][36][63]
Ecuador	27	145	14 April 2021	[36]
Sweden	68	141	20 February 2021	[64][36]
Aruba	96	121	29 March 2021	[36]
Japan	96	118	6 January 2021	[65][66][36]
Suriname	106	117	11 April 2021	[36]
Peru	103	42	4 February 2021	[67][68][69][70][71]
Costa Rica	32	69	11 April 2021	[36]
Denmark	40	63	3 March 2021	[72][73][36]
Paraguay	53	54	25 March 2021	[74][36]
Haiti	46	47	15 May 2021	[36]
Dominican Republic	4	38	11 March 2021	[36]
Malta	22	32	18 April 2021	[36]
Ireland	25	29	19 February 2021	[75][76][77][78][79][36]
Austria	17	28	15 April 2021	[36]
Poland	5	24	13 April 2021	[36]
Czech Republic	9	20	21 April 2021	[36]
Israel	9	19	11 April 2021	[36]
Venezuela	17	17	10 February 2021	[36]
Bolivia	10	17	19 March 2021	[36]