SARS-CoV-2 Gamma variant

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SARS-CoV-2 Variant
Gamma
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom. Coronavirus. SARS-CoV-2.png
Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom.
General details
WHO DesignationGamma
Other Names20J/501Y.V3, Variant of Concern 202101/02 (VOC-202101/02), [1] Brazilian variant or Brazil variant' [2] [3] [4]
LineageP.1
First detectedTokyo, Japan
Date reported6 January 2021;3 years ago (2021-01-06)
Status Variant of concern
Cases map
Total number of P.1 sequences by country as of 21 April 2021 Legend: .mw-parser-output .legend{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .legend-color{display:inline-block;min-width:1.25em;height:1.25em;line-height:1.25;margin:1px 0;text-align:center;border:1px solid black;background-color:transparent;color:black}.mw-parser-output .legend-text{} 1,000+ confirmed sequences 500-999 confirmed sequences 100-499 confirmed sequences 2-99 confirmed sequences 1 confirmed sequence 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
Major variants

The Gamma variant (P.1) [lower-alpha 1] 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]

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, [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
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
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]

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. [25]

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

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. [4] 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%. [4] [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. [27] 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 about 2.0 times (50% CrI, 1.7–2.4 times) more transmissible and was shown to be capable of evading about 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 about 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]

Extinction

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. [11]

See also

Notes

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

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  40. ↑ Biernath, André (14 January 2021). "Coronavirus: qué se sabe sobre la nueva variante encontrada en Brasil (y que llegó a Japón)" [Coronavirus: what is known about the new variant found in Brazil (and that reached Japan)]. BBC Brasil (in Spanish). São Paulo . Retrieved 18 January 2021. Los científicos analizaron el material genético de 31 muestras de pacientes con covid-19 en la ciudad de Manaos... ...De ellos, 13 individuos (el 42% del total) presentaban justamente ese nuevo linaje del virus. Scientists analyzed the genetic material of 31 samples from patients with covid-19 in the city of Manaus... ...Of them, 13 individuals (42% of the total) presented precisely this new lineage of the virus.
  41. ↑ "Circulación de variantes SARS-CoV-2 en Chile" [Circulation of SARS-CoV-2 variants in Chile](PDF).
  42. ↑ "Covid, variante brasiliana: primo caso identificato a Varese" [Covid, Brazilian variant: first case identified in Varese]. ADN Kronos (in Italian). Italy. 25 January 2021. Retrieved 26 January 2021.
  43. ↑ "Covid, first case of Brazilian variant in Italy". Italy 24 News. Italy. 26 January 2021. Archived from the original on 30 January 2021. Retrieved 26 January 2021.
  44. ↑ Ronza, Veronica (26 January 2021). "Covid, è allarme per la variante brasiliana: altri tre casi rilevati in Italia" [Covid alarm for the Brazilian variant: three other cases detected in Italy]. Vesuvio Live (in Italian). Retrieved 2 February 2021.
  45. ↑ "Coronavirus live news: France death toll surpasses 72,000; Brazil variant found in Germany". The Guardian . London. 22 January 2021. Retrieved 22 January 2021.
  46. ↑ "France registers four cases of Brazilian coronavirus variant, says minister". Reuters . Paris. 4 February 2021. Retrieved 5 February 2021.
  47. ↑ "Brazilian coronavirus variants (P1 and P2) found in the Netherlands" (Press release). The Netherlands: RIVM. National Institute for Public Health and the Environment. 29 January 2021. Retrieved 31 January 2021.
  48. ↑ "Colombia mantiene vigilancia de cepa brasileña de covid-19" [Colombia maintains surveillance of the Brazilian strain of covid-19]. minsalud.gov.co (in Spanish). Bogotá. 30 January 2021. Retrieved 31 January 2021. The case of a Colombian-Brazilian woman who acquired the new strain and consulted the health services in Leticia is confirmed.
  49. ↑ "Colombia detecta su primer caso de variante brasileña del coronavirus" [Colombia detects its first case of Brazilian variant of the coronavirus]. La Vanguardia (in Spanish). Bogotá. 30 January 2021. Retrieved 31 January 2021.
  50. ↑ "First Brazilian variants of COVID-19 identified in Buenos Aires". Semana . Buenos Aires. 8 February 2021. Retrieved 10 February 2021. Officials said on Monday that two patients who had recently travelled from Brazil has tested positive for the P.1 COVID-19 mutation.
  51. ↑ Ministry of Health, Trinidad and Tobago (23 April 2021). "Brazilian Variant Found in Additional COVID-19 Samples". Government of Trinidad and Tobago Ministry of Health. Retrieved 24 May 2021.
  52. ↑ Ministry of Health, Trinidad and Tobago (26 April 2021). "5 Additional COVID-19 samples Confirmed to be the Brazilian Variant". Government of Trinidad and Tobago Ministry of Health. Retrieved 24 May 2021.
  53. ↑ "5 more cases of Brazilian covid19 variant in Trinidad and Tobago". Trinidad and Tobago Newsday. 26 April 2021. Retrieved 24 May 2021.
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  55. ↑ "Covid: Four more cases of Brazil variant found in England". BBC News . London. 11 March 2021. Retrieved 11 March 2021.
  56. ↑ "COVID-19: New Philippines-linked coronavirus variant investigated in England after two cases found". Sky News . UK. 16 March 2021. Retrieved 17 March 2021.
  57. ↑ "Portugal detecta primeiros casos da variante brasileira" [Portugal detects first cases of the Brazilian variant]. terra.com. Portugal. 11 February 2021. Retrieved 11 February 2021.
  58. ↑ "Portugal detects first cases of Brazilian COVID-19 variant". The Portugal News . Portugal. 11 February 2021. Retrieved 11 February 2021.
  59. ↑ "INSA identifica mais três casos da variante brasileira (a somar aos sete já conhecidos)" [INSA identifies three more cases of the Brazilian variant (in addition to the seven already known)]. Observador. Retrieved 4 March 2021.
  60. ↑ "Coronavirus: variante P.1 se detectó en casos de Artigas, Canelones, Fray Bentos, Montevideo, Rocha, Salto y San José" [Coronavirus: variant P.1 was detected in cases from Artigas, Canelones, Fray Bentos, Montevideo, Rocha, Salto and San José]. Retrieved 23 March 2021.
  61. ↑ "Turkey: 2 S. Africa, 1 Brazil variant detected". aa.com.tr. Istanbul. 4 February 2021. Retrieved 4 February 2021. Two Turkish citizens have contracted the South African variant...
  62. ↑ "Turkey: Turkey reports cases of South Africa, Brazil variants of coronavirus". dailysabah.com. Istanbul. 4 February 2021. Retrieved 4 February 2021. Two people in Turkey have contracted the South African variant...
  63. ↑ Jeyhun Aliyev, Dilara Hamit Turkey: 85% of new COVID-19 cases due to UK variant S.Africa COVID variant seen in 285 people in 11 of Turkey's 81 provinces, Brazil strain seen in 166 people: Health minister 12 April 2021 www.aa.com.tr, accessed 24 April 2021
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  67. ↑ "Loreto: Diresa reporta caso de variante de Covid-19 procedente de Manaos" [ Loreto: Diresa reports case of variant of Covid-19 from Manaus]. Peru.21 (in Spanish). Iquitos. 20 January 2021. Retrieved 21 January 2021.
  68. ↑ "Loreto: DIRESA aclara que variante de Manaos aún no llega a la región" [Loreto: DIRESA clarifies that Manaus variant has not yet reached the region]. Canal N (in Spanish). Peru. 21 January 2021. Retrieved 27 January 2021.
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