SARS-CoV-2 Gamma variant
Gamma variant, also known as lineage P.1,[a] is one of the variants of SARS-CoV-2, the virus that causes COVID-19. 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. 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. It was subsequently declared to be in circulation in Brazil. 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.
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, with a study indicating high seroprevalence of antibodies for SARS-CoV-2. 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.
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.
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.
Initial reports claimed that both P.1 and P.2 were two separate and different descendants of the Brazilian lineage B.1.1.248. However, B.1.1.248 later lost its status as a distinct lineage and was reclassified to B.1.1.28. P.1 has also been called B.126.96.36.199, while P.2 has been B.188.8.131.52 or VUI-202101/01. Since only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation of B.184.108.40.206 to P.1 and B.220.127.116.11 to P.2.
Amino acid mutations of SARS-CoV-2 Gamma variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.
|del11288-11296 (3675-3677 SGF)|
|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.
Descendant and sublineagesEdit
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.18.104.22.168, 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. 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.
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. 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.
|Development of the Gamma variant|
(share of analyzed SARS-CoV-2–positive tests in a given week)
|Country||Region||Sector||Test||Week 12||Week 13||Week 14||Week 15||Week 16||Week 17|
|Madre de Dios||Unknown||52.50%|
|Cases by country (PANGO)|
|Country||Confirmed cases||Suspected cases||First detection||References|
|Canada||19,643||0||7 February 2021|||
|Brazil||10,556||0||14 January 2021|||
|Italy||838||0||25 January 2021|||
|Germany||276||0||22 January 2021|||
|Japan||96||0||6 January 2021|||
|Denmark||40||0||3 March 2021|||
|South Korea||3||0||18 January 2021|||
|Faroe Islands||1||0||18 January 2021|||
|Finland||2||0||18 February 2021|||
|Ireland||25||0||19 February 2021|||
|United States||15,786||0||25 January 2021|||
|Peru||103||0||4 February 2021|||
|Netherlands||499||0||29 January 2021|||
|Colombia||165||0||30 January 2021|||
|Croatia||2||0||18 February 2021|||
|Turkey||166||0||3 February 2021|||
|France||219||0||4 February 2021|||
|Argentina||230||0||8 February 2021|||
|Portugal||148||0||11 February 2021|||
|Belgium||1,333||0||16 February 2021|||
|French Guiana||225||0||16 February 2021|||
|Spain||635||0||16 February 2021|||
|Switzerland||153||0||16 February 2021|||
|Mexico||814||0||28 January 2021|||
|Sweden||68||0||20 February 2021|||
|United Kingdom||155||0||28 February 2021|||
|India||2||0||17 February 2021|||
|Australia||5||0||6 March 2021|||
|Romania||5||0||8 March 2021|||
|Sint Maarten||1||0||10 March 2021|||
|Philippines||2||0||13 March 2021|||
|New Zealand||7||0||18 March 2021|||
|Slovenia||4||0||21 March 2021|||
|Uruguay||112||0||22 March 2021|||
|Chile||975||0||24 March 2021|||
|Paraguay||53||0||25 March 2021|||
|Aruba||96||0||29 March 2021|||
|Luxembourg||43||0||30 March 2021|||
|Jordan||5||0||4 April 2021|||
|Costa Rica||32||0||11 April 2021|||
|Suriname||106||0||11 April 2021|||
|Ecuador||27||0||14 April 2021|||
|Singapore||8||0||16 April 2021|||
|Norway||4||0||24 February 2021|||
|Poland||5||0||13 April 2021|||
|Thailand||1||0||5 April 2021|||
|Guyane||1||0||3 May 2021|||
|Bangladesh||1||0||3 May 2021|||
|China||2||0||10 May 2021|||
|Lithuania||3||0||10 May 2021|||
|Curacao||6||0||24 April 2021|||
|Malta||22||0||18 April 2021|||
|Austria||17||0||15 April 2021|||
|Trinidad and Tobago||14||0||23 April 2021|||
|Haiti||46||0||15 May 2021|||
|Cayman Islands||1||0||17 June 2021|||
|Bolivia||10||0||19 March 2021|||
|Czech Republic||9||0||21 April 2021|||
|Dominican Republic||4||0||11 March 2021|||
|Israel||9||0||11 April 2021|||
|Venezuela||17||0||10 February 2021|||
|Taiwan||4||0||20 February 2021|||
|Hungary||1||0||22 July 2021|||
Total: 63 countries
|Total: 52,079||Total: 0||Total as of 27 June 2021|
|Cases by country (Updated as of 9 August 2021) GISAID|
|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|
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. 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%.
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. 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). The study also found the E484K mutation as "widely spread" across all analysed P.2 samples (36 out of 38).
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.
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. 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. 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.
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These lineages have already formed new sublineages. B.1.1.248 has evolved in N.1 (USA lineage), N.2 (French), N.3 (Argentinian), and N.4 (Chilean). Furthermore, B.1.1.248 has evolved in P.1 (Manaus lineage associated with a constellation of Spike mutations like B.1.1.7 and B.1.351 (Faria et al. 2021)) and P.2 (Rio de Janeiro lineage found in this study).
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Brazilian lineage [B.1.1.248] reassigned B.1.1.28
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P.2...Alias of B.22.214.171.124, Brazilian lineage
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EPI_ISL_792680, EPI_ISL_792681, EPI_ISL_792682, EPI_ISL_792683 - Pathogen Genomics Center, National Institute of Infectious Diseases Pathogen Genomics Center, National Institute of Infectious Diseases - Tsuyoshi Sekizuka, Kentaro Itokawa, Rina Tanaka, Masanori Hashino, Makoto Kuroda
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In an update published Thursday night, federal health officials reported a total of 4,499 variant of concern cases, including: *4,169 cases of the B117 variant, which was first reported in the U.K. *241 cases of the B1351 variant, which was first reported in South Africa. *89 cases of the P1 variant, which was first reported in travellers from Brazil.
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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.
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厚生労働省は10日、ブラジルから羽田空港に2日に到着した10～40代の男女4人が、新型コロナウイルスでこれまで確認されていないタイプの変異種に感染していたと発表した。国内での変異種への感染確認は計34人になった (The Ministry of Health, Labor and Welfare announced on the 10th that four men and women in their teens and 40s who arrived at Haneda Airport from Brazil on the 2nd were infected with a type of mutation that had not been confirmed so far with the new coronavirus.)
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This is the first report in the United States of the P.1 variant...
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