Gamma variant, also known as lineage P.1,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.22.214.171.124, while P.2 has been B.126.96.36.199 or VUI-202101/01. Since only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation of B.188.8.131.52 to P.1 and B.184.108.40.206 to P.2.
Following its detection, genome data for four samples of the new variant were shared to GISAID having been assigned the ID range:
|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.
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.220.127.116.11, 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.
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.
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.
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), also known as the coronavirus, is the virus that causes COVID-19, the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019. First identified in the city of Wuhan, Hubei, China, the World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. As described by the US National Institutes of Health, it is the successor to SARS-CoV-1, the virus that caused the 2002–2004 SARS outbreak.
"Cluster 5", also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), is a variant of SARS-CoV-2, the virus that causes COVID-19, that is believed to be extinct. It was discovered in North Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of North Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic.
The Alpha variant, also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several variants of concern, the variant is estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. It was first detected in November 2020 from a sample taken in September in the United Kingdom, and began to spread quickly by mid-December, around the same time as infections surged. This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant is also notable for having more mutations than normally seen.
Beta variant, also known as lineage B.1.351, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa in October 2020, which was reported by the country's health department on 18 December 2020. Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay area in July or August 2020.
The COVID-19 Genomics UK Consortium (COG-UK) is a group of public health agencies and academic institutions in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the Wellcome Sanger Institute. The consortium is known for first identifying the SARS-CoV-2 Alpha variant in November 2020. As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to the GISAID sequencing database originated from COG-UK.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them.
The following is a timeline of the COVID-19 pandemic in the United States during 2021.
The term variant of concern (VOC) for severe acute respiratory syndrome coronavirus 2 is a category used when mutations in Receptor Binding Domain (RBD) substantially increase binding affinity in RBD-hACE2 complex, while also being linked to rapid spread in human populations.
Iota variant, also known as lineage B.1.526, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in New York City in November 2020. The variant has appeared with two notable mutations: the E484K spike mutation, which may help the virus evade antibodies, and the S477N mutation, which may help the virus bind more tightly to human cells.
The Delta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The Delta variant was named on 31 May 2021 and had spread to over 163 countries by 24 August 2021. The World Health Organization (WHO) indicated that the Delta variant is becoming the dominant strain globally.
Theta variant, also known as lineage P.3, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. The variant was first identified in the Philippines on February 18, 2021, when two mutations of concern were detected in Central Visayas. It was detected in Japan on March 12, 2021, when a traveler from the Philippines arrived at Narita International Airport in Tokyo.
INSACOG is the forum set up under the Ministry of Health and Family Welfare by the Government of India on 25 December 2020, to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India. Initially it was tasked to study the virus variant Lineage B.1.1.7 earlier found in United Kingdom in December 2020. INSACOG works as a consortium of 28 national laboratories for genome sequencing located in different parts of India. All these 10 laboratories are required to share 5% of positive samples to INSACOG for further research and studies. A National Centre for Disease Control (NCDC) nodal unit maintain a database of all samples of the new variants. Two national genomic sequencing database centers are appointed 1) National Institute of Biomedical Genomics and 2) CSIR Institute of Genomics and Integrative Biology. In its early research INSACOG identefied virus variant Lineage B.1.617 referred to as a double mutation variant.
Kappa variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It is one of the three sublineages of Pango lineage B.1.617. The SARS-CoV-2 Kappa variant is also known as lineage B.1.617.1 and was first detected in India in December 2020. By the end of March 2021, the Kappa sub-variant accounted for more than half of the sequences being submitted from India. On 1 April 2021, it was designated a Variant Under Investigation (VUI-21APR-01) by Public Health England.
Lineage B.1.617 is a lineage of SARS-CoV-2, the virus that causes COVID-19. It first came to international attention in late March 2021 after the newly established INSACOG performed genome sequencing on positive samples throughout various Indian states. Analysis of samples from Maharashtra had revealed that compared to December 2020, there was an increase in the fraction of samples with the E484Q and L452R mutations. Lineage B.1.617 later came to be dubbed a double mutant by news media.
Lambda variant, also known as lineage C.37, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Peru in August 2020. On 14 June 2021, the World Health Organization (WHO) named it Lambda variant and designated it as a variant of interest. It has spread to at least 30 countries around the world and is known to be more resistant to neutralizing antibodies compared to other strains. There is evidence that suggests the Lambda variant is both more infectious and resistant to vaccines than the Alpha and/or Gamma variant.
Epsilon variant, also known as CAL.20C and referring to two PANGO lineages B.1.427 and B.1.429, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in California, USA in July 2020.
Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.
The Eta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. The Eta variant or lineage B.1.525, also called VUI-21FEB-03 by Public Health England (PHE) and formerly known as UK1188, 21D or 20A/S:484K, does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion as found in Alpha, N439K variant and Y453F variant.
The Mu variant, also known as lineage B.1.621 or VUI-21JUL-1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Colombia in January 2021 and was designated by the WHO as a variant of interest on August 30, 2021. The WHO said the variant has mutations that indicate a risk of resistance to the current vaccines and stressed that further studies were needed to better understand it. Outbreaks of the Mu variant were reported in South America and Europe. The B.1.621 lineage has a sublineage, labeled B.1.621.1 under the PANGO nomenclature, which has already been detected in more than 20 countries worldwide.
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).
Brazilian lineage [B.1.1.248] reassigned B.1.1.28
P.2...Alias of B.18.104.22.168, Brazilian lineage
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
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.
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.
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.)
This is the first report in the United States of the P.1 variant...
The case of a Colombian-Brazilian woman who acquired the new strain and consulted the health services in Leticia is confirmed.
Two Turkish citizens have contracted the South African variant...
Two people in Turkey have contracted the South African variant...
Officials said on Monday that two patients who had recently travelled from Brazil has tested positive for the P.1 COVID-19 mutation.
Tests by the National Public Health Centre (NNK) showed the presence of the Delta variant of the coronavirus in 14 new cases and the gamma variant in one new case, the prime minister's chief of staff said on Thursday.