SARS-CoV-2 Gamma Variant
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The Gamma variant (P.1) was one of the
variants of SARS-CoV-2 There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or have been stated, to be of particular importance due to their potential ...
, the virus that causes
COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first known case was COVID-19 pandemic in Hubei, identified in Wuhan, China, in December ...
. This
variant Variant may refer to: In arts and entertainment * ''Variant'' (magazine), a former British cultural magazine * Variant cover, an issue of comic books with varying cover art * ''Variant'' (novel), a novel by Robison Wells * " The Variant", 2021 e ...
of
SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...
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 There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or have been stated, to be of particular importance due to their potential ...
,
E484K There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or have been stated, to be of particular importance due to their potenti ...
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 Tokyo (; ja, 東京, , ), officially the Tokyo Metropolis ( ja, 東京都, label=none, ), is the capital and largest city of Japan. Formerly known as Edo, its metropolitan area () is the most populous in the world, with an estimated 37.468 ...
having visited Amazonas,
Brazil Brazil ( pt, Brasil; ), officially the Federative Republic of Brazil (Portuguese: ), is the largest country in both South America and Latin America. At and with over 217 million people, Brazil is the world's fifth-largest country by area ...
, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the
World Health Organization The World Health Organization (WHO) is a specialized agency of the United Nations responsible for international public health. The WHO Constitution states its main objective as "the attainment by all peoples of the highest possible level of h ...
, P.1 has been labeled Gamma variant, and is currently considered a
variant of concern The term variant of concern (VOC) for SARS-CoV-2, which causes COVID-19, is a category used for variants of the virus where mutations in their spike protein receptor binding domain (RBD) substantially increase binding affinity (e.g., N501Y) in ...
. Gamma caused widespread infection in early 2021 in the city of
Manaus Manaus () is the capital and largest city of the Brazilian state of Amazonas. It is the seventh-largest city in Brazil, with an estimated 2020 population of 2,219,580 distributed over a land area of about . Located at the east center of the s ...
, the capital of Amazonas, although the city had already experienced widespread infection in May 2020, with a study indicating high
seroprevalence Seroprevalence is the number of persons in a population who test positive for a specific disease based on serology (blood serum) specimens; often presented as a percent of the total specimens tested or as a proportion per 100,000 persons tested. As ...
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 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.


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. 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.1.1.28.1, while P.2 has been B.1.1.28.2 or VUI-202101/01. 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. Following its detection, genome data for four samples of the new variant were shared to
GISAID GISAID (Global Initiative on Sharing Avian Influenza Data) is a global science initiative and primary source established in 2008 that provides open access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pan ...
having been assigned the ID range: EPI_ISL_792680 to EPI_ISL_792683.


Mutations

File: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. Variants of SARS-CoV-2 As well as having eight mutations (four of these synonymous genetic mutations) in its
open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readin ...
s (ORF1a and ORF1b) – one of which is a set of deletions – Gamma has 10 defining mutations in its
spike protein In virology, a spike protein or peplomer protein is a protein that forms a large structure known as a spike or peplomer projecting from the surface of an enveloped virus. as cited in The proteins are usually glycoproteins that form dimers or ...
, including N501Y and E484K. It also has two mutations – one an insertion – in its
ORF8 ORF8 is a gene that encodes a viral accessory protein, Betacoronavirus NS8 protein, in coronaviruses of the subgenus ''Sarbecovirus''. It is one of the least well conserved and most variable parts of the genome. In some viruses, a deletion sp ...
gene and one in its N gene.


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 Rio de Janeiro () is one of the 27 federative units of Brazil. It has the second largest economy of Brazil, with the largest being that of the state of São Paulo. The state, which has 8.2% of the Brazilian population, is responsible for 9.2% of ...
, 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 The Philippines (; fil, Pilipinas, links=no), officially the Republic of the Philippines ( fil, Republika ng Pilipinas, links=no), * bik, Republika kan Filipinas * ceb, Republika sa Pilipinas * cbk, República de Filipinas * hil, Republ ...
on 18 February 2021 when two mutations of concern were detected in
Central Visayas Central Visayas ( ceb, Tunga-tungang Kabisay-an; tl, Gitnang Kabisayaan) is an administrative region in the Philippines, numerically designated as Region VII. It consists of four provinces: (Cebu, Bohol, Negros Oriental, and Siquijor) and thr ...
. 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 Itirapina is a municipality in the state of São Paulo in Brazil. The population is 18,387 (2020 est.) in an area of 565 km2. The elevation is 770 m. The municipality contains 56% of the Itirapina Ecological Station The Itirapina Ecological ...
, Brazil, and was already circulating in various municipalities in the
state of São Paulo State may refer to: Arts, entertainment, and media Literature * ''State Magazine'', a monthly magazine published by the U.S. Department of State * ''The State'' (newspaper), a daily newspaper in Columbia, South Carolina, United States * ''Our S ...
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 Delta commonly refers to: * Delta (letter) (Δ or δ), a letter of the Greek alphabet * River delta, at a river mouth * D ( NATO phonetic alphabet: "Delta") * Delta Air Lines, US * Delta variant of SARS-CoV-2 that causes COVID-19 Delta may also ...
and
Kappa Kappa (uppercase Κ, lowercase κ or cursive ; el, κάππα, ''káppa'') is the 10th letter of the Greek alphabet, representing the voiceless velar plosive sound in Ancient and Modern Greek. In the system of Greek numerals, has a value o ...
variants) detected in India, Epsilon variant (lineages B.1.427 and B.1.429) from
California California is a U.S. state, state in the Western United States, located along the West Coast of the United States, Pacific Coast. With nearly 39.2million residents across a total area of approximately , it is the List of states and territori ...
, United States. The branch of this lineage is P.4.1 (VUI-NP13L)—suspected to have arisen in
Goiás Goiás () is a Brazilian state located in the Center-West region. Goiás borders the Federal District and the states of (from north clockwise) Tocantins, Bahia, Minas Gerais, Mato Grosso do Sul and Mato Grosso. The state capital is Goiânia. ...
, Brazil, around June–July 2020— also rapidly spread to the southeast of the country, where for example
Taquara Taquara is a municipality in Rio Grande do Sul, Brazil. Taquara is located 72 kilometers (44 miles) from Porto Alegre Porto Alegre (, , Brazilian ; ) is the capital and largest city of the Brazilian state of Rio Grande do Sul. Its pop ...
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.


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. 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 Rio de Janeiro ( , , ; literally 'River of January'), or simply Rio, is the capital of the state of the same name, Brazil's third-most populous state, and the second-most populous city in Brazil, after São Paulo. Listed by the GaWC as a b ...
. 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 The Oswaldo Cruz Foundation (Portuguese ''Fundação Oswaldo Cruz'', also known as FIOCRUZ) is a scientific institution for research and development in biological sciences located in Rio de Janeiro, Brazil; it is considered one of the world's ma ...
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 about more transmissible and was shown to be capable of evading about 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 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 CoronaVac, also known as the Sinovac COVID-19 vaccine, is a whole inactivated virus COVID-19 vaccine developed by the Chinese company Sinovac Biotech. It was Phase III clinical trialled in Brazil, Chile, Indonesia, the Philippines, and Turk ...
-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 Pfizer Inc. ( ) is an American multinational pharmaceutical and biotechnology corporation headquartered on 42nd Street in Manhattan, New York City. The company was established in 1849 in New York by two German entrepreneurs, Charles Pfizer ...
and Moderna vaccines have significantly decreased neutralisation with P.1—in a preprint work.


Extinction

In March 2022, the World Health Organization listed the
Alpha Alpha (uppercase , lowercase ; grc, ἄλφα, ''álpha'', or ell, άλφα, álfa) is the first letter of the Greek alphabet. In the system of Greek numerals, it has a value of one. Alpha is derived from the Phoenician letter aleph , whic ...
,
Beta Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiod ...
and Gamma variants as previously circulating citing lack of any detected cases in the prior weeks and months.


See also

*
Variants of SARS-CoV-2 There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or have been stated, to be of particular importance due to their potential ...
:
Alpha Alpha (uppercase , lowercase ; grc, ἄλφα, ''álpha'', or ell, άλφα, álfa) is the first letter of the Greek alphabet. In the system of Greek numerals, it has a value of one. Alpha is derived from the Phoenician letter aleph , whic ...
,
Beta Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiod ...
,
Delta Delta commonly refers to: * Delta (letter) (Δ or δ), a letter of the Greek alphabet * River delta, at a river mouth * D ( NATO phonetic alphabet: "Delta") * Delta Air Lines, US * Delta variant of SARS-CoV-2 that causes COVID-19 Delta may also ...
,
Epsilon Epsilon (, ; uppercase , lowercase or lunate ; el, έψιλον) is the fifth letter of the Greek alphabet, corresponding phonetically to a mid front unrounded vowel or . In the system of Greek numerals it also has the value five. It was der ...
,
Zeta Zeta (, ; uppercase Ζ, lowercase ζ; grc, ζῆτα, el, ζήτα, label= Demotic Greek, classical or ''zē̂ta''; ''zíta'') is the sixth letter of the Greek alphabet. In the system of Greek numerals, it has a value of 7. It was derived f ...
,
Eta Eta (uppercase , lowercase ; grc, ἦτα ''ē̂ta'' or ell, ήτα ''ita'' ) is the seventh letter of the Greek alphabet, representing the close front unrounded vowel . Originally denoting the voiceless glottal fricative in most dialects, ...
,
Theta Theta (, ; uppercase: Θ or ; lowercase: θ or ; grc, ''thē̂ta'' ; Modern: ''thī́ta'' ) is the eighth letter of the Greek alphabet, derived from the Phoenician letter Teth . In the system of Greek numerals, it has a value of 9. Gr ...
,
Iota Iota (; uppercase: Ι, lowercase: ι; ) is the ninth letter of the Greek alphabet. It was derived from the Phoenician letter Yodh. Letters that arose from this letter include the Latin alphabet, Latin I and J, the Cyrillic І (І, і), Yi (Cy ...
,
Kappa Kappa (uppercase Κ, lowercase κ or cursive ; el, κάππα, ''káppa'') is the 10th letter of the Greek alphabet, representing the voiceless velar plosive sound in Ancient and Modern Greek. In the system of Greek numerals, has a value o ...
,
Lambda Lambda (}, ''lám(b)da'') is the 11th letter of the Greek alphabet, representing the voiced alveolar lateral approximant . In the system of Greek numerals, lambda has a value of 30. Lambda is derived from the Phoenician Lamed . Lambda gave rise ...
, Mu,
Omicron Omicron (; uppercase Ο, lowercase ο, ell, όμικρον) is the 15th letter of the Greek alphabet. This letter is derived from the Phoenician letter ayin: . In classical Greek, omicron represented the close-mid back rounded vowel in contras ...


Notes


References


External links


PANGO lineages: New variant report -Report on global distribution of 3 variants including P.1, a descendent of B.1.1.28

COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK
{{COVID-19 pandemic COVID-19 pandemic in Brazil S003