Lineage P.1

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Total number of P.1 sequences by country as of 21 April 2021[1]
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

Lineage P.1, also known as 20J/501Y.V3, Variant of Concern 202101/02 (VOC-202101/02)[2] or colloquially known as the Brazil(ian) variant[3][4][5] is one of the variants of SARS-CoV-2, the virus that causes COVID-19.[6] This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid changes, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T.[5][7] This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID), Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier.[5][8] It was subsequently declared to be in circulation in Brazil.[5]

It caused widespread infection in early 2021 in the city of Manaus, capital of Amazonas, although the city had already experienced widespread infection in May 2020[9] with a study[10] indicating high seroprevalence of antibodies for SARS-CoV-2.[11] Early studies, not yet peer-reviewed, indicated as of March 2021 that P.1 infections can produce nearly 10 times more viral load than in other COVID-19-infected persons and showed 1.4–2.2 times higher transmissibility; were more successful infecting younger humans with no gender differential; can be 10–80% more lethal; are capable of evading 25–61% of immunity from previous coronavirus diseases, leading to the possibility of reinfection. At least some vaccines were found to be significantly less effective than against other variants. P.1 has also been called 'B.1.1.28.1',[12] although strictly only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation 'P.1'.[5][13]

P.1 comprises the two distinct subvariants 28-AM-1 and 28-AM-2, which both carry the K417T, E484K, N501Y mutations, and both developed independently of each other within the same Brazilian Amazonas region.[14]

P.1 is notably different from the other Brazilian P.2 lineage (also called 'B.1.1.28.2'[15] or 'VUI-202101/01', which originated from Rio de Janeiro state). In particular, P.2 only carries the E484K mutation and has neither of the other two mutations of concern, N501Y and K417T.[14][7]

Initial reports claimed that both P.1 and P.2 were two separate and different descendants of the Brazilian B.1.1.248 variant.[16][17] However, B.1.1.248 later lost its status as a distinct variant and was reclassified to B.1.1.28.[18]

Research[edit]

On 12 January 2021, the Brazil–United Kingdom CADDE Centre confirmed 13 local cases of the P.1 lineage in Manaus, Amazonas state, the largest city of the Amazon rain forest.[5] The new lineage was absent in 27 samples collected from March to November 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 and 85.4% (n=41/48) during 1–9 January 2021. Most notably, the P2 was rapidly outcompeted by P1 going from the second half of December to 1–9 January, where the P2 variant share for Manaus decreased from 25.4% to 6.3%.[5][19]

A study of 180 sequenced Brazilian samples collected in the state of Rio de Janeiro during 2020, identified emergence of the novel P.2 lineage 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.[20] 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 variants behind the COVID-19 positives were B.1.1.33 (70%) and B.1.1.28 (20%), whereas by September the main variants 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 variant with a share close to 50% (according to the Pangolin tool).[21] The study also found the E484K mutation as "widely spread" across all analyzed P.2 samples (36 out of 38).[21]

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 B.1.1.28 and B.1.195 lineages. The variant 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 lineages are more successful at infecting younger humans with no gender differential.[22]

The Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)[23] produced another preprint manuscript of samples collected in Manaus between November 2020 and January 2021.[non-primary source needed] The study indicated P.1 lineage to be 1.4–2.2 times more transmissible and was shown to be capable of evading 25–61% 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 10–80% more lethal.[24][25][26] As part of ongoing research, the variant's capacity to neutralize antibodies has been evaluated by scientists in a published preprint work demonstrating that 8 CoronaVac-immunized 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.[27] Scientists at MIT, Harvard and Cambridge, and physicians of Boston Hospitals, corroborated that people fully vaccinated with Pfizer and Moderna vaccines have significantly decreased neutralization with P.1—in a preprint work.[28][non-primary source needed]

Mutations[edit]

Defining mutations in Lineage P.1
Gene Amino acid
ORFlab 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 – Lineage P.1 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.[5][29]

In comparison, the mutations of the P.2 lineage (B.1.1.28.2) only share one mutation with P.1, which is the E484K mutation. 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.[20]

Detection[edit]

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.[30]

Circulation of Lineage P.1[edit]

Development of Variant P.1
(share of analyzed SARS-CoV-2–positive tests in a given week)
Country Region Sector Test Week 12[31] Week 13 Week 14[32] Week 15 Week 16 Week 17
 Peru Lima Lima Metropolitana 39.70%
Lima Este 63.20%
Lima Norte 50.00%
Lima Sur 41.90%
Central Lima 25.00%
Cajamarca Unknown 75.00%
Cuzco Unknown 70.00%
Madre de Dios Unknown 52.50%
Ucayali Unknown 47.60%
Piura Unknown 25.00%
La Libertad Unknown 25.00%
Ayacucho Unknown 20.00%
Loreto Unknown 08.10% 08.10%
Ancash Unknown 02.50%

Statistics[edit]

Cases by country
Country Confirmed cases Suspected cases First detection References
 Japan 17 0 6 January 2021 [33][34][35]
 Brazil 1557 0 14 January 2021 [36][5][35]
 South Korea 4 0 18 January 2021 [37]
 Faroe Islands 1 0 18 January 2021 [38][35]
 Denmark 1 0 3 March 2021 [39][40]
 Finland 1 0 18 February 2021 [41]
 Germany 117 0 22 January 2021 [42][35]
 Italy 616 0 25 January 2021 [43][44][45][35]
 Ireland 26 0 19 February 2021 [46][47][48][49][50][35]
 USA 3879 0 25 January 2021 [51][52][53][35]
 Peru 103 0 4 February 2021 [54][55][56][57][58]
 The Netherlands 223 0 29 January 2021 [59][35]
 Colombia 37 0 30 January 2021 [60][61][35]
 Croatia 1 0 18 February 2021 [62]
 Turkey 166 0 3 February 2021 [63][64][35][65]
 France 155 0 4 February 2021 [35][66]
 Canada 4538 0 7 February 2021 [35][67][68][69]
 Argentina 2 0 8 February 2021 [70]
 Portugal 60 0 11 February 2021 [71][72][73]
 Belgium 493 0 16 February 2021 [35]
 French Guiana 61 0 16 February 2021 [35]
 Spain 133 0 16 February 2021 [35]
  Switzerland 45 0 16 February 2021 [35]
 Mexico 29 0 28 January 2021 [35]
 Sweden 33 0 20 February 2021 [74][35]
 United Kingdom 82 0 28 February 2021 [75][76][77][78]
 India 2 0 17 February 2021 [79]
 Australia 6 0 6 March 2021 [35]
 Romania 2 0 8 March 2021 [80]
 Sint Maarten 1 0 10 March 2021 [35]
 Philippines 2 0 13 March 2021 [81][82]
 New Zealand 4 0 18 March 2021 [35]
 Slovenia 1 0 21 March 2021 [35]
 Uruguay 24 0 22 March 2021 [83]
 Chile 156 0 24 March 2021 [84]
 Paraguay 5 0 25 March 2021 [85][35]
 Aruba 11 0 29 March 2021 [35]
 Luxembourg 3 0 30 March 2021 [35]
 Jordan 3 0 4 April 2021 [35]
 Costa Rica 6 0 11 April 2021 [35]
 Suriname 8 0 11 April 2021 [35]
 Ecuador 6 0 14 April 2021 [35]
 Singapore 3 0 16 April 2021 [35]
 Norway 3 0 24 February 2021 [35]
 Poland 2 0 13 April 2021 [35]
 Thailand 1 0 5 April 2021 [35]
 Guyane 1 0 3 May 2021 [35]
 Bangladesh 1 0 3 May 2021 [35]
  World
Total: 48 countries		 Total: 12,631 Total: 0 Total as of 3 May 2021

See also[edit]

References[edit]

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External links[edit]

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