Lineage P.1

From Wikipedia the free encyclopedia

Countries with confirmed cases of Lineage P.1 as of 8 February 2021.[1]
Legend:
  Local transmission
  Imported transmission
  Unknown method of transmission

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 unique amino acid changes, 10 of which are in its spike protein, including these 3 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 has caused widespread infection in the city of Manaus, despite the fact that the city had already experienced widespread infection in May[9] with a study[10] indicating high seroprevalence of antibodies for SARS-CoV-2.[11] 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]

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.[13]

P.1 is notably different from the other Brazilian P.2 lineage (also called 'B.1.1.28.2' or 'VUI-202101/01', which originated from Rio de Janeiro). In particular, P.2 only carries the E484K mutation and has neither of the other two concerning N501Y and K417T mutations.[13][7]

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, largest city of the Amazon rain forest.[5] The new lineage was absent in samples from March to November from Manaus, but it was identified in 42% of the samples from December 2020 collected in the same city, suggesting a recent increase in frequency.[5][14]

A preprint of a paper by Carolina M Voloch et al. described relationships between Brazilian samples sequenced during 2020 and identified a novel lineage of SARS-CoV-2, 'B.1.1.248', in circulation in Brazil, which originated from B.1.1.28. The paper described it as first emerging in July and first detected by themselves in October, but as of publishing (December 2020), although significantly increased in frequency, it was still largely (61% of cases) confined to the state capital of Rio de Janeiro.[15] In May the majority of their samples had been of lineage B.1.1.33, whereas by September there was significant spread of B.1.1.28, and during October and November, P.1 predominated over respectively 3 and 4 other classifications using the Pangolin tool.[16] The paper identified the change E484K (present in both B.1.1.28 and P.1) as "widely spread" across the samples (for example, 36 out of the 38 samples in one set).[16]

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

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][17]

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.[18]

Statistics[edit]

Cases by country
Country Confirmed cases Suspected cases First detection References
 Japan 6 0 6 January 2021 (2021-01-06) [19][20][21]
 Brazil 258 0 14 January 2021 (2021-01-14) [22][5][21]
 South Korea 1 0 18 January 2021 (2021-01-18) [23]
 Faroe Islands 1 0 18 January 2021 (2021-01-18) [24][21]
 Germany 4 0 22 January 2021 (2021-01-22) [25][21]
 Italy 27 0 25 January 2021 (2021-01-25) [26][27][28][21]
 Ireland 3 0 19 February 2021 (2021-02-19) [29][30][31][32]
 USA 10 0 25 January 2021 (2021-01-25) [33][34][35][21]
 Peru 22 0 4 February 2021 (2021-02-04) [36][37][38][39]
 The Netherlands 5 0 29 January 2021 (2021-01-29) [40]
 Colombia 9 0 30 January 2021 (2021-01-30) [41][42][21]
 Croatia 1 0 18 February 2021 (2021-02-18) [43]
 Turkey 1 0 3 February 2021 (2021-02-03) [44][45]
 France 8 0 4 February 2021 (2021-02-04) [21][46]
 Canada 3 0 7 February 2021 (2021-02-07) [47][21]
 Argentina 2 0 8 February 2021 (2021-02-08) [48]
 Portugal 2 0 11 February 2021 (2021-02-11) [49][50]
 Belgium 15 0 16 February 2021 (2021-02-16) [21]
 French Guiana 2 0 16 February 2021 (2021-02-16) [21]
 Spain 1 0 16 February 2021 (2021-02-16) [21]
  Switzerland 14 0 16 February 2021 (2021-02-16) [21]
 Mexico 1 0 28 January 2021 (2021-01-28) [21]
 Sweden 4 0 20 February 2021 (2021-02-20) [51]
 United Kingdom 6 0 28 February 2021 (2021-02-28) [52]
  World
Total: 24 countries
Total: 406 Total: 0 Total as of 28 February 2021

References[edit]

  1. ^ "P.1 report". cov-lineages.org. Retrieved 8 February 2021.
  2. ^ Public Health England (27 February 2021). "Variants: distribution of cases data". GOV.UK. Retrieved 27 February 2021.
  3. ^ Covid-19: Brazil virus already in UK ‘not variant of concern’, scientist says 15 January 2021 www.bbc.com accessed 15 January 2021
  4. ^ COVID-19: Virologist says Brazilian coronavirus variant detected in UK is not the one 'of concern' 15 January 2021 news.sky.com accessed 15 January 2021
  5. ^ a b c d e f g h i Faria, Nuno R.; et al. (12 January 2021). "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological. Retrieved 23 January 2021.
  6. ^ Third concerning coronavirus variant should be a 'wake up call' to the world, experts warn 12 January 2021 www.telegraph.co.uk, accessed 17 January 2021
  7. ^ a b Covid-19 Genomics UK Consortium (15 January 2021). "COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK" (PDF). www.cogconsortium.uk. Retrieved 25 January 2021.
  8. ^ "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Retrieved 14 January 2021.
  9. ^ Matt Rivers. "Is a new coronavirus variant to blame for this Brazilian city's collapse?". CNN. Retrieved 31 January 2021.
  10. ^ Buss, Lewis F.; Prete, Carlos A.; Abrahim, Claudia M. M.; Mendrone, Alfredo; Salomon, Tassila; de Almeida-Neto, Cesar; França, Rafael F. O.; Belotti, Maria C.; Carvalho, Maria P. S. S.; Costa, Allyson G.; et al. (8 December 2020). "Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic". Science. American Association for the Advancement of Science. 371 (6526): 288–292. doi:10.1126/science.abe9728. ISSN 0036-8075.
  11. ^ Sabino, Ester C.; Buss, Lewis F.; Carvalho, Maria P. S.; Prete, Carlos A.; Crispim, Myuki A. E.; Fraiji, Nelson A.; Pereira, Rafael H. M.; Parag, Kris V.; Peixoto, Pedro da Silva; Kraemer, Moritz U. G.; Oikawa, Marcio K. (27 January 2021). "Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence". The Lancet. 0 (0). doi:10.1016/S0140-6736(21)00183-5. ISSN 0140-6736.
  12. ^ Marlúcia Seixas (25 January 2021). "Fiocruz Amazon confirms reinfection by a new variation of the Sars-CoV-2". Fiocruz Amazon. Fiocruz, Oswaldo Cruz Foundation.
  13. ^ a b Oliver T.R. Toovey, Kirsty N. Harvey, Paul W. Bird, and Julian Wei-Tze Wei-Tze Tang (3 February 2021). "Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK". Elsevier Public Health Emergency Collection. doi:10.1016/j.jinf.2021.01.025. PMC 7857057. PMID 33548358.CS1 maint: multiple names: authors list (link)
  14. ^ Danner, Chas (25 January 2021). "What We Know About the New P.1 Strain of the Coronavirus". nymag.com. Retrieved 28 January 2021.
  15. ^ Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil (Abstract) Carolina M Voloch et al. via www.medrxiv.org, accessed 15 January 2021 doi.org/10.1101/2020.12.23.20248598
  16. ^ a b Voloch, Carolina M.; et al. (2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil". Figure 5. Retrieved 15 January 2021. doi:10.1101/2020.12.23.20248598 – via MedRxiv.
  17. ^ Corum, Jonathan; Zimmer, Carl (24 February 2021). "Coronavirus Variants and Mutations (Section: The P.1 Lineage)". www.nytimes.com. Retrieved 25 February 2021.
  18. ^ "Supplementary Table 1 Acknowledgement Table GISAID" (PDF). virological.org. GISAID. 14 January 2021. p. 10. Retrieved 14 January 2021. 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
  19. ^ "Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil" (PDF) (Press release). Japan: NIID (National Institute of Infectious Diseases). 12 January 2021. Retrieved 14 January 2021.
  20. ^ "新たなコロナ変異種を確認 ブラジルから入国の4人" [New coronavirus Mutation Confirmed in 4 people from Brazil]. The Nikkei (in Japanese). Japan. 10 January 2020. Retrieved 14 January 2021. 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.)
  21. ^ a b c d e f g h i j k l m n "PANGO Lineages - B.1.28". cov-lineages.org. 22 January 2021. Retrieved 14 February 2021.
  22. ^ 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). Sao 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.
  23. ^ "S. Korea reports 1st COVID-19 variant case from Brazil". Yonhap News Agency. 18 January 2021. Retrieved 20 January 2021.
  24. ^ Egholm, Sverri (18 January 2021). "In a first European case, Brazilian Covid variant confirmed in Faroe". Local.fo. Retrieved 22 January 2021.
  25. ^ "Coronavirus live news: France death toll surpasses 72,000; Brazil variant found in Germany". The Guardian. London. 22 January 2021. Retrieved 22 January 2021.
  26. ^ "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.
  27. ^ "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.
  28. ^ 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.
  29. ^ "Statement from the National Public Health Emergency Team on the detection of P1 variant in Ireland - Friday 19 February". Government of Ireland. Department of Health. 19 February 2021. Retrieved 19 February 2021.
  30. ^ McQuinn, Cormac; Cullen, Paul (19 February 2021). "Coronavirus: Three cases of Brazil variant identified in the State for first time". The Irish Times. Retrieved 19 February 2021.
  31. ^ "Three cases of Brazilian virus variant identified in Ireland". RTÉ News and Current Affairs. 19 February 2021. Retrieved 19 February 2021.
  32. ^ Halpin, Hayley (19 February 2021). "Three cases of new Covid-19 variant, first identified in Brazil, reported in Ireland". TheJournal.ie. Retrieved 19 February 2021.
  33. ^ Achenbach, Joel (25 January 2021). "First U.S. case of highly transmissible Brazil coronavirus variant identified in Minnesota". The Washington Post. USA. Retrieved 26 January 2021. This is the first report in the United States of the P.1 variant...
  34. ^ Massie, Graeme (26 January 2021). "First case of Brazil coronavirus variant found in the US". The Independent. Los Angeles. Retrieved 26 January 2021.
  35. ^ "US COVID-19 Cases Caused by Variants". cdc.gov. Centers for Disease Control and Prevention. 2 February 2021. Retrieved 3 February 2021.
  36. ^ "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.
  37. ^ "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.
  38. ^ "Pilar Mazzetti confirma que en Lima, Loreto y Huánuco se ha encontrado la variante brasilera del coronavirus" [Pilar Mazzetti confirms that the Brazilian variant of the coronavirus has been found in Lima, Loreto and Huánuco]. El Comercio (in Spanish). Peru. 4 February 2021. Retrieved 4 February 2021.
  39. ^ "INS identifica 22 casos de variante brasileña" [NIS identifies 22 cases of Brazilian variant]. Diario Correo (in Spanish). Lima. 26 February 2021. Retrieved 26 February 2021.
  40. ^ "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.
  41. ^ "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.
  42. ^ "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.
  43. ^ "Mutated Brazilian Variant of Coronavirus Detected in Croatia by RBI Researchers". total-croatia-news.com. Retrieved 18 February 2021.
  44. ^ "Turkey: 2 S. Africa, 1 Brazil variant detected". aa.com.tr. İstanbul. 4 February 2021. Retrieved 4 February 2021. Two Turkish citizens have contracted the South African variant...
  45. ^ "Turkey: Turkey reports cases of South Africa, Brazil variants of coronavirus". dailysabah.com. İstanbul. 4 February 2021. Retrieved 4 February 2021. Two people in Turkey have contracted the South African variant...
  46. ^ "France registers four cases of Brazilian coronavirus variant, says minister". Reuters. Paris. 4 February 2021. Retrieved 5 February 2021.
  47. ^ "First Brazilian and South African variants of COVID-19 identified in Toronto". CityNews. Toronto. 7 February 2021. Retrieved 10 February 2021. Officials said on Sunday that a patient who had recently travelled from Brazil has tested positive for the P.1 COVID-19 mutation.
  48. ^ "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.
  49. ^ "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.
  50. ^ "Portugal detects first cases of Brazilian COVID-19 variant". The Portugal News. Portugal. 11 February 2021. Retrieved 11 February 2021.
  51. ^ "Brasilianska mutationen i Sverige – saknas resekoppling" [Brazilian mutation in Sweden - no travel connection]. expressen.se (in Swedish). Retrieved 21 February 2021.
  52. ^ "Covid-19: Brazil 'variant of concern' detected in UK". BBC News. UK. 28 February 2021. Retrieved 28 February 2021.

External links[edit]