Lineage P.1

Lineage P.1, colloquially known as the Brazil(ian) variant,[1][2][3] is one of the variants of SARS-CoV-2, the virus that causes COVID-19.[4] This variant of SARS-CoV-2 has been named P.1 lineage and has 17 unique amino acid changes, 10 of which in its spike protein, including N501Y and E484K.[5][6] 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.[3][7] 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[8] with a study[9] indicating high seroprevalence of antibodies for SARS-CoV-2.[10]

Research

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][11]

A preprint of a paper by Carolina M Voloch et al. describes relationships between Brazillian 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. It describes 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.[12] It has also been called 'B.1.1.28.1'.[13] 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.[14] The paper identifies 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).[14]

Mutations

This lineage of SARS-CoV-2 has 10 mutations in its spike protein, including N501Y and E484K.[3]

Detection

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.[15]

Statistics
Cases by country
Country Confirmed cases Suspected cases First detection References
 Japan406 January 2021 (2021-01-06)[16][17]
 Brazil51014 January 2021 (2021-01-14)[18][19][20]
 South Korea1018 January 2021 (2021-01-18)[21]
 Faroe Islands1018 January 2021 (2021-01-18)[22][20]
 Germany1022 January 2021 (2021-01-22)[23]
 Italy4025 January 2021 (2021-01-25)[24][25][26]
 USA3025 January 2021 (2021-01-25)[27][28][29][20]
 Peru304 February 2021 (2021-02-04)[30][31][32]
 The Netherlands2029 January 2021 (2021-01-29)[33]
 Colombia1030 January 2021 (2021-01-30)[34][35]
 Turkey103 February 2021 (2021-02-03)[36][37]
 France404 February 2021 (2021-02-04)[20][38]
  WorldTotal: 76Total: 0First detected 6 January 2021
Total as of 5 February 2021		Total: 12 countries

References
  1. Covid-19: Brazil virus already in UK ‘not variant of concern’, scientist says 15 January 2021 www.bbc.com accessed 15 January 2021
  2. 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
  3. "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological. 12 January 2021. Retrieved 23 January 2021.
  4. 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
  5. "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological. 12 January 2021. Retrieved 23 January 2021.
  6. COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK www.cogconsortium.uk, Accessed 25 January 2021
  7. "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Retrieved 14 January 2021.
  8. CNN, Matt Rivers. "Is a new coronavirus variant to blame for this Brazilian city's collapse?". CNN. Retrieved 31 January 2021.
  9. 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.
  10. 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.
  11. Danner, Chas (25 January 2021). "What We Know About the New P.1 Strain of the Coronavirus". nymag.com. Retrieved 28 January 2021.
  12. 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
  13. Marlúcia Seixas (25 January 2021). "Fiocruz Amazon confirms reinfection by a new variation of the Sars-CoV-2". Fiocruz Amazon. Fiocruz, Oswaldo Cruz Foundation.
  14. 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.
  15. "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
  16. "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.
  17. "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.)
  18. 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.
  19. "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". Virological. 12 January 2021. Retrieved 23 January 2021.
  20. "PANGO Lineages - B.1.28". cov-lineages.org. 22 January 2021. Retrieved 22 January 2021.
  21. "S. Korea reports 1st COVID-19 variant case from Brazil". Yonhap News Agency. 18 January 2021. Retrieved 20 January 2021.
  22. Egholm, Sverri (18 January 2021). "In a first European case, Brazilian Covid variant confirmed in Faroe". Local.fo. Retrieved 22 January 2021.
  23. "Coronavirus live news: France death toll surpasses 72,000; Brazil variant found in Germany". The Guardian. London. 22 January 2021. Retrieved 22 January 2021.
  24. "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.
  25. "Covid, first case of Brazilian variant in Italy". Italy 24 News. Italy. 26 January 2021. Retrieved 26 January 2021.
  26. 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.
  27. 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...
  28. Massie, Graeme (26 January 2021). "First case of Brazil coronavirus variant found in the US". The Independent. Los Angeles. Retrieved 26 January 2021.
  29. "US COVID-19 Cases Caused by Variants". cdc.gov. Centers for Disease Control and Prevention. 2 February 2021. Retrieved 3 February 2021.
  30. "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.
  31. "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.
  32. "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.
  33. "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.
  34. "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.
  35. "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.
  36. "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...
  37. "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...
  38. "France registers four cases of Brazilian coronavirus variant, says minister". Reuters. Paris. 4 February 2021. Retrieved 5 February 2021.
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