P.1 2024-10-16



Description

A lineage first identified in Brazil with variants of biological significance E484K, N501Y and K417T, described in a recent virological post: here. P.1 lineage is an alias of lineage B.1.1.28.1. As described in Rambaut et al., 2020 when the lineage heirarchy reaches a certain depth (length of 5) lineage names are given an alias to prevent them from becoming infinitely long.
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.

Table 1 | Summary of P.1 data

Statistic Information
Countries with sequences 76
Sequence count 73862
Countries Brazil 43136, United States of America 18691, Chile 1853, Argentina 1061, Spain 992, Mexico 805, French Guiana 751, Uruguay 689, France 554, Colombia 521, Peru 415, Germany 353, Suriname 342, Paraguay 333, Trinidad and Tobago 284, Ecuador 282, Canada 213, Netherlands 207, Panama 207, Venezuela 185, Switzerland 174, Sweden 172, Haiti 172, Costa Rica 164, Portugal 159, Turkey 138, Italy 134, United Kingdom 96, Belgium 84, Bolivia 71, Dominican Republic 60, Nicaragua 52, Guatemala 49, Denmark 47, Luxembourg 46, Puerto Rico 40, Japan 38, Aruba 37, Austria 29, Ireland 27, Canary Islands 20, Saint Vincent and the Grenadines 18, South Korea 13, Iceland 13, Israel 12, Jordan 11, Curaçao 11, Norway 10, Romania 10, Malta 10, Finland 7, New Zealand 6, Taiwan 6, Czech Republic 5, Slovenia 5, El Salvador 5, Martinique 4, Poland 3, India 3, Bosnia and Herzegovina 3, Australia 3, Montenegro 3, The Bahamas 2, Philippines 2, Croatia 2, Singapore 2, Lithuania 1, Honduras 1, U.S. Virgin Islands 1, Cayman Islands 1, Angola 1, Guadeloupe 1, Bonaire 1, Laos 1, Antigua and Barbuda 1, Faroe Islands 1
First detected Brazil
Earliest sample date 2020-09-22
Defining SNPs aa:orf1ab:S1188L
aa:orf1ab:K1795Q
del:11288:9
aa:S:L18F
aa:S:T20N
aa:S:P26S
aa:S:D138Y
aa:S:R190S
aa:S:K417T
aa:S:E484K
aa:S:N501Y
aa:S:H655Y
aa:S:T1027I
aa:orf3a:G174C
aa:orf8:E92K
aa:N:P80R

Figure 1 | Cumulative sequence count over time P.1

Bars show the number of new sequences on GISAID over time, binned by epi-week. The line shows the cumulative number of sequences over time.


Figure 2 | Date of earliest_P.1 detected

Schematic map showing the date of the first sequence sample date in each country containing the lineage. Darker countries have earlier first sample dates.


Figure 3 | Map of P.1 sequence counts

Map showing the logged number of sequences of the variant in each country. Countries with more sequences are shown in darker colours.


Figure 4 | Sequence count per country P.1

The number of sequences of the lineage recorded in each country. The height of the bar is the logged number and the numbers above the bar are the raw counts.


Figure 5 | Frequency P.1 in sequences produced since first new variant reported per country

The overall frequency of the lineage, defined as the number of sequences assigned the lineage divided by the total number of sequences from that country in the time since the variant was first sequenced in that country.


Figure 6 | P.1 count per continent

Seven day rolling average of sequence counts per continent. Please note that recent declines may be due to delay in reporting rather than reflecting a change in the underlying virus population.


Figure 7 | Rolling average P.1 frequency per continent

Seven day rolling average of frequency of sequences of the lineage of interest. Frequency is calculated by dividing the number of sequences of the lineage of interest by the total sequences for each continent for each day.


Figure 9 | Air traffic by destination P.1

The number of ticketed origin-to-destination journeys from Manaus, Brazil to countries outside Brazil during October 2020.

Colours indicate numbers of published genomes of P.1 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published P.1 sequences on GISAID. White bars indicate countries with no reports of P.1.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased.



Table 2 | Reported P.1 imports | Country count: 37




Country Earliest report Date local transmission Local transmission Method of surveillance Source
Brazil 2020-12-15 2020-12-15 1 community_sequencing https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
Japan 2021-01-12 0 travellers https://www.niid.go.jp/niid/en/2019-ncov-e/10108-covid19-33-en.html
Italy 2021-01-17 0 travellers https://www.business-standard.com/article/current-affairs/italy-bans-flights-from-brazil-after-covid-variant-detected-in-4-passengers-121011700080_1.html
South Korea 2021-01-10 0 travellers GISAID
Germany 2021-01-22 0 travellers https://www.faz.net/aktuell/rhein-main/nachweis-in-frankfurt-neue-corona-mutation-in-deutschland-17159476.html
Faroe Islands 2021-01-12 0 travellers https://local.fo/in-a-first-european-case-brazilian-coronavirus-variant-confirmed-in-the-faroe-islands/
United States of America 2021-01-25 0 travellers https://twitter.com/SeanW_PHLNGS/status/1353831578342981632?s=20
Netherlands 2021-01-29 community_sequencing https://www.rivm.nl/en/news/brazilian-coronavirus-variants-p1-and-p2-found-in-netherlands
Colombia 2021-01-30 2021-01-31 1 community_sequencing https://twitter.com/INSColombia/status/1356012753656422403?s=20; https://twitter.com/INSColombia/status/1355531730422263809?s=20
Turkey 2021-02-03 community_sequencing https://www.aa.com.tr/en/health/turkey-2-s-africa-1-brazil-variant-detected/2133077
France 2021-01-22 0 community_sequencing https://www.reuters.com/article/health-coronavirus-france-variant/france-registers-four-cases-of-brazilian-coronavirus-variant-says-minister-idUSP6N2I8010
Peru 2021-02-05 0 community_sequencing https://noticias.uol.com.br/ultimas-noticias/afp/2021/02/04/peru-confirma-presenca-da-variante-brasileira-do-coronavirus.htm
Spain 2021-02-05 0 travellers https://www.lavanguardia.com/vida/20210205/6226594/detectado-madrid-primer-caso-variante-brasilena-covid-espana.html
Canada 2021-02-07 0 travellers https://toronto.ctvnews.ca/toronto-reports-canada-s-first-known-case-of-covid-19-variant-first-seen-in-brazil-1.5299345
Argentina 2021-02-08 0 travellers https://g1.globo.com/mundo/noticia/2021/02/08/argentina-detecta-primeiros-casos-de-variantes-brasileiras-do-coronavirus.ghtml
Portugal 2021-02-10 0 community_sequencing https://www.reuters.com/article/health-coronavirus-portugal/portugal-detects-first-cases-of-brazilian-covid-19-variant-sic-tv-says-idUSL8N2KG7KT
Venezuela 2021-02-10 0 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---9-february-2021
Switzerland 2021-02-09 0 community_sequencing https://www.thelocal.ch/20210209/switzerland-records-first-case-of-brazilian-coronavirus-mutation
Belgium 2021-01-31 2021-01-31 1 community_sequencing https://twitter.com/GuyBaele/status/1361414538281672704
India 2021-02-05 0 travellershttps://timesofindia.indiatimes.com/india/south-africa-brazil-mutated-covid-strains-have-reached-india/articleshow/81014842.cms
Mexico 2021-02-16 1 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---16-february-2021
Taiwan 2021-02-20 0 travellers https://www.channelnewsasia.com/news/asia/covid-19-taiwan-confirms-brazil-variant-3-cases-quarantine-14248914
Ireland 2021-02-19 0 travellers https://www.thejournal.ie/three-cases-covid-19-variant-brazil-ireland-5360414-Feb2021/
Finland 2021-02-18 0 travellers https://valtioneuvosto.fi/en/-/1271139/current-covid-19-situation-in-finland-new-virus-variants-cause-concern
Sweden 2021-02-25 1 community_sequencing https://www.foreigner.fi/articulo/coronavirus/sweden-detects-first-brazilian-variant-cases/20210221112458010335.html
Denmark 2021-03-03 0 travellers https://www.reuters.com/article/health-coronavirus-denmark-idUSL5N2L14OT
Aruba 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Chile 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Guadeloupe 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Philippines 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Reunion 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Romania 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Saint Martin 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
United Kingdom 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
United Arab Emirates 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Uruguay 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Panama 2021-04-09 community_sequencing https://www.prensa.com/impresa/panorama/variante-brasilena-se-propaga-en-panama/

Table 3 | Raw data for figures




Country Earliest sequence Number of variant sequences Total sequences since first variant sequence
France 2021-01-22 821 554900
United States Of America 2021-01-05 27902 4529868
Brazil 2020-09-22 56299 234790
Belgium 2021-01-29 1920 170399
Spain 2021-01-29 1310 249543
Sweden 2021-01-27 183 265308
Peru 2020-12-16 2193 54640
Argentina 2021-01-24 3020 19115
Chile 2021-01-08 4594 45345
Mexico 2021-01-28 2734 88124
Canada 2020-12-04 13141 572485
Colombia 2021-01-04 564 18341
Nicaragua 2021-04-20 63 553
Ireland 2021-02-02 32 102154
Luxembourg 2021-02-02 973 52136
Suriname 2021-02-22 343 866
Poland 2021-04-09 23 84636
Italy 2021-01-04 2399 177193
Germany 2021-02-04 995 917536
Bahrain 2021-07-24 1 10377
United Kingdom 2021-02-04 221 2701666
Switzerland 2021-01-27 242 136546
Denmark 2021-02-22 66 611993
Portugal 2021-02-09 188 45161
Trinidad And Tobago 2021-04-23 284 2586
Ecuador 2021-03-31 299 9215
Uruguay 2021-02-19 706 1554
Puerto Rico 2021-03-25 64 20533
New Zealand 2021-03-06 7 46431
Japan 2021-01-02 121 654971
Czech Republic 2021-04-21 18 53825
India 2021-03-24 4 182428
Norway 2021-03-14 12 71252
Netherlands 2021-01-25 579 166477
Austria 2021-04-15 33 67540
South Korea 2021-01-10 17 156786
The Bahamas 2021-07-22 2 258
Australia 2021-03-01 6 195180
Turkey 2021-01-28 157 100805
Lithuania 2021-04-13 8 33609
Costa Rica 2021-03-03 184 12739
Dominican Republic 2020-12-22 64 3222
Venezuela 2021-01-01 185 1212
Panama 2021-02-17 217 5698
Slovenia 2021-02-27 10 74927
Israel 2021-04-11 19 114883
Aruba 2021-02-15 123 3915
Croatia 2021-04-16 7 41596
Paraguay 2021-01-31 348 3214
Iceland 2021-03-20 15 17997
Finland 2021-02-01 19 49063
Bosnia And Herzegovina 2021-06-28 3 1327
Romania 2021-02-25 17 19609
Bolivia 2021-02-07 74 315
Haiti 2021-05-12 180 630
China 2021-04-17 15 83293
Philippines 2021-02-21 2 23381
Guyana 2021-09-07 2 112
Guatemala 2021-04-11 59 5794
Russia 2021-04-08 3 72821
Belize 2021-05-07 21 987
Honduras 2021-05-19 4 416
El Salvador 2021-05-01 5 895
Jordan 2021-03-01 11 912
Singapore 2021-04-04 8 50068
Malta 2021-04-18 30 655
Taiwan 2021-01-28 6 5890
Bangladesh 2021-02-18 1 5707
Montenegro 2021-07-27 3 1029
Curaçao 2021-04-24 14 2019
Cayman Islands 2021-06-17 1 320
Angola 2021-03-22 1 574
Guadeloupe 2021-07-07 1 2114
Laos 2021-11-24 1 1245
Latvia 2021-04-01 2 23042
Guam 2021-04-30 1 901
Thailand 2021-04-05 1 36251
Faroe Islands 2021-01-12 1 3
Greece 2021-05-14 1 32765

Data source and processing

The data on this page is recent as of 2024-10-16, 14:27 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here. The sequences were then assigned lineages with pangolin 4.2, pangoLEARN version 2022-07-09.

Pangolin assigns P.1 to sequences with at least 10 of the 17 defining P.1 SNPs – defined here.

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Acknowledgements

Created by: Áine O'Toole and Verity Hill, Rambaut Group, University of Edinburgh. Flight volume data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer. Sequences sourced from GISAID, full acknowledgements table here.

We have a publication in Wellcome Open Research here describing this web tracker.