P.1 2022-06-24



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 74
Sequence count 66066
Countries Brazil 37543, United States of America 18415, Chile 1738, Argentina 1049, Spain 842, Mexico 709, Colombia 473, France 454, French Guiana 407, Peru 359, Suriname 342, Paraguay 328, Trinidad and Tobago 282, Ecuador 262, Germany 225, Netherlands 206, Canada 202, Panama 192, Switzerland 173, Sweden 171, Turkey 168, Costa Rica 164, Portugal 158, Uruguay 136, Italy 134, United Kingdom 101, Belgium 84, Venezuela 70, Bolivia 65, Dominican Republic 59, Haiti 51, Luxembourg 47, Denmark 45, Puerto Rico 41, Nicaragua 39, Japan 38, Aruba 37, Guatemala 35, Austria 27, Ireland 27, Saint Vincent and the Grenadines 18, Israel 12, South Korea 12, Iceland 11, Jordan 11, Curaçao 11, Malta 10, Romania 10, Norway 9, Finland 7, New Zealand 6, Taiwan 6, Slovenia 5, Czech Republic 5, Poland 3, Australia 3, Montenegro 3, India 3, Bosnia and Herzegovina 3, Canary Islands 3, Singapore 2, Croatia 2, The Bahamas 2, Lithuania 1, Antigua and Barbuda 1, U.S. Virgin Islands 1, Philippines 1, Faroe Islands 1, El Salvador 1, Cayman Islands 1, Honduras 1, Bonaire 1, Guyana 1, Angola 1
First detected Brazil
Earliest sample date 2020-10-01
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
Chile 2021-01-08 4344 24965
Guyana 2021-01-18 3 125
United States Of America 2021-01-09 27592 3011677
Brazil 2020-09-22 49637 140707
Canada 2020-12-04 13097 303252
Guatemala 2021-04-11 42 1622
Puerto Rico 2021-03-25 65 8227
Spain 2021-01-29 1130 116391
Mexico 2021-01-28 2707 56416
France 2021-01-22 702 273300
Germany 2021-02-04 865 653981
Italy 2021-01-04 2380 110510
Belgium 2021-01-29 1918 116177
Switzerland 2021-01-27 239 114064
Israel 2021-04-11 19 58267
Portugal 2021-02-09 188 32131
Colombia 2021-01-04 504 10733
Panama 2021-03-04 201 3590
Austria 2021-04-15 32 19094
Peru 2020-12-17 2156 20135
Netherlands 2021-01-25 581 112587
United Kingdom 2021-02-04 221 2376221
Argentina 2021-01-24 2939 12160
Belize 2021-05-07 21 546
Venezuela 2021-01-01 70 412
Romania 2021-02-25 17 13088
Costa Rica 2021-03-03 185 4333
Iceland 2021-03-20 15 4173
Finland 2021-02-01 19 30702
Turkey 2021-01-28 195 90930
Ecuador 2021-03-31 286 4549
Suriname 2021-02-22 343 866
Aruba 2021-02-15 123 3070
New Zealand 2021-03-06 7 10352
Japan 2021-01-02 121 281236
Sweden 2021-01-27 182 183563
Bolivia 2021-02-07 68 130
Poland 2021-04-09 23 72408
Dominican Republic 2020-12-22 62 1053
Ireland 2021-02-02 31 63833
Luxembourg 2021-02-02 973 30633
Denmark 2021-02-22 64 459511
Singapore 2021-04-04 8 16355
Norway 2021-03-14 11 57612
Malta 2021-04-18 30 655
Trinidad And Tobago 2021-04-23 283 1211
Australia 2021-03-01 6 84411
Uruguay 2021-02-23 146 403
Croatia 2021-04-16 7 28474
Haiti 2021-05-15 55 132
Honduras 2021-05-19 4 157
Jordan 2021-03-01 11 731
Czech Republic 2021-04-21 18 38553
Lithuania 2021-04-13 8 30277
Montenegro 2021-07-27 3 613
Paraguay 2021-01-31 348 1496
Latvia 2021-04-01 2 9070
South Korea 2021-01-10 17 38579
Curaçao 2021-04-24 14 1371
Philippines 2021-02-21 2 15751
Nicaragua 2021-04-20 47 346
Russia 2021-05-08 1 10272
Bangladesh 2021-02-18 1 4650
India 2021-03-24 4 125684
Taiwan 2021-01-28 6 192
Bosnia And Herzegovina 2021-06-28 3 1193
Slovenia 2021-02-27 10 57345
Guam 2021-04-30 1 653
Greece 2021-05-14 1 10110
The Bahamas 2021-07-22 2 152
Faroe Islands 2021-01-12 1 3
China 2021-04-17 2 823
El Salvador 2021-05-01 1 356
Cayman Islands 2021-06-17 1 41
Bahrain 2021-07-24 1 1657
Thailand 2021-04-05 1 20042
Angola 2021-03-22 1 532

Data source and processing

The data on this page is recent as of 2022-06-24, 20:45 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 3.1.20, pangoLEARN version 2022-02-02.

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.