P.1 2023-10-14



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 72773
Countries Brazil 42600, United States of America 18701, Chile 1854, Argentina 1074, Spain 985, Mexico 804, French Guiana 751, France 555, Colombia 512, Peru 417, Germany 353, Suriname 342, Paraguay 333, Trinidad and Tobago 284, Ecuador 283, Canada 213, Netherlands 207, Panama 207, Venezuela 185, Switzerland 174, Sweden 172, Haiti 172, Costa Rica 164, Portugal 159, Uruguay 143, Turkey 140, Italy 131, United Kingdom 96, Belgium 84, Bolivia 69, Dominican Republic 60, Nicaragua 52, Denmark 47, Luxembourg 47, Puerto Rico 40, Japan 38, Aruba 37, Guatemala 36, Austria 29, Ireland 28, 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, Taiwan 6, New Zealand 6, Slovenia 5, Czech Republic 5, Martinique 4, Australia 3, Bosnia and Herzegovina 3, Montenegro 3, India 3, Poland 3, The Bahamas 2, Singapore 2, Philippines 2, Croatia 2, U.S. Virgin Islands 1, Bonaire 1, Laos 1, Angola 1, Honduras 1, El Salvador 1, Lithuania 1, Faroe Islands 1, Cayman Islands 1, Antigua and Barbuda 1, Guadeloupe 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
United States Of America 2021-01-05 27887 4284053
Germany 2021-02-04 995 906251
Brazil 2020-09-22 55544 218480
Sweden 2021-01-27 183 248754
Italy 2021-01-04 2386 163317
France 2021-01-22 821 524287
Peru 2020-12-16 2193 50418
Trinidad And Tobago 2021-04-23 284 2552
Lithuania 2021-04-13 8 31699
Suriname 2021-02-22 343 866
Canada 2020-12-04 13140 490030
Colombia 2021-01-04 542 17624
Portugal 2021-02-09 188 43140
United Kingdom 2021-02-04 221 2645878
Spain 2021-01-29 1294 210981
Belgium 2021-01-29 1920 166203
Netherlands 2021-01-25 579 154697
Argentina 2021-01-24 3008 18079
Ecuador 2021-03-31 300 8220
Chile 2021-01-08 4595 41946
Mexico 2021-01-28 2720 83703
Ireland 2021-02-02 32 96295
Switzerland 2021-01-27 242 132682
Czech Republic 2021-04-21 18 52859
Costa Rica 2021-03-03 184 11273
Poland 2021-04-09 23 81848
Uruguay 2021-02-23 146 609
Austria 2021-04-15 33 64848
Guatemala 2021-04-11 42 4596
Puerto Rico 2021-03-25 64 16447
Japan 2021-01-02 121 605413
Israel 2021-04-11 19 110630
Luxembourg 2021-02-02 974 49608
Haiti 2021-05-12 180 526
Turkey 2021-01-28 159 99153
Australia 2021-03-01 6 177572
Bosnia And Herzegovina 2021-06-28 3 1327
Denmark 2021-02-22 66 585764
Norway 2021-03-14 12 69941
Montenegro 2021-07-27 3 880
Romania 2021-02-25 17 18988
Finland 2021-02-01 19 46119
Malta 2021-04-18 30 655
Paraguay 2021-01-31 348 2897
India 2021-03-24 4 178223
South Korea 2021-01-10 17 130948
Singapore 2021-04-04 8 37892
Aruba 2021-02-15 123 3915
Jordan 2021-03-01 11 837
Taiwan 2021-01-28 6 3856
Nicaragua 2021-04-20 63 553
Curaçao 2021-04-24 14 1898
The Bahamas 2021-07-22 2 246
Slovenia 2021-02-27 10 72812
Dominican Republic 2020-12-22 64 2908
Bolivia 2021-02-07 72 309
New Zealand 2021-03-06 7 36968
Venezuela 2021-01-01 185 1071
Croatia 2021-04-16 7 40287
Laos 2021-11-24 1 972
Iceland 2021-03-20 15 16897
Panama 2021-02-17 217 5573
Belize 2021-05-07 21 987
Bangladesh 2021-02-18 1 5499
Bahrain 2021-07-24 1 10008
Latvia 2021-04-01 2 22873
China 2021-04-17 15 58889
Philippines 2021-02-21 2 22467
Thailand 2021-04-05 1 33344
Russia 2021-04-08 3 63651
Honduras 2021-05-19 4 233
Guyana 2021-09-07 2 112
Angola 2021-03-22 1 574
El Salvador 2021-05-01 1 588
Faroe Islands 2021-01-12 1 3
Greece 2021-05-14 1 25867
Cayman Islands 2021-06-17 1 320
Guadeloupe 2021-07-07 1 2060
Guam 2021-04-30 1 856

Data source and processing

The data on this page is recent as of 2023-10-14, 03:19 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.