P.1 2022-09-13



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 77
Sequence count 68795
Countries Brazil 39591, United States of America 18566, Chile 1738, Argentina 1065, Spain 839, Mexico 750, French Guiana 719, France 553, Colombia 477, Peru 376, Suriname 342, Paraguay 330, Trinidad and Tobago 283, Ecuador 274, Germany 227, Netherlands 207, Canada 204, Panama 193, Switzerland 171, Sweden 171, Turkey 171, Costa Rica 164, Portugal 159, Italy 141, Uruguay 134, United Kingdom 101, Belgium 84, Venezuela 70, Bolivia 65, Dominican Republic 55, Luxembourg 47, Denmark 45, Puerto Rico 41, Nicaragua 39, Haiti 39, Japan 38, Aruba 37, Guatemala 36, Austria 28, Ireland 27, Canary Islands 20, Saint Vincent and the Grenadines 18, South Korea 13, Iceland 13, Israel 12, Curaçao 11, Jordan 11, Romania 10, Malta 10, Norway 9, Finland 8, New Zealand 6, Czech Republic 6, Taiwan 6, Slovenia 5, Martinique 4, Poland 3, India 3, Australia 3, Bosnia and Herzegovina 3, Montenegro 3, Singapore 2, Philippines 2, South Africa 2, The Bahamas 2, Croatia 2, Honduras 1, Lithuania 1, Antigua and Barbuda 1, Angola 1, Guadeloupe 1, El Salvador 1, Cayman Islands 1, Guyana 1, U.S. Virgin Islands 1, Bonaire 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
Brazil 2020-09-22 51721 165178
United States Of America 2021-01-09 27649 3444670
Argentina 2021-01-24 2944 13122
Canada 2020-12-04 13130 352160
Italy 2021-01-04 2386 127555
Belgium 2021-01-29 1919 146100
Mexico 2021-01-28 2724 69221
France 2021-01-22 822 426361
Dominican Republic 2020-12-22 59 1446
Spain 2021-01-29 1129 132697
Colombia 2021-01-04 506 13187
Switzerland 2021-01-27 239 119633
Chile 2021-01-08 4344 31720
Suriname 2021-02-22 343 866
Costa Rica 2021-03-03 185 6244
Trinidad And Tobago 2021-04-23 283 1772
Netherlands 2021-01-25 580 124753
Uruguay 2021-02-23 146 403
Luxembourg 2021-02-02 974 38049
Germany 2021-02-04 866 743915
Panama 2021-03-04 201 4396
Austria 2021-04-15 32 28052
Puerto Rico 2021-03-25 65 9866
Paraguay 2021-01-31 348 1818
Ecuador 2021-03-31 295 5882
Venezuela 2021-01-01 70 485
Sweden 2021-01-27 182 199266
United Kingdom 2021-02-04 221 2471640
Peru 2020-12-16 2161 28359
Japan 2021-01-02 121 365785
Honduras 2021-05-19 4 157
Turkey 2021-01-28 193 93718
Israel 2021-04-11 19 90544
Poland 2021-04-09 23 75382
Belize 2021-05-07 21 788
Lithuania 2021-04-13 8 30277
Bolivia 2021-02-07 68 179
Portugal 2021-02-09 188 35986
Singapore 2021-04-04 8 20643
Denmark 2021-02-22 64 502408
Nicaragua 2021-04-20 47 351
Romania 2021-02-25 17 14742
Malta 2021-04-18 30 655
Ireland 2021-02-02 31 77122
South Korea 2021-01-10 17 51119
Slovenia 2021-02-27 10 60701
Guatemala 2021-04-11 42 1956
Aruba 2021-02-15 123 3329
Finland 2021-02-01 20 34421
Iceland 2021-03-20 15 5353
Bangladesh 2021-02-18 1 4994
Curaçao 2021-04-24 14 1625
New Zealand 2021-03-06 7 18840
Philippines 2021-02-21 2 16962
Haiti 2021-05-15 55 132
Angola 2021-03-22 1 533
Australia 2021-03-01 6 108117
Czech Republic 2021-04-21 19 43801
Guadeloupe 2021-07-07 1 1898
India 2021-03-24 4 151379
South Africa 2021-07-28 2 21777
Jordan 2021-03-01 11 766
The Bahamas 2021-07-22 2 152
El Salvador 2021-05-01 1 408
Taiwan 2021-01-28 6 2319
Bosnia And Herzegovina 2021-06-28 3 1213
Cayman Islands 2021-06-17 1 41
Montenegro 2021-07-27 3 769
Croatia 2021-04-16 7 32691
Russia 2021-05-08 1 13422
Norway 2021-03-14 11 61882
Thailand 2021-04-05 1 23333
Guyana 2021-01-18 3 125
Bahrain 2021-07-24 1 6913
Guam 2021-04-30 1 716
Latvia 2021-04-01 2 13762
Faroe Islands 2021-01-12 1 3
China 2021-04-17 2 1044
Greece 2021-05-14 1 12700

Data source and processing

The data on this page is recent as of 2022-09-13, 04:50 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.