P.1 2021-10-25



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 72
Sequence count 46637
Countries Brazil 20733, United States of America 17092, Chile 1532, Peru 885, Spain 815, Argentina 728, Mexico 664, France 439, French Guiana 395, Colombia 376, Suriname 341, Netherlands 205, Ecuador 196, Germany 187, Turkey 176, Switzerland 170, Sweden 159, Portugal 156, Canada 142, Costa Rica 139, Italy 118, Uruguay 104, United Kingdom 94, Belgium 85, Paraguay 84, Trinidad and Tobago 63, Haiti 49, Luxembourg 48, Denmark 42, Puerto Rico 39, Aruba 38, Japan 36, Dominican Republic 34, Panama 27, Ireland 26, Austria 25, Finland 17, Venezuela 17, Guatemala 16, South Korea 12, Iceland 11, Bolivia 11, Romania 10, Malta 10, Jordan 10, Israel 10, Curaçao 9, Norway 8, New Zealand 6, Taiwan 5, Czech Republic 5, Guyana 4, Slovenia 4, Australia 3, India 3, Poland 3, Montenegro 3, Russia 2, Singapore 2, Croatia 2, The Bahamas 1, Faroe Islands 1, El Salvador 1, Lithuania 1, Cayman Islands 1, Angola 1, U.S. Virgin Islands 1, Antigua and Barbuda 1, Greece 1, Bonaire 1, Philippines 1, Bosnia and Herzegovina 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
France 2021-01-22 439 79602
Canada 2021-02-24 142 92316
Colombia 2021-01-04 376 3258
United States Of America 2021-01-09 17092 1113719
Mexico 2021-01-28 664 28404
Brazil 2020-10-01 20733 43708
Spain 2021-01-29 815 52499
Peru 2020-12-16 885 6513
Suriname 2021-02-22 341 553
Costa Rica 2021-03-03 139 943
Germany 2021-02-05 187 209428
Switzerland 2021-01-27 170 51408
Italy 2021-01-18 118 52059
Chile 2021-01-08 1532 9855
Japan 2021-01-02 36 106793
South Korea 2021-01-10 12 9084
Ireland 2021-02-02 26 30700
Guyana 2021-01-18 4 5
Guatemala 2021-04-30 16 360
Argentina 2021-01-24 728 3615
Turkey 2021-01-28 176 65217
Belgium 2021-01-29 85 50567
Netherlands 2021-01-25 205 56145
Puerto Rico 2021-03-25 39 2534
Sweden 2021-01-27 159 104477
Portugal 2021-02-09 156 14365
New Zealand 2021-03-06 6 1671
Panama 2021-03-11 27 293
Aruba 2021-02-15 38 2556
Luxembourg 2021-02-26 48 9840
Norway 2021-03-14 8 20308
United Kingdom 2021-02-04 94 778252
Trinidad And Tobago 2021-04-23 63 74
Finland 2021-05-03 17 7734
The Bahamas 2021-07-22 1 37
Uruguay 2021-02-23 104 267
Australia 2021-03-01 3 16156
Romania 2021-02-25 10 3789
Ecuador 2021-03-31 196 1678
Malta 2021-04-18 10 158
Curaçao 2021-05-19 9 397
Austria 2021-04-15 25 5258
Haiti 2021-05-15 49 61
Faroe Islands 2021-01-12 1 3
Paraguay 2021-02-13 84 236
Denmark 2021-03-01 42 117224
Slovenia 2021-05-10 4 11996
El Salvador 2021-05-01 1 47
Taiwan 2021-01-28 5 78
Lithuania 2021-04-13 1 12780
Jordan 2021-03-01 10 186
Cayman Islands 2021-06-17 1 28
Angola 2021-03-22 1 274
Dominican Republic 2021-03-11 34 231
Iceland 2021-03-20 11 4168
India 2021-03-24 3 35183
Czech Republic 2021-06-02 5 4846
Bolivia 2021-02-07 11 25
Poland 2021-05-26 3 6561
Montenegro 2021-07-27 3 137
Israel 2021-04-11 10 4106
Russia 2021-05-12 2 3280
Singapore 2021-06-11 2 5542
Venezuela 2021-01-01 17 42
Greece 2021-03-15 1 6830
Philippines 2021-02-21 1 3787
Bosnia And Herzegovina 2021-07-05 1 39
Croatia 2021-04-16 2 5070

Data source and processing

The data on this page is recent as of 2021-10-25, 14:33 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 3.1.3, pangoLEARN version 2021-06-15.

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 pre-print up on virological here describing this web tracker.