P.1 2021-09-23



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 68850
Countries Brazil 20619, United States of America 20399, Canada 11192, Chile 3419, Mexico 2419, Belgium 1671, Argentina 1065, Spain 926, Luxembourg 925, Peru 782, Italy 760, France 569, Netherlands 549, Germany 435, French Guiana 388, Suriname 324, Colombia 279, Turkey 201, United Kingdom 196, Switzerland 193, Portugal 176, Sweden 168, Ecuador 157, Costa Rica 129, Uruguay 111, Japan 110, Paraguay 81, Trinidad and Tobago 60, Denmark 54, Haiti 47, Puerto Rico 45, Aruba 39, Dominican Republic 36, Austria 28, Ireland 24, Guatemala 22, Malta 22, Finland 19, Czech Republic 18, Venezuela 17, South Korea 15, Curaçao 14, Israel 14, Iceland 14, Bolivia 12, Romania 10, Jordan 10, Poland 9, Norway 8, Singapore 8, New Zealand 7, Slovenia 7, Belize 7, Australia 5, Lithuania 4, Guyana 4, Taiwan 4, Montenegro 3, China 2, Philippines 2, Croatia 2, India 2, Bosnia and Herzegovina 2, Togo 1, Bahamas 1, Angola 1, Faroe Islands 1, Cayman Islands 1, Republic of the Congo 1, Bangladesh 1, U.S. Virgin Islands 1, Antigua and Barbuda 1, Bonaire 1, Sint Maarten 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 20619 33903
Spain 2021-01-29 926 46266
United States Of America 2021-01-09 20399 796243
Chile 2021-01-08 3419 6466
France 2021-01-22 569 71869
Switzerland 2021-01-27 193 40934
Belgium 2021-01-29 1671 39103
Ecuador 2021-03-31 157 1313
Italy 2021-01-04 760 45465
Czech Republic 2021-04-21 18 3980
Turkey 2021-01-28 201 61006
Colombia 2021-01-04 279 1454
Mexico 2021-01-28 2419 23520
Germany 2021-02-05 435 167113
New Zealand 2021-03-06 7 1158
Canada 2021-02-08 11192 64538
Guatemala 2021-04-11 22 327
Peru 2020-12-17 782 4565
United Kingdom 2021-02-04 196 614538
Sweden 2021-01-27 168 95947
Puerto Rico 2021-03-25 45 2111
Portugal 2021-02-09 176 11863
Ireland 2021-02-02 24 25730
Australia 2021-03-01 5 10384
Paraguay 2021-02-13 81 236
Slovenia 2021-04-20 7 9488
Luxembourg 2021-02-02 925 7993
Netherlands 2021-01-25 549 49900
Curaçao 2021-04-24 14 319
Aruba 2021-02-15 39 2266
Austria 2021-04-15 28 4521
Romania 2021-02-25 10 1709
Togo 2021-06-15 1 114
Norway 2021-03-14 8 16071
Singapore 2021-04-04 8 5237
Denmark 2021-02-22 54 107027
Lithuania 2021-04-13 4 9942
Japan 2021-01-02 110 73242
South Korea 2021-01-10 15 7367
Trinidad And Tobago 2021-04-23 60 72
Poland 2021-04-13 9 10571
Venezuela 2021-01-01 17 42
Israel 2021-04-11 14 4106
Iceland 2021-03-20 14 4168
Uruguay 2021-02-23 111 267
Argentina 2021-01-24 1065 2451
Angola 2021-03-22 1 231
Suriname 2021-02-22 324 447
Costa Rica 2021-03-03 129 770
Finland 2021-03-02 19 11641
Jordan 2021-03-01 10 83
Faroe Islands 2021-01-12 1 3
Guyana 2021-01-18 4 5
Cayman Islands 2021-06-17 1 17
China 2021-04-17 2 116
Republic Of Congo 2021-07-01 1 12
Montenegro 2021-07-27 3 55
Bolivia 2021-03-19 12 18
Malta 2021-04-18 22 158
Philippines 2021-02-21 2 2172
Bangladesh 2021-02-18 1 1314
Dominican Republic 2021-03-11 36 231
Haiti 2021-05-15 47 61
Croatia 2021-04-16 2 3540
Belize 2021-05-07 7 62
India 2021-03-24 2 25821
Taiwan 2021-01-28 4 66
Bosnia And Herzegovina 2021-06-28 2 49

Data source and processing

The data on this page is recent as of 2021-09-23, 10:46 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.