P.1 2022-01-22



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 61869
Countries Brazil 34621, United States of America 17923, Chile 1649, Argentina 1015, Spain 837, Mexico 703, Colombia 459, France 439, French Guiana 400, Suriname 342, Peru 333, Paraguay 255, Ecuador 222, Germany 211, Netherlands 204, Canada 176, Switzerland 174, Turkey 174, Sweden 173, Costa Rica 162, Portugal 156, Italy 135, Trinidad and Tobago 120, Uruguay 113, United Kingdom 95, Belgium 84, Bolivia 61, Dominican Republic 53, Haiti 50, Luxembourg 48, Venezuela 47, Denmark 44, Puerto Rico 40, Japan 37, Aruba 37, Guatemala 33, Panama 27, Ireland 26, Austria 25, Israel 12, South Korea 12, Curaçao 11, Jordan 11, Iceland 11, Malta 10, Saint Vincent and the Grenadines 10, Romania 10, Finland 8, Norway 8, New Zealand 6, Taiwan 6, Czech Republic 5, India 5, Slovenia 5, Lithuania 4, Philippines 4, Australia 3, Montenegro 3, Canary Islands 3, Poland 3, Croatia 2, Singapore 2, Bonaire 1, U.S. Virgin Islands 1, The Bahamas 1, Cayman Islands 1, South Africa 1, Antigua and Barbuda 1, Bosnia and Herzegovina 1, Republic of Serbia 1, Angola 1, El Salvador 1, Guyana 1, Faroe Islands 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
United States Of America 2021-01-09 17923 1963713
Italy 2021-01-18 135 76112
Spain 2021-01-29 837 74195
Switzerland 2021-01-27 174 85469
France 2021-01-22 439 140923
United Kingdom 2021-02-04 95 1435630
Brazil 2020-10-01 34621 91406
Chile 2021-01-08 1649 16125
Peru 2020-12-16 333 13149
Mexico 2021-01-28 703 41078
Japan 2021-01-02 37 160102
Suriname 2021-02-22 342 744
Costa Rica 2021-03-03 162 2050
Colombia 2021-01-04 459 7879
Lithuania 2021-04-13 4 20709
Netherlands 2021-01-25 204 79588
Aruba 2021-02-15 37 2881
Puerto Rico 2021-03-25 40 4957
Ecuador 2021-03-31 222 2896
Curaçao 2021-04-24 11 694
Belgium 2021-01-29 84 72550
Sweden 2021-01-27 173 132066
Uruguay 2021-02-23 113 269
Turkey 2021-01-28 174 80172
Luxembourg 2021-02-26 48 16024
Germany 2021-02-05 211 329616
Dominican Republic 2021-03-11 53 735
Portugal 2021-02-09 156 20650
Ireland 2021-02-02 26 41813
New Zealand 2021-03-06 6 5047
Canada 2021-02-24 176 162596
Australia 2021-03-01 3 34751
Czech Republic 2021-06-02 5 18269
Argentina 2021-01-24 1015 7660
Trinidad And Tobago 2021-04-23 120 418
Malta 2021-04-18 10 600
Paraguay 2021-01-31 255 655
India 2021-03-24 5 60902
Denmark 2021-02-22 44 248909
Guatemala 2021-04-30 33 973
Jordan 2021-03-01 11 534
Venezuela 2021-01-01 47 112
Austria 2021-04-15 25 6924
Israel 2021-04-11 12 21408
Montenegro 2021-07-27 3 404
South Korea 2021-01-10 12 20483
Haiti 2021-05-15 50 61
Slovenia 2021-05-05 5 29596
Bolivia 2021-02-20 61 113
Finland 2021-04-02 8 15146
The Bahamas 2021-07-22 1 37
Iceland 2021-03-20 11 4168
Norway 2021-03-14 8 32494
Cayman Islands 2021-06-17 1 41
Taiwan 2021-01-28 6 81
South Africa 2020-12-10 1 18125
Panama 2021-03-11 27 294
Bosnia And Herzegovina 2021-07-05 1 967
Republic Of Serbia 2021-01-26 1 274
Philippines 2020-12-15 4 10950
Croatia 2021-04-16 2 14202
Romania 2021-02-25 10 7696
Singapore 2021-06-11 2 8957
Poland 2021-04-09 3 36903
Angola 2021-03-22 1 381
El Salvador 2021-05-01 1 197
Guyana 2021-01-18 1 51
Faroe Islands 2021-01-12 1 3

Data source and processing

The data on this page is recent as of 2022-01-22, 20:37 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 publication in Wellcome Open Research here describing this web tracker.