P.1 2021-03-07



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 reported 26
Countries with sequences 21
Sequence count 502
Countries Brazil 281, Italy 80, Belgium 24, Peru 23, Switzerland 15, United States of America 14, Germany 14, Colombia 13, France 8, Japan 6, Netherlands 4, Portugal 4, Ireland 3, French Guiana 3, United Kingdom 3, Turkey 2, Mexico 1, Faroe Islands 1, Australia 1, Spain 1, South Korea 1
First detected Brazil
Earliest sample date 2020-12-04
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 8 | Map of P.1 local transmission

Colours indicate reports of imported cases (pink) or of local transmission (darker purple). Data is obtained from news reports and similar sources and is manually maintained.


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: 26

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

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 14 46888
Italy 2021-01-07 80 2958
Switzerland 2021-01-27 15 2966
France 2021-01-22 8 2484
Brazil 2020-12-04 281 674
Netherlands 2021-01-25 4 2676
Colombia 2021-01-04 13 79
Belgium 2021-01-29 24 2199
Mexico 2021-01-28 1 191
Faroe Islands 2021-01-12 1 1
Japan 2021-01-02 6 1911
Portugal 2021-02-09 4 525
Ireland 2021-02-02 3 917
Germany 2021-02-08 14 6493
United Kingdom 2021-02-13 3 14807
Australia 2021-03-01 1 5
Spain 2021-01-29 1 810
South Korea 2021-01-10 1 254
Peru 2020-12-17 23 168
Turkey 2021-01-28 2 812

Data source and processing

The data on this page is recent as of 2021-03-07, 07:38 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 2.3.3, pangoLEARN version 2021-02-21.

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.