Table 1 | Summary of P.1 data
|Countries with sequences||72|
|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|
|Earliest sample date||2020-10-01|
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.
|Country||Earliest sequence||Number of variant sequences||Total sequences since first variant sequence|
|United States Of America||2021-01-09||17092||1113719|
|Trinidad And Tobago||2021-04-23||63||74|
|Bosnia And Herzegovina||2021-07-05||1||39|
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.
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.