A lineage first identified in South Africa and defined by new variant of concern 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here.
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.
Table 1 | Summary of B.1.351 data
|Countries with sequences||86|
|Countries||South Africa 2644, Germany 1646, France 1547, United States of America 1369, Sweden 1016, Belgium 866, United Kingdom 720, Luxembourg 640, Reunion 604, Netherlands 577, Mayotte 362, Norway 340, Bangladesh 248, Austria 240, Israel 235, Switzerland 213, Zimbabwe 194, Qatar 174, Singapore 173, Turkey 168, Spain 157, Malawi 152, Botswana 116, Denmark 95, Portugal 86, India 77, Ireland 72, Finland 68, Malaysia 66, Australia 62, Kenya 61, Mozambique 58, Japan 58, Czech Republic 53, Equatorial Guinea 46, Italy 45, Slovenia 31, Zambia 31, Greece 31, Eswatini 29, Poland 27, New Zealand 25, Slovakia 23, South Korea 22, Canada 21, Angola 20, Madagascar 17, Lesotho 14, Croatia 11, Rwanda 11, Russia 10, Lithuania 10, Costa Rica 9, Estonia 8, Mexico 8, Philippines 8, Thailand 7, Bahrain 7, Comoros 6, United Arab Emirates 5, Brazil 5, Aruba 4, Democratic Republic of the Congo 4, Sri Lanka 4, Jordan 4, Romania 4, Ghana 4, Suriname 4, Latvia 3, Mauritius 3, Cameroon 3, Panama 2, Chile 2, Guadeloupe 2, Pakistan 2, Sint Maarten 1, Togo 1, Cote d'Ivoire 1, Indonesia 1, Brunei 1, Monaco 1, North Macedonia 1, Gabon 1, Hong Kong 1, Malta 1, French Guiana 1|
|First detected||South Africa|
|Earliest sample date||2020-10-08|
Figure 1 | Cumulative sequence count over time B.1.351
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_B.1.351 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 B.1.351 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 B.1.351
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 B.1.351 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 | B.1.351 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 B.1.351 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 B.1.351 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 B.1.351
The number of ticketed origin-to-destination journeys from South African airports to destinations outside of South Africa during October 2020.
Colours indicate numbers of published genomes of B.1.351 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.351 sequences on GISAID. White bars indicate countries with no reports of B.1.351.
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 count: 68
|Country||Earliest sequence||Number of variant sequences||Total sequences since first variant sequence|
|United States Of America||2021-01-01||1369||311558|
|Democratic Republic Of The Congo||2021-01-22||4||13|
|United Arab Emirates||2020-12-26||5||64|
Data source and processing
The data on this page is recent as of 2021-05-15, 23:02 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 2.4.2, pangoLEARN version 2021-05-12.
Pangolin assigns B.1.351 to sequences with at least 5 of the 9 defining B.1.351 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.