South African lineage defined by new variant 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here
This report is recent as of 2021-01-22 17:25 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 v2.1.7, pangoLEARN version 2021-01-11.
Pangolin assigns B.1.351 to any sequences with more than 5 of the 9 defining B.1.351 SNPs, defined in the preprint here.
| Lineage | Country count | Country | Sequence count | Earliest sequence | Travel history |
|---|---|---|---|---|---|
| B.1.351 | 18 | South_Africa 447, UK 73, Australia 7, France 6, Belgium 6, Botswana 6, Germany 5, Ireland 3, Kenya 2, Switzerland 2, Finland 2, South_Korea 1, Sweden 1, Norway 1, Netherlands 1, New_Zealand 1, Denmark 1, Spain 1 | 566 | 2020-10-08 | 1 Maldives/South; |
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.
| Statistic | Information |
|---|---|
| Count | 566 |
| Likely origin | South Africa |
| SNPs | aa:E:P71L aa:N:T205I aa:orf1a:K1655N aa:S:D80A aa:S:D215G aa:S:K417N aa:S:A701V aa:S:N501Y aa:S:E484K |
The number of ticketed origin-to-destination journeys from South African airports to countries outside 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 >300 passengers.
Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased. Also, this data will not reflect volume of traffic over land or other modes of transport.
Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer
Country count: 24
| Country | Earliest sequence | Number of variant sequences | Total sequences since first variant sequence |
|---|---|---|---|
| South Korea | 2020-12-26 | 1 | 9 |
| United Kingdom | 2020-12-10 | 73 | 35822 |
| Sweden | 2020-12-24 | 1 | 75 |
| France | 2020-12-22 | 6 | 133 |
| Australia | 2020-12-10 | 7 | 341 |
| Germany | 2020-12-21 | 5 | 132 |
| Kenya | 2020-12-15 | 2 | 6 |
| South Africa | 2020-10-08 | 447 | 813 |
| Norway | 2020-12-27 | 1 | 21 |
| Switzerland | 2020-12-14 | 2 | 1339 |
| Finland | 2020-12-19 | 2 | 40 |
| Ireland | 2020-12-22 | 3 | 127 |
| Netherlands | 2020-12-22 | 1 | 461 |
| New Zealand | 2020-12-29 | 1 | 26 |
| Denmark | 2021-01-04 | 1 | 4195 |
| Belgium | 2020-12-20 | 6 | 290 |
| Botswana | 2020-12-17 | 6 | 6 |
| Spain | 2020-12-24 | 1 | 231 |