This report is recent as of 2021-01-18 19:03 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.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here
|Lineage||Country count||Country||Sequence count||Earliest sequence||Travel history|
|B.1.1.7||39||UK 16847, Denmark 192, Netherlands 95, Israel 89, USA 84, Portugal 73, Spain 67, Ireland 49, Finland 40, Italy 36, Australia 29, Slovakia 22, Turkey 21, Iceland 21, Norway 20, France 20, India 19, Switzerland 17, New_Zealand 16, Singapore 15, Sweden 15, Germany 12, Belgium 8, Brazil 5, Hungary 5, Ecuador 4, Jamaica 4, Greece 4, Luxembourg 3, Hong_Kong 3, South_Korea 3, Pakistan 2, Oman 1, Lebanon 1, Peru 1, Canada 1, Sri_Lanka 1, Mexico 1, Romania 1||17847||2020-09-20||15 UK;|
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.
|Countries with sequences||39|
|Likely origin||United Kingdom|