Data source and processing

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

Table 1 | Summary of sequence data

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;

Lineage B.1.1.7

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.

Table B.1.1.7 | Lineage B.1.1.7

Statistic	Information
Sequence count	17847
Countries with sequences	39
Countries reported	57
Likely origin	United Kingdom
SNPs	aa:orf1ab:T1001I aa:orf1ab:A1708D aa:orf1ab:I2230T del:11288:9 del:21765:6 del:21991:3 aa:S:N501Y aa:S:A570D aa:S:P681H aa:S:T716I aa:S:S982A aa:S:D1118H aa:Orf8:Q27* aa:Orf8:R52I aa:Orf8:Y73C aa:N:D3L aa:N:S235F