grinch | global report investigating novel coronavirus haplotypes

B.1.1.7 report 2021-01-18



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

Figure 1 | Cumulative sequence count over time B.1.1.7

2021-01-18T20:32:14.906967 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 2 | Date of earliest B.1.1.7 detected

2021-01-18T20:32:12.993806 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/