B.1.1.529 2022-01-22



Description

A lineage detected in a number of countries with a high number of spike protein mutations, since named the Omicron Variant of Concern by the WHO. Designated through GitHub issues https://github.com/cov-lineages/pango-designation/issues/343
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.

Table 1 | Summary of B.1.1.529 data

Statistic Information
Countries with sequences 51
Sequence count 2597
Countries United States of America 1614, Turkey 368, India 94, Germany 76, Italy 67, United Kingdom 36, Thailand 32, Switzerland 25, Poland 25, Nepal 23, Brazil 22, Denmark 18, Belgium 16, South Africa 14, Spain 14, Botswana 13, Israel 13, Cambodia 12, France 12, Czech Republic 11, Mexico 11, Slovakia 9, Morocco 9, Puerto Rico 8, Slovenia 5, Kazakhstan 5, Colombia 4, Chile 4, Indonesia 3, Australia 3, Singapore 3, Antigua and Barbuda 2, Saint Vincent and the Grenadines 2, Finland 2, Ireland 2, New Zealand 2, Canada 2, Malta 2, Peru 2, Barbados 1, Romania 1, Nigeria 1, Saint-Martin 1, Ghana 1, Jordan 1, South Korea 1, Malaysia 1, Sweden 1, Mali 1, Mauritius 1, Sri Lanka 1
First detected South Africa and Botswana
Earliest sample date 2021-11-12
Defining SNPs del:6513:3
del:11283:9
nuc:C241T
ORF1A:K856R
nuc:C3037T
nuc:T5386G
ORF1A:A2710T
ORF1A:T3255I
ORF1A:P3395H
ORF1A:I3758V
nuc:T13195C
ORF1B:P314L
nuc:C15240T
ORF1B:I1566V
S:A67V
S:T95I
S:G339D
S:S371L
S:S373P
S:K417N
S:N440K
S:G446S
S:S477N
S:T478K
S:E484A
S:Q493R
S:G496S
S:Q498R
S:N501Y
S:T547K
S:D614G
S:H655Y
S:N679K
S:P681H
S:N764K
S:D796Y
S:N856K
S:Q954H
S:N969K
nuc:C25000T
E:T9I
M:D3G
M:Q19E
M:A63T
nuc:A27259C
nuc:C27807T
N:RG203KR


Table 3 | Raw data for figures




Country Earliest sequence Number of variant sequences Total sequences since first variant sequence
United Kingdom 2021-12-02 36 305159
Denmark 2021-12-12 18 34674
India 2021-11-12 94 5828
Botswana 2021-11-15 13 793
United States Of America 2021-11-29 1614 295718
Italy 2021-12-08 67 8038
Germany 2021-12-03 76 46412
Israel 2021-12-13 13 3223
Nepal 2021-11-25 23 101
Belgium 2021-12-10 16 5875
Barbados 2021-12-16 1 1
Indonesia 2021-12-31 3 1014
Cambodia 2021-12-25 12 240
Thailand 2021-12-13 32 1177
Turkey 2021-12-15 368 4236
South Africa 2021-11-18 14 2887
Spain 2021-12-03 14 7977
Slovenia 2021-12-04 5 4111
Switzerland 2021-11-28 25 15384
Puerto Rico 2021-12-10 8 732
France 2021-12-12 12 14324
Slovakia 2021-12-15 9 440
Romania 2021-12-15 1 547
Finland 2021-12-13 2 480
Brazil 2021-12-09 22 2814
Morocco 2021-12-10 9 42
Kazakhstan 2021-12-21 5 7
Colombia 2021-12-04 4 536
Czech Republic 2021-12-22 11 1525
Poland 2021-12-21 25 5592
Mexico 2021-12-05 11 3378
Chile 2021-12-09 4 857
Ireland 2021-12-14 2 1536
New Zealand 2021-12-22 2 744
Nigeria 2021-12-13 1 62
Australia 2021-12-24 3 3171
Saint-Martin 2021-12-15 1 45
Ghana 2021-12-08 1 15
Jordan 2022-01-04 1 5
Canada 2021-12-22 2 2361
South Korea 2021-12-21 1 1096
Malaysia 2022-01-01 1 52
Singapore 2021-12-28 3 706
Sweden 2021-12-15 1 2656
Malta 2022-01-05 2 18
Mali 2021-12-23 1 1
Peru 2021-12-23 2 139
Sri Lanka 2022-01-10 1 9

Data source and processing

The data on this page is recent as of 2022-01-22, 20:37 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 3.1.3, pangoLEARN version 2021-06-15.

Pangolin assigns B.1.1.529 to sequences with at least 32 of the 47 defining B.1.1.529 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.

Acknowledgements

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 publication in Wellcome Open Research here describing this web tracker.