B.1.1.529 2024-09-04



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 106
Sequence count 7655
Countries United States of America 2598, Germany 1038, India 672, Turkey 416, Russia 403, United Kingdom 339, France 227, Italy 180, Spain 134, Belgium 123, Czech Republic 120, Brazil 110, Iceland 71, Argentina 71, Poland 69, Switzerland 65, Thailand 56, Austria 50, Mexico 48, Paraguay 44, Romania 42, Botswana 41, Saudi Arabia 40, Nigeria 37, Australia 34, Chile 30, South Africa 30, Bahrain 29, Slovakia 27, Ireland 24, Pakistan 23, Senegal 23, Egypt 22, Morocco 21, Kazakhstan 21, Indonesia 20, Iran 18, Sweden 16, New Zealand 16, United Arab Emirates 16, Israel 15, Philippines 14, Puerto Rico 13, Colombia 13, Bangladesh 13, Canada 12, Ecuador 12, South Korea 12, Malaysia 11, Slovenia 10, Denmark 10, Peru 10, Ghana 10, Japan 8, Mauritius 7, Panama 6, Vietnam 6, Sri Lanka 6, Lithuania 6, Croatia 6, Kuwait 5, Kenya 5, Netherlands 5, Tunisia 5, Qatar 5, Finland 5, Reunion 4, Brunei 3, Sudan 3, Singapore 3, Guatemala 2, Republic of Serbia 2, Antigua and Barbuda 2, Luxembourg 2, Northern Mariana Islands 2, Cameroon 2, Latvia 2, Ukraine 2, China 2, Belarus 2, Seychelles 2, Venezuela 2, Cote d'Ivoire 1, Portugal 1, Grenada 1, Guinea 1, Malta 1, Jordan 1, Trinidad and Tobago 1, Cabo Verde 1, Norway 1, Syria 1, Cambodia 1, Montenegro 1, Mali 1, Hong Kong 1, Uganda 1, Togo 1, Democratic Republic of the Congo 1, Saint Lucia 1, Guyana 1, Zambia 1, Estonia 1, Uruguay 1, Liechtenstein 1, Saint Vincent and the Grenadines 1
First detected South Africa and Botswana
Earliest sample date 2021-09-29
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 States Of America 2021-09-02 2180564 3448954
France 2021-11-05 319966 419226
Spain 2021-09-01 121268 181394
Belgium 2021-10-11 88574 117325
Israel 2021-09-29 89545 104789
Philippines 2021-11-20 11445 13913
Denmark 2021-10-18 370726 485340
Canada 2021-10-29 288565 404248
Netherlands 2021-11-13 75309 98027
Malaysia 2021-11-08 25677 33892
Germany 2021-11-08 549746 666388
Italy 2021-10-07 80018 115437
India 2021-09-07 83486 131312
Japan 2021-11-27 428841 486310
Switzerland 2021-11-21 50967 68833
United Kingdom 2021-10-07 1342743 1920443
Montenegro 2021-12-04 458 722
South Africa 2021-10-12 21371 25074
Taiwan 2021-12-13 3830 5342
Aruba 2021-12-16 945 1073
Austria 2021-09-25 45819 62017
China 2021-12-04 43125 80287
Romania 2021-12-01 10388 12567
South Korea 2021-11-24 89857 139063
Curaçao 2021-12-16 1211 1352
Peru 2021-11-28 28457 41767
Colombia 2021-10-09 7478 11833
Australia 2021-10-09 128900 174806
Costa Rica 2021-12-10 7336 10312
Sweden 2021-11-19 106783 139616
Benin 2021-12-14 454 455
Chile 2021-10-26 23210 31390
Puerto Rico 2021-11-29 12244 14807
Croatia 2021-12-01 22529 31824
Ireland 2021-11-25 53572 63457
Indonesia 2021-11-29 30757 39067
Myanmar 2021-11-30 93 178
Lithuania 2021-12-09 10245 14557
Brazil 2021-10-31 103977 135722
Poland 2021-09-21 41589 70743
Norway 2021-11-24 34372 40637
Czech Republic 2021-11-11 31579 40385
Slovenia 2021-11-30 33144 41541
Mexico 2021-11-16 40096 50660
Portugal 2021-11-19 22044 27403
Bangladesh 2021-11-27 1736 2541
Brunei 2021-12-16 3962 6597
Thailand 2021-09-12 22249 32099
Namibia 2021-12-02 499 515
Republic Of Serbia 2021-12-12 1618 1656
Guadeloupe 2021-11-02 582 691
New Zealand 2021-12-07 31978 42170
Argentina 2021-10-27 8292 12674
Nigeria 2021-09-03 1929 2723
Slovakia 2021-09-17 25641 38342
Turkey 2021-12-02 20504 27444
Guatemala 2021-12-07 2388 4364
Pakistan 2021-10-07 2358 3323
Hong Kong 2021-11-13 14060 16276
Finland 2021-11-23 21711 28944
Greece 2021-11-29 18413 27450
Luxembourg 2021-12-06 31660 37741
Reunion 2021-09-24 9653 14407
Estonia 2021-12-15 6230 6612
Paraguay 2021-10-10 1920 2467
Trinidad And Tobago 2021-12-16 1562 1988
Botswana 2021-11-11 1508 1644
Sri Lanka 2021-11-24 752 1193
Ecuador 2021-12-02 4527 6066
Latvia 2021-12-07 14126 15531
Cambodia 2021-12-12 1882 2183
Guam 2021-12-20 513 536
Kenya 2021-09-04 3612 4561
Bahrain 2021-12-05 6200 7509
Russia 2021-09-29 40632 63981
Moldova 2021-12-18 645 756
Malawi 2021-12-02 197 199
Georgia 2021-12-14 1947 2567
Singapore 2021-12-02 24745 41374
Panama 2021-12-11 2633 3478
Kyrgyzstan 2021-12-24 42 49
Kosovo 2021-12-16 660 794
Mayotte 2021-12-14 325 373
Iceland 2021-12-01 10691 13794
Dominican Republic 2021-12-02 1251 2373
Jamaica 2021-12-09 2899 3397
Ukraine 2021-12-14 2089 4906
Morocco 2021-12-07 1537 1708
Liechtenstein 2021-12-10 661 793
Bulgaria 2021-12-13 7147 9220
Algeria 2021-12-10 543 665
New Caledonia 2021-12-31 86 97
Egypt 2021-12-01 1625 2370
Mongolia 2021-12-02 757 1085
Iran 2021-11-26 1559 1785
Malta 2021-12-13 138 267
Zambia 2021-11-30 295 371
Qatar 2021-11-27 1393 1731
North Macedonia 2021-12-28 303 439
Kuwait 2022-01-16 525 798
Hungary 2021-12-14 437 637
Saint-Martin 2021-12-14 296 314
Bosnia And Herzegovina 2021-12-08 231 541
Zimbabwe 2021-11-26 249 249
Libya 2022-03-23 22 22
Vietnam 2021-12-21 4744 6112
Venezuela 2021-12-11 600 715
Lebanon 2021-12-03 496 677
Haiti 2021-12-20 326 389
Albania 2021-10-12 776 1570
Mozambique 2021-11-26 325 413
Tunisia 2021-12-02 708 875
Jordan 2021-12-07 248 347
Democratic Republic Of The Congo 2021-10-02 146 204
Senegal 2021-11-25 840 890
Djibouti 2021-12-16 629 632
Saudi Arabia 2021-12-13 587 651
Nepal 2021-11-25 1079 1342
Syria 2022-01-05 72 83
Vanuatu 2022-02-16 93 93
Ivory Coast 2021-12-03 184 261
Oman 2021-12-01 433 761
Kazakhstan 2021-12-10 1836 2354
Uganda 2021-11-23 487 783
Guinea 2021-12-21 287 346
Republic Of Congo 2021-09-12 72 178
Central African Republic 2021-12-20 41 64
Chad 2021-12-30 11 11
Eswatini 2021-11-23 583 652
Papua New Guinea 2021-12-26 775 786
Laos 2022-02-25 711 1073
Ghana 2021-11-10 1337 1399
Andorra 2021-12-17 138 152
Barbados 2021-12-16 214 279
Gibraltar 2021-12-07 112 323
El Salvador 2021-12-05 433 677
Lesotho 2021-11-12 80 82
Gambia 2021-12-17 159 159
Suriname 2021-12-24 132 143
Iraq 2021-11-27 252 380
Ethiopia 2021-12-27 246 250
Saint Lucia 2022-01-21 136 207
Cameroon 2021-10-29 1027 1077
Sudan 2022-01-03 161 183
Belize 2021-12-20 583 642
Uruguay 2021-12-27 226 323
Togo 2021-12-12 257 290
Armenia 2022-01-11 5 7
Bolivia 2021-12-18 115 173
United Arab Emirates 2021-11-10 732 1272
Bhutan 2022-01-05 86 103
Cyprus 2021-12-04 4345 4843
British Virgin Islands 2021-12-17 37 57
Solomon Islands 2022-03-27 218 238
South Sudan 2021-12-13 38 38
Angola 2021-12-21 112 112
Honduras 2021-12-14 163 305
Niger 2022-01-06 31 31
Rwanda 2021-12-09 70 71
Afghanistan 2022-02-13 5 15
Burkina Faso 2021-11-03 37 65
Nicaragua 2021-12-23 63 142
Tanzania 2021-12-18 2 2
Belarus 2022-01-20 40 48
Azerbaijan 2022-01-10 28 36
Mali 2021-12-23 44 59
Cayman Islands 2022-10-10 210 279
Mauritania 2022-05-12 11 14
Palestine 2022-01-19 18 60
Burundi 2021-12-25 9 9
Guyana 2022-01-02 72 74
Liberia 2021-12-14 16 17
Madagascar 2021-12-12 57 69
Uzbekistan 2022-05-26 34 36
The Bahamas 2021-12-15 101 108
Equatorial Guinea 2022-01-03 2 2
East Timor 2022-01-31 1 1
Gabon 2022-06-29 2 2

Data source and processing

The data on this page is recent as of 2024-09-04, 11:04 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 4.2, pangoLEARN version 2022-07-09.

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.