B.1.1.529 2023-08-24



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 7974
Countries United States of America 2755, Germany 1082, India 682, Turkey 429, Russia 404, United Kingdom 342, France 237, Italy 173, Spain 130, Belgium 129, Czech Republic 121, Brazil 116, Argentina 71, Switzerland 69, Philippines 69, Poland 68, Iceland 67, Thailand 58, Austria 51, Romania 49, Mexico 48, Paraguay 44, Botswana 41, Nigeria 40, Saudi Arabia 40, Australia 34, Slovakia 33, Chile 32, Bahrain 31, South Africa 26, Ireland 25, Senegal 24, Pakistan 23, Indonesia 23, United Arab Emirates 22, Morocco 21, Kazakhstan 21, Iran 19, Egypt 17, Puerto Rico 16, Israel 16, Sweden 15, Peru 14, Malaysia 13, Canada 13, Colombia 13, Ecuador 13, Bangladesh 12, Slovenia 10, New Zealand 10, South Korea 9, Japan 9, Ghana 9, Vietnam 7, Mauritius 7, Denmark 7, Tunisia 7, Sri Lanka 6, Croatia 6, Lithuania 6, Panama 6, Kuwait 5, Kenya 5, Qatar 5, Netherlands 4, Reunion 4, Singapore 3, Sudan 3, Venezuela 3, Brunei 3, Belarus 3, Cameroon 2, Latvia 2, Guatemala 2, Northern Mariana Islands 2, Ukraine 2, Republic of Serbia 2, Guyana 2, Uruguay 2, Antigua and Barbuda 2, Luxembourg 2, Seychelles 2, Zambia 1, Cambodia 1, Guinea 1, Hong Kong 1, Uganda 1, Democratic Republic of the Congo 1, Saint Vincent and the Grenadines 1, Estonia 1, Portugal 1, Saint Lucia 1, Mali 1, Syria 1, Jordan 1, Cabo Verde 1, Malta 1, Greece 1, Trinidad and Tobago 1, Montenegro 1, Liechtenstein 1, China 1, Norway 1, Grenada 1, Togo 1, Cote d'Ivoire 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 2058627 3171848
Luxembourg 2021-12-06 30232 34939
Australia 2021-10-09 118733 155860
Indonesia 2021-11-29 29636 37318
Brazil 2021-10-31 97725 119803
Ireland 2021-11-25 49669 57262
Germany 2021-11-08 543771 655291
Malaysia 2021-11-08 23557 30708
Nigeria 2021-09-03 1666 2436
Italy 2021-10-07 75123 102619
Japan 2021-11-27 405348 428162
Belgium 2021-10-11 86699 111955
India 2021-09-07 80807 126893
Trinidad And Tobago 2021-12-16 1548 1856
Saint Lucia 2022-01-21 136 175
Sweden 2021-11-19 99251 122131
New Zealand 2021-12-07 25935 30192
Republic Of Serbia 2021-12-12 1616 1654
France 2021-11-05 304739 383660
United Kingdom 2021-10-07 1303243 1856026
Argentina 2021-10-27 7867 11595
Chile 2021-10-26 21523 27835
Norway 2021-11-24 33653 39151
Poland 2021-09-21 40754 68256
Portugal 2021-11-19 20670 25068
Israel 2021-09-29 86059 99400
Mexico 2021-11-16 37829 44656
Croatia 2021-12-01 22221 29896
Netherlands 2021-11-13 68621 86583
Denmark 2021-11-22 344639 400930
Canada 2021-10-29 250029 319977
Turkey 2021-12-02 20035 25725
Kazakhstan 2021-12-10 1357 1570
Austria 2021-09-25 44842 59122
Philippines 2021-11-20 11203 12959
Switzerland 2021-11-21 49088 64585
Kenya 2021-09-04 3322 4010
South Africa 2021-10-12 20143 23146
Djibouti 2021-12-16 629 632
Puerto Rico 2021-11-29 9616 11186
Bulgaria 2021-12-13 7084 8747
Ecuador 2021-12-02 4165 5084
Andorra 2021-12-17 138 152
Brunei 2021-12-16 3761 6187
Czech Republic 2021-11-11 31118 39158
Peru 2021-11-28 26201 36889
Mayotte 2021-12-14 323 371
Cambodia 2021-12-12 1702 1974
Hong Kong 2021-11-13 12436 13453
Singapore 2021-12-02 16827 28089
Finland 2021-11-23 20512 25453
Spain 2021-09-01 99262 142850
Estonia 2021-12-15 6148 6518
Thailand 2021-09-12 20418 28907
Pakistan 2021-12-08 2157 2809
Slovenia 2021-11-30 32608 39437
Reunion 2021-09-24 9579 13638
Georgia 2021-12-14 1878 2216
Lithuania 2021-12-09 9739 12647
Curaçao 2021-12-16 1148 1227
Guadeloupe 2021-11-02 551 631
Moldova 2021-12-18 587 685
Paraguay 2021-10-10 1809 2164
Russia 2021-09-29 37558 54773
Greece 2021-11-29 16644 20151
Latvia 2021-12-07 13585 14968
Montenegro 2021-12-04 437 571
Liechtenstein 2021-12-10 661 793
Romania 2021-12-01 10184 11305
North Macedonia 2021-12-28 239 256
South Korea 2021-11-24 78768 106009
Jamaica 2021-12-09 2891 3187
Slovakia 2021-09-17 25173 36877
Costa Rica 2021-12-10 6836 9364
Venezuela 2021-12-11 492 574
Uganda 2021-11-23 440 581
Kosovo 2021-12-16 643 752
Colombia 2021-10-09 7316 11121
Syria 2022-01-05 72 80
Panama 2021-12-11 2524 3347
Bangladesh 2021-11-27 1637 2295
China 2021-12-04 29453 52185
Taiwan 2021-12-13 2631 3264
Mozambique 2021-11-26 306 392
Kuwait 2022-01-16 469 680
Ghana 2021-11-10 1334 1395
Angola 2021-12-21 112 112
Jordan 2021-12-07 200 267
Iran 2021-11-26 1547 1694
Zimbabwe 2021-11-26 249 249
Senegal 2021-11-25 714 726
Belize 2021-12-20 583 642
Vietnam 2021-12-21 4627 5802
Dominican Republic 2021-12-02 952 2031
Botswana 2021-11-11 1480 1616
Sudan 2022-01-03 161 183
Algeria 2021-12-10 466 550
Morocco 2021-12-07 1164 1268
Guinea 2021-12-21 281 329
Ukraine 2021-12-14 1275 2675
Mongolia 2021-12-02 737 933
Nepal 2021-11-25 1000 1259
Malta 2021-12-13 138 267
Barbados 2021-12-16 149 175
Iceland 2021-12-01 9858 12459
Myanmar 2021-11-30 61 121
Guam 2021-12-20 483 489
Saint-Martin 2021-12-14 295 313
Nicaragua 2021-12-23 63 142
Zambia 2021-11-30 293 369
Hungary 2021-12-14 381 439
Bosnia And Herzegovina 2021-12-08 194 495
Sri Lanka 2021-11-24 741 1179
Guatemala 2021-12-07 1736 3432
Haiti 2021-12-20 302 324
Papua New Guinea 2021-12-26 775 786
Laos 2022-02-25 605 796
Malawi 2021-12-02 197 199
Gibraltar 2021-12-07 112 323
Bahrain 2021-12-05 6183 7142
Aruba 2021-12-16 945 1043
Bolivia 2021-12-18 115 173
Iraq 2021-11-27 248 357
Ivory Coast 2021-12-03 159 195
Egypt 2021-12-01 1157 1652
Eswatini 2021-11-23 560 563
Palestine 2022-01-19 12 25
Qatar 2021-11-27 1364 1539
Lebanon 2021-12-03 472 604
Oman 2021-12-01 121 324
Solomon Islands 2022-03-27 218 238
Namibia 2021-12-02 498 512
Rwanda 2021-12-09 70 71
Democratic Republic Of The Congo 2021-10-02 121 174
Cameroon 2021-10-29 988 1037
New Caledonia 2021-12-31 59 60
Republic Of Congo 2021-09-12 71 177
Gambia 2021-12-17 159 159
South Sudan 2021-12-13 28 28
Lesotho 2021-11-12 79 81
Niger 2022-01-06 31 31
El Salvador 2021-12-05 302 390
Honduras 2021-12-14 60 122
Saudi Arabia 2021-12-13 578 610
Central African Republic 2021-12-20 39 60
Suriname 2021-12-24 132 143
Uruguay 2021-12-27 202 224
Tunisia 2021-12-02 561 634
Kyrgyzstan 2021-12-24 42 49
Albania 2021-10-12 767 1340
Benin 2021-12-14 454 454
British Virgin Islands 2021-12-17 37 57
Cyprus 2021-12-21 396 420
Mali 2021-12-23 44 59
United Arab Emirates 2021-11-10 732 1272
Togo 2021-12-12 182 208
Ethiopia 2021-12-27 96 98
Libya 2022-03-23 22 22
Armenia 2022-01-11 5 7
Madagascar 2021-12-12 57 69
Burkina Faso 2021-11-03 29 54
Cayman Islands 2022-10-10 210 279
Chad 2021-12-30 4 4
Guyana 2022-01-02 72 74
Liberia 2021-12-14 12 12
The Bahamas 2021-12-15 90 96
Mauritania 2022-05-12 1 1
Afghanistan 2022-02-13 2 3
Bhutan 2022-01-05 82 92
Burundi 2021-12-25 9 9
Azerbaijan 2022-01-10 20 20
Vanuatu 2022-02-16 93 93
Belarus 2022-01-20 40 48
Tanzania 2021-12-18 2 2
Equatorial Guinea 2022-01-03 2 2
Uzbekistan 2022-05-26 34 36
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 2023-08-24, 10:12 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.