B.1.1.529 2024-05-24



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 7652
Countries United States of America 2598, Germany 1038, India 672, Turkey 416, Russia 401, 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 29, Bahrain 29, Slovakia 27, Ireland 24, Senegal 23, Pakistan 23, Egypt 22, Kazakhstan 21, Morocco 21, Indonesia 20, Iran 18, Sweden 16, New Zealand 16, United Arab Emirates 16, Israel 15, Philippines 14, Bangladesh 13, Puerto Rico 13, Colombia 13, Ecuador 12, South Korea 12, Canada 12, Malaysia 11, Slovenia 10, Peru 10, Ghana 10, Denmark 10, Japan 8, Mauritius 7, Vietnam 6, Croatia 6, Panama 6, Sri Lanka 6, Lithuania 6, Netherlands 5, Kenya 5, Tunisia 5, Qatar 5, Kuwait 5, Finland 5, Reunion 4, Singapore 3, Sudan 3, Brunei 3, Seychelles 2, Venezuela 2, Latvia 2, China 2, Antigua and Barbuda 2, Northern Mariana Islands 2, Cameroon 2, Luxembourg 2, Republic of Serbia 2, Ukraine 2, Guatemala 2, Belarus 2, Saint Lucia 1, Cambodia 1, Trinidad and Tobago 1, Malta 1, Liechtenstein 1, Mali 1, Uruguay 1, Zambia 1, Jordan 1, Guinea 1, Estonia 1, Guyana 1, Montenegro 1, Cote d'Ivoire 1, Syria 1, Uganda 1, Hong Kong 1, Grenada 1, Democratic Republic of the Congo 1, Togo 1, Saint Vincent and the Grenadines 1, Norway 1, Portugal 1, Cabo Verde 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
Germany 2021-11-08 547983 664597
Morocco 2021-12-07 1191 1341
United Kingdom 2021-10-07 1331290 1908832
Iceland 2021-12-01 10344 13434
South Korea 2021-11-24 88365 137544
Netherlands 2021-11-13 72780 95442
Poland 2021-09-21 41492 70645
France 2021-11-05 314888 413977
United States Of America 2021-09-02 2136983 3403118
Philippines 2021-11-20 11383 13849
Dominican Republic 2021-12-02 1095 2217
Sweden 2021-11-19 105395 138213
New Zealand 2021-12-07 29715 39869
Japan 2021-11-27 417970 474241
Saudi Arabia 2021-12-13 584 648
Indonesia 2021-11-29 30610 38909
Malaysia 2021-11-08 25333 33544
Australia 2021-10-09 124823 170701
Vanuatu 2022-02-16 93 93
Italy 2021-10-07 78839 114228
Switzerland 2021-11-21 50531 68383
Denmark 2021-10-18 369359 483971
Canada 2021-10-29 272774 388250
Portugal 2021-11-19 21217 26572
Israel 2021-09-29 88105 103344
Spain 2021-09-01 110219 169339
Barbados 2021-12-16 165 230
Austria 2021-09-25 45756 61952
Pakistan 2021-10-07 2324 3289
India 2021-09-07 83000 130675
Brazil 2021-10-31 102859 134405
Norway 2021-11-24 34255 40517
South Africa 2021-10-12 21124 24787
Costa Rica 2021-12-10 7268 10229
Ireland 2021-11-25 51564 61444
Reunion 2021-09-24 9652 14406
Thailand 2021-09-12 21528 31278
Luxembourg 2021-12-06 31116 37185
Puerto Rico 2021-11-29 11041 13601
Slovenia 2021-11-30 32940 41336
Algeria 2021-12-10 469 583
Uganda 2021-11-23 460 756
Estonia 2021-12-15 6230 6612
Belgium 2021-10-11 88214 116958
Czech Republic 2021-11-11 31526 40321
Mexico 2021-11-16 39911 50456
Bulgaria 2021-12-13 7147 9219
Singapore 2021-12-02 20787 37412
Chile 2021-10-26 23124 31296
Croatia 2021-12-01 22499 31781
Romania 2021-12-01 10343 12520
Taiwan 2021-12-13 3329 4839
Turkey 2021-12-02 20500 27439
Eswatini 2021-11-23 583 652
Nigeria 2021-09-03 1872 2666
Colombia 2021-10-09 7450 11796
Latvia 2021-12-07 14126 15531
Greece 2021-11-29 18110 27146
Peru 2021-11-28 27866 41066
Botswana 2021-11-11 1501 1637
Argentina 2021-10-27 8182 12490
Malawi 2021-12-02 197 199
Kazakhstan 2021-12-10 1836 2354
Oman 2021-12-01 356 684
Ecuador 2021-12-02 4356 5888
Panama 2021-12-11 2616 3461
Mongolia 2021-12-02 757 1085
China 2021-12-04 38401 75488
Lithuania 2021-12-09 10243 14554
Hong Kong 2021-11-13 12705 13855
Laos 2022-02-25 647 1009
Slovakia 2021-09-17 25641 38342
Vietnam 2021-12-21 4744 6112
Guam 2021-12-20 486 509
Finland 2021-11-23 21431 28658
Djibouti 2021-12-16 629 632
Montenegro 2021-12-04 445 695
Guadeloupe 2021-11-02 556 665
Brunei 2021-12-16 3921 6556
Paraguay 2021-10-10 1911 2457
New Caledonia 2021-12-31 79 90
Trinidad And Tobago 2021-12-16 1562 1988
Democratic Republic Of The Congo 2021-10-02 146 204
Jordan 2021-12-07 219 318
Republic Of Serbia 2021-12-12 1618 1656
Zambia 2021-11-30 295 371
Egypt 2021-12-01 1601 2345
Bangladesh 2021-11-27 1705 2496
Russia 2021-09-29 38794 61712
Cambodia 2021-12-12 1756 2056
Afghanistan 2022-02-13 5 15
Mayotte 2021-12-14 325 373
Iran 2021-11-26 1559 1785
Cameroon 2021-10-29 1020 1069
North Macedonia 2021-12-28 303 439
Ukraine 2021-12-14 1864 4615
Republic Of Congo 2021-09-12 72 178
Andorra 2021-12-17 138 152
Haiti 2021-12-20 326 389
Lebanon 2021-12-03 496 677
Aruba 2021-12-16 945 1073
Sri Lanka 2021-11-24 752 1193
Curaçao 2021-12-16 1182 1319
Guinea 2021-12-21 287 346
Jamaica 2021-12-09 2899 3397
Georgia 2021-12-14 1915 2535
Albania 2021-10-12 776 1570
Guatemala 2021-12-07 2094 4070
Belize 2021-12-20 583 642
El Salvador 2021-12-05 391 624
Nepal 2021-11-25 1009 1272
Kosovo 2021-12-16 660 794
Saint Lucia 2022-01-21 136 207
Tunisia 2021-12-02 697 864
Ghana 2021-11-10 1337 1399
Venezuela 2021-12-11 494 600
Moldova 2021-12-18 587 689
Nicaragua 2021-12-23 63 142
Kenya 2021-09-04 3612 4561
Senegal 2021-11-25 748 798
Qatar 2021-11-27 1393 1731
Liechtenstein 2021-12-10 661 793
Kuwait 2022-01-16 472 745
Bahrain 2021-12-05 6200 7509
Uruguay 2021-12-27 202 289
Hungary 2021-12-14 435 634
Mozambique 2021-11-26 317 405
Suriname 2021-12-24 132 143
Zimbabwe 2021-11-26 249 249
Saint-Martin 2021-12-14 296 314
United Arab Emirates 2021-11-10 732 1272
Gibraltar 2021-12-07 112 323
Bosnia And Herzegovina 2021-12-08 231 541
Niger 2022-01-06 31 31
Malta 2021-12-13 138 267
Mali 2021-12-23 44 59
Ivory Coast 2021-12-03 184 261
Benin 2021-12-14 454 455
Central African Republic 2021-12-20 41 64
Togo 2021-12-12 257 290
Bhutan 2022-01-05 83 100
Belarus 2022-01-20 40 48
Ethiopia 2021-12-27 243 247
Iraq 2021-11-27 252 380
South Sudan 2021-12-13 28 28
Solomon Islands 2022-03-27 218 238
Syria 2022-01-05 72 83
Cyprus 2021-12-04 4345 4843
Rwanda 2021-12-09 70 71
Namibia 2021-12-02 499 515
Uzbekistan 2022-05-26 34 36
Myanmar 2021-11-30 93 178
Chad 2021-12-30 11 11
Gambia 2021-12-17 159 159
Papua New Guinea 2021-12-26 775 786
British Virgin Islands 2021-12-17 37 57
Sudan 2022-01-03 161 183
Burkina Faso 2021-11-03 37 65
Armenia 2022-01-11 5 7
Bolivia 2021-12-18 115 173
Equatorial Guinea 2022-01-03 2 2
Honduras 2021-12-14 122 263
Lesotho 2021-11-12 80 82
Tanzania 2021-12-18 2 2
Libya 2022-03-23 22 22
Palestine 2022-01-19 18 60
Burundi 2021-12-25 9 9
The Bahamas 2021-12-15 101 108
Angola 2021-12-21 112 112
Cayman Islands 2022-10-10 210 279
Azerbaijan 2022-01-10 20 20
Guyana 2022-01-02 72 74
Mauritania 2022-05-12 1 1
Madagascar 2021-12-12 57 69
East Timor 2022-01-31 1 1
Liberia 2021-12-14 16 17
Gabon 2022-06-29 2 2
Kyrgyzstan 2021-12-24 42 49

Data source and processing

The data on this page is recent as of 2024-05-24, 18:05 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.