B.1.1.529 2024-02-22



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 107
Sequence count 7778
Countries United States of America 2665, Germany 1077, India 674, Turkey 427, Russia 396, United Kingdom 336, France 237, Italy 185, Spain 128, Belgium 117, Brazil 116, Czech Republic 115, Argentina 71, Iceland 68, Poland 67, Switzerland 65, Thailand 59, Austria 49, Mexico 48, Paraguay 44, Botswana 42, Romania 40, Saudi Arabia 40, Nigeria 39, Australia 36, Chile 32, Bahrain 31, South Africa 30, Slovakia 29, Indonesia 24, Senegal 24, Pakistan 22, Egypt 21, Ireland 21, Morocco 21, Kazakhstan 19, Iran 19, United Arab Emirates 19, Sweden 16, Puerto Rico 16, Israel 15, Bangladesh 13, Ecuador 13, New Zealand 13, Colombia 13, Peru 13, Canada 12, Philippines 12, Malaysia 11, Slovenia 10, South Korea 9, Ghana 9, Japan 8, Denmark 8, Tunisia 8, Mauritius 7, Vietnam 7, Panama 6, Lithuania 6, Croatia 6, Sri Lanka 6, Qatar 5, Kenya 5, Kuwait 5, Reunion 4, Netherlands 4, Finland 4, Belarus 3, Sudan 3, Brunei 3, Singapore 3, Guatemala 3, Antigua and Barbuda 2, Venezuela 2, Uruguay 2, Luxembourg 2, China 2, Northern Mariana Islands 2, Latvia 2, Cameroon 2, Seychelles 2, Ukraine 2, Republic of Serbia 2, Hong Kong 1, Saint Vincent and the Grenadines 1, Jordan 1, Cote d'Ivoire 1, Cabo Verde 1, Togo 1, Malta 1, Estonia 1, Syria 1, Liechtenstein 1, Guinea 1, Democratic Republic of the Congo 1, Montenegro 1, Saint Lucia 1, Norway 1, Bosnia and Herzegovina 1, Zambia 1, Guyana 1, Mali 1, Uganda 1, Cambodia 1, Trinidad and Tobago 1, Portugal 1, Grenada 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
France 2021-11-05 313675 412627
Norway 2021-11-24 33921 40150
United States Of America 2021-09-02 2094917 3350212
Sweden 2021-11-19 104801 137534
United Kingdom 2021-10-07 1322560 1899560
Taiwan 2021-12-13 2904 4351
Dominican Republic 2021-12-02 1065 2186
Denmark 2021-11-22 357623 420618
Japan 2021-11-27 409238 459392
Panama 2021-12-11 2608 3452
Switzerland 2021-11-21 50362 68202
Italy 2021-10-07 78208 113430
Chile 2021-10-26 21911 29870
South Korea 2021-11-24 81557 130251
Austria 2021-09-25 45684 61876
Spain 2021-09-01 106976 165101
Cameroon 2021-10-29 1020 1069
Mexico 2021-11-16 38700 48853
Poland 2021-09-21 41325 70450
Belgium 2021-10-11 88119 116846
Brazil 2021-10-31 99972 129820
India 2021-09-07 82204 129402
Canada 2021-10-29 262241 376703
Australia 2021-10-09 120855 166541
Puerto Rico 2021-11-29 9848 12336
Djibouti 2021-12-16 629 632
Germany 2021-11-08 546916 663407
Argentina 2021-10-27 7914 12160
Colombia 2021-10-09 7350 11532
Nigeria 2021-09-03 1667 2458
Hong Kong 2021-11-13 12627 13734
Guinea 2021-12-21 287 346
Finland 2021-11-23 21139 28344
Romania 2021-12-01 10259 12395
Belarus 2022-01-20 40 48
Albania 2021-10-12 776 1570
Ecuador 2021-12-02 4227 5734
Israel 2021-09-29 87633 102862
Namibia 2021-12-02 499 515
Malaysia 2021-11-08 24857 32982
Czech Republic 2021-11-11 31389 40155
South Africa 2021-10-12 20778 24410
Pakistan 2021-10-07 2221 3186
China 2021-12-04 30241 66063
Netherlands 2021-11-13 72110 94681
Ireland 2021-11-25 50868 60687
Slovenia 2021-11-30 32893 41268
Philippines 2021-11-20 11316 13759
Georgia 2021-12-14 1900 2520
Turkey 2021-12-02 20168 26762
Portugal 2021-11-19 21138 26485
Iceland 2021-12-01 10182 13265
Thailand 2021-09-12 21044 30529
Uganda 2021-11-23 442 597
Belize 2021-12-20 583 642
Montenegro 2021-12-04 445 694
Moldova 2021-12-18 587 689
Reunion 2021-09-24 9652 14406
Croatia 2021-12-01 22421 31604
Indonesia 2021-11-29 30283 38528
Liechtenstein 2021-12-10 661 793
Iran 2021-11-26 1549 1771
Sri Lanka 2021-11-24 752 1193
Russia 2021-09-29 37710 60275
Singapore 2021-12-02 20006 36620
Ukraine 2021-12-14 1340 3825
New Zealand 2021-12-07 28012 37990
Zambia 2021-11-30 293 369
Luxembourg 2021-12-06 30727 36776
Peru 2021-11-28 26957 40013
Kazakhstan 2021-12-10 1836 2354
Bangladesh 2021-11-27 1705 2496
Trinidad And Tobago 2021-12-16 1554 1980
Guadeloupe 2021-11-02 554 663
El Salvador 2021-12-05 390 594
Jordan 2021-12-07 201 284
Lithuania 2021-12-09 10050 13929
Laos 2022-02-25 615 963
Ghana 2021-11-10 1334 1396
Slovakia 2021-09-17 25559 38254
North Macedonia 2021-12-28 284 413
Kuwait 2022-01-16 472 745
Oman 2021-12-01 187 513
Vietnam 2021-12-21 4630 5976
Greece 2021-11-29 17523 26421
Kenya 2021-09-04 3533 4391
Jamaica 2021-12-09 2901 3397
Mongolia 2021-12-02 737 1061
Aruba 2021-12-16 945 1073
Curaçao 2021-12-16 1178 1314
Andorra 2021-12-17 138 152
Bosnia And Herzegovina 2021-12-08 232 541
Cambodia 2021-12-12 1737 2036
Bulgaria 2021-12-13 7107 9149
Guam 2021-12-20 483 506
Kosovo 2021-12-16 660 794
Qatar 2021-11-27 1368 1705
Syria 2022-01-05 72 81
Costa Rica 2021-12-10 6954 9905
Paraguay 2021-10-10 1853 2381
Morocco 2021-12-07 1187 1336
Botswana 2021-11-11 1501 1637
Guatemala 2021-12-07 1807 3760
Nepal 2021-11-25 1009 1272
Algeria 2021-12-10 469 583
Uruguay 2021-12-27 203 290
Brunei 2021-12-16 3821 6450
Iraq 2021-11-27 252 380
Mayotte 2021-12-14 325 373
British Virgin Islands 2021-12-17 37 57
Egypt 2021-12-01 1600 2345
Republic Of Serbia 2021-12-12 1618 1656
Barbados 2021-12-16 165 230
Solomon Islands 2022-03-27 218 238
Latvia 2021-12-07 14126 15531
Malta 2021-12-13 138 267
Madagascar 2021-12-12 57 69
Honduras 2021-12-14 80 220
Sudan 2022-01-03 161 183
New Caledonia 2021-12-31 61 68
Saint Lucia 2022-01-21 136 207
Zimbabwe 2021-11-26 249 249
Tunisia 2021-12-02 718 884
Gibraltar 2021-12-07 112 323
Mozambique 2021-11-26 316 404
Suriname 2021-12-24 132 143
Bahrain 2021-12-05 6200 7509
Lebanon 2021-12-03 478 631
Togo 2021-12-12 244 271
Eswatini 2021-11-23 560 563
Saint-Martin 2021-12-14 295 313
Gambia 2021-12-17 159 159
Angola 2021-12-21 112 112
Ivory Coast 2021-12-03 182 224
Estonia 2021-12-15 6148 6518
Venezuela 2021-12-11 494 600
Hungary 2021-12-14 397 592
Chad 2021-12-30 11 11
Senegal 2021-11-25 741 791
United Arab Emirates 2021-11-10 732 1272
Malawi 2021-12-02 197 199
Cyprus 2021-12-04 4345 4843
Ethiopia 2021-12-27 165 167
Bolivia 2021-12-18 115 173
Burkina Faso 2021-11-03 30 58
Azerbaijan 2022-01-10 20 20
Cayman Islands 2022-10-10 210 279
Myanmar 2021-11-30 71 153
Armenia 2022-01-11 5 7
South Sudan 2021-12-13 28 28
Tanzania 2021-12-18 2 2
Lesotho 2021-11-12 80 82
Saudi Arabia 2021-12-13 583 648
Haiti 2021-12-20 302 357
Libya 2022-03-23 22 22
Papua New Guinea 2021-12-26 775 786
Republic Of Congo 2021-09-12 72 178
Democratic Republic Of The Congo 2021-10-02 121 179
Mali 2021-12-23 44 59
Vanuatu 2022-02-16 93 93
Afghanistan 2022-02-13 2 3
Rwanda 2021-12-09 70 71
Uzbekistan 2022-05-26 34 36
Benin 2021-12-14 454 455
Central African Republic 2021-12-20 39 62
Burundi 2021-12-25 9 9
Bhutan 2022-01-05 83 100
Palestine 2022-01-19 12 54
The Bahamas 2021-12-15 90 96
Kyrgyzstan 2021-12-24 42 49
Nicaragua 2021-12-23 63 142
Guyana 2022-01-02 72 74
Liberia 2021-12-14 12 12
Niger 2022-01-06 31 31
Equatorial Guinea 2022-01-03 2 2
East Timor 2022-01-31 1 1
Gabon 2022-06-29 2 2
Mauritania 2022-05-12 1 1

Data source and processing

The data on this page is recent as of 2024-02-22, 22:41 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.