B.1.1.529 2023-01-31



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 87
Sequence count 6036
Countries United States of America 2898, Germany 652, Turkey 332, India 279, Italy 215, Russia 183, France 181, United Kingdom 117, Belgium 115, Spain 101, Brazil 82, Argentina 69, Czech Republic 68, Switzerland 60, Bahrain 52, Thailand 49, Poland 44, Austria 38, Mexico 34, Saudi Arabia 31, Chile 29, Nigeria 26, Indonesia 21, South Africa 20, Senegal 20, Morocco 19, Slovakia 18, Australia 17, Kazakhstan 15, Sweden 14, Romania 14, Paraguay 13, Puerto Rico 11, Israel 11, Malaysia 10, Colombia 10, Bangladesh 10, Slovenia 10, Peru 9, Ecuador 8, Pakistan 8, Philippines 8, Botswana 7, South Korea 6, Canada 6, Egypt 6, Iran 6, New Zealand 5, Lithuania 5, Panama 5, Sri Lanka 5, Denmark 4, Vietnam 4, Ireland 4, Netherlands 3, Japan 3, Qatar 3, Ghana 3, Reunion 3, Mauritius 3, Guatemala 2, Kenya 2, Republic of Serbia 2, Venezuela 2, Luxembourg 2, Kuwait 2, Ukraine 2, Belarus 1, Saint Lucia 1, Croatia 1, Antigua and Barbuda 1, Greece 1, Tunisia 1, Cote d'Ivoire 1, Guyana 1, Cameroon 1, Northern Mariana Islands 1, Singapore 1, Seychelles 1, Norway 1, Zambia 1, Hong Kong 1, Guinea 1, Portugal 1, Saint Vincent and the Grenadines 1, Democratic Republic of the Congo 1, Liechtenstein 1
First detected South Africa and Botswana
Earliest sample date 2021-11-08
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 1952158 2892546
Canada 2021-10-29 229617 264061
Denmark 2021-11-22 341490 392968
France 2021-11-05 295733 356438
United Kingdom 2021-10-07 1265937 1782279
Slovakia 2021-09-17 24570 35269
Germany 2021-11-17 509200 586649
Mexico 2021-11-16 34481 38750
Australia 2021-10-09 108904 124991
Poland 2021-09-21 39686 65026
India 2021-09-07 79867 115410
Israel 2021-09-29 84418 94257
South Africa 2021-10-12 18782 19427
Spain 2021-09-01 89978 118883
Croatia 2021-12-01 21147 27654
Austria 2021-09-25 40583 43846
Switzerland 2021-11-21 48545 62210
Malaysia 2021-11-08 22334 26539
Slovenia 2021-11-30 31527 36873
Sweden 2021-11-19 84549 99353
Netherlands 2021-11-13 64714 77470
Belgium 2021-10-11 84290 106061
Norway 2021-11-24 31776 35967
Indonesia 2021-11-29 28628 32310
Japan 2021-11-27 346965 351330
Czech Republic 2021-11-11 30651 37526
Italy 2021-10-07 68960 90242
Romania 2021-12-01 9291 9965
Peru 2021-11-28 24665 29228
Portugal 2021-11-19 19836 22393
Turkey 2021-12-02 19966 25669
Hong Kong 2021-11-13 10837 11223
Lithuania 2021-12-09 9215 11745
Ireland 2021-11-25 47930 51972
Brazil 2021-10-31 86666 101948
South Korea 2021-11-24 57362 62978
Colombia 2021-12-04 6927 7360
Estonia 2021-12-15 6148 6518
Republic Of Congo 2021-09-12 68 169
Russia 2021-12-03 35462 42848
Luxembourg 2021-12-06 29204 31113
Gambia 2021-12-17 159 159
Greece 2021-11-29 13479 15015
Thailand 2021-09-12 18023 24270
Ecuador 2021-12-11 4027 4199
Botswana 2021-11-11 1428 1568
Bangladesh 2021-11-27 1632 2211
Puerto Rico 2021-11-29 7716 8035
Singapore 2021-12-02 15924 19232
Reunion 2021-09-24 8123 11444
New Zealand 2021-12-07 22885 24265
Costa Rica 2021-12-10 6445 6840
Brunei 2021-12-16 3622 4478
Chile 2021-10-26 19908 23588
Bulgaria 2021-12-13 6752 8100
Argentina 2021-10-27 5249 8479
Cambodia 2021-12-12 1691 1909
Moldova 2021-12-18 544 577
Vietnam 2021-12-21 4319 4831
Sri Lanka 2021-11-24 724 1148
Georgia 2021-12-14 1678 1823
Paraguay 2021-12-14 1456 1504
Nepal 2021-11-25 998 1193
Iraq 2021-11-27 248 357
Philippines 2021-11-20 10436 11005
Malta 2021-12-13 137 267
Kenya 2021-09-04 2966 3480
Guatemala 2021-12-07 1678 2592
Kosovo 2021-12-16 624 642
Finland 2021-11-23 19092 21824
Laos 2022-02-25 494 538
Iran 2021-11-26 1413 1472
Pakistan 2021-12-08 2124 2304
Ghana 2021-11-10 1078 1130
Trinidad And Tobago 2021-12-16 1471 1605
Tunisia 2021-12-02 222 266
Jamaica 2021-12-09 1660 1734
Guam 2021-12-20 476 479
Algeria 2021-12-10 389 427
Latvia 2021-12-07 13582 14966
Oman 2021-12-01 106 149
Nigeria 2021-09-03 1647 2392
Malawi 2021-12-02 169 169
Republic Of Serbia 2021-12-12 1490 1504
Liechtenstein 2021-12-10 661 793
Kuwait 2022-01-16 439 458
North Macedonia 2021-12-28 239 256
Uganda 2021-11-29 308 337
Montenegro 2021-12-04 369 475
Kazakhstan 2021-12-10 771 906
Eswatini 2021-11-23 442 443
Panama 2021-12-11 2458 3018
Curaçao 2021-12-16 1114 1148
Taiwan 2021-12-13 2258 2266
Mongolia 2021-12-02 703 736
Saudi Arabia 2021-12-13 535 544
New Caledonia 2021-12-31 57 57
Ukraine 2021-12-14 671 822
Iceland 2022-03-14 2972 3060
Bahrain 2021-12-05 6018 6357
Guadeloupe 2021-11-02 541 561
Mayotte 2021-12-14 323 363
Guinea 2021-12-21 278 280
Bosnia And Herzegovina 2021-12-08 138 427
Cameroon 2021-10-29 436 485
Liberia 2021-12-14 12 12
Saint Lucia 2022-01-21 127 129
Barbados 2021-12-16 117 117
Belize 2021-12-20 526 552
El Salvador 2021-12-05 294 306
Zambia 2021-11-30 275 275
Democratic Republic Of The Congo 2021-10-26 103 141
Dominican Republic 2021-12-02 941 1496
Morocco 2021-12-07 1122 1175
Vanuatu 2022-02-16 93 93
Lebanon 2021-12-03 404 526
Benin 2021-12-14 450 450
Djibouti 2021-12-16 504 505
Qatar 2021-11-27 1362 1538
Mozambique 2021-11-26 273 306
China 2021-12-08 8909 9085
Aruba 2021-12-16 857 889
Suriname 2021-12-24 132 143
Gibraltar 2021-12-07 112 323
Papua New Guinea 2021-12-26 775 786
Uruguay 2021-12-27 166 178
Egypt 2021-12-01 673 869
Andorra 2021-12-17 138 152
Namibia 2021-12-02 479 481
Ivory Coast 2021-12-03 153 156
Jordan 2021-12-07 163 225
Lesotho 2021-11-12 79 81
Togo 2021-12-12 103 105
Saint-Martin 2021-12-14 295 308
Honduras 2021-12-14 48 48
Syria 2022-01-05 72 80
Senegal 2021-11-25 693 705
Belarus 2022-01-20 40 48
Hungary 2021-12-14 135 160
Angola 2021-12-21 112 112
Bolivia 2021-12-18 42 52
Haiti 2021-12-20 161 163
Cyprus 2021-12-21 396 420
Madagascar 2021-12-12 57 69
East Timor 2022-01-31 1 1
Equatorial Guinea 2022-01-03 2 2
Zimbabwe 2021-11-26 214 214
Solomon Islands 2022-03-27 218 238
Central African Republic 2022-01-03 8 17
Nicaragua 2021-12-23 57 57
Mali 2021-12-23 31 32
Azerbaijan 2022-01-10 20 20
Venezuela 2021-12-11 293 318
Guyana 2022-01-02 72 74
South Sudan 2021-12-13 28 28
Ethiopia 2021-12-27 80 82
Albania 2022-04-07 1 1
Rwanda 2021-12-09 70 71
Myanmar 2021-11-30 36 50
Kyrgyzstan 2021-12-24 42 49
Sudan 2022-01-05 99 101
Niger 2022-01-06 28 28
Burundi 2021-12-25 9 9
British Virgin Islands 2021-12-17 37 57
Uzbekistan 2022-05-26 34 36
Armenia 2022-01-11 5 7
Libya 2022-03-23 22 22
Chad 2021-12-30 4 4
Tanzania 2021-12-18 2 2
Gabon 2022-06-29 2 2
Palestine 2022-01-19 1 1
The Bahamas 2021-12-15 1 2
United Arab Emirates 2022-07-10 1 1
Afghanistan 2022-02-13 2 3
Mauritania 2022-05-12 1 1

Data source and processing

The data on this page is recent as of 2023-01-31, 22:14 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 3.1.20, pangoLEARN version 2022-02-02.

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.