B.1.1.529 2022-11-25



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 0
Sequence count 0
Countries
First detected South Africa and Botswana
Earliest sample date
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 2021-11-17 443286 542146
Denmark 2021-11-22 304810 366030
United States Of America 2021-09-02 1707608 2676872
United Kingdom 2021-10-07 1195539 1737842
Japan 2021-11-27 268475 272846
France 2021-11-05 261705 329317
Mexico 2021-11-16 31430 36591
Estonia 2021-12-15 6055 6518
Australia 2021-10-09 92217 108547
Canada 2021-10-29 196922 232999
Belgium 2021-10-11 75196 102074
Brazil 2021-10-31 69503 86192
Italy 2021-10-07 52451 80083
India 2021-10-02 69318 105062
Slovenia 2021-11-30 25458 31942
Portugal 2021-11-19 17940 20754
Reunion 2021-09-24 7324 10608
Czech Republic 2021-11-11 25977 35770
Poland 2021-09-21 37912 64256
Hong Kong 2021-11-13 9469 9923
Lithuania 2021-12-10 8689 11089
Switzerland 2021-11-21 43416 57851
Bulgaria 2021-12-13 6692 8100
Sweden 2021-11-19 59467 87129
Thailand 2021-09-12 14541 21050
Croatia 2021-12-04 19181 25693
Spain 2021-11-25 66713 78447
Turkey 2021-12-02 15828 24223
Philippines 2021-11-20 9624 10010
Puerto Rico 2021-11-29 7047 7623
Netherlands 2021-11-13 53386 67798
Israel 2021-09-29 78814 90356
Norway 2021-11-24 30385 34589
Kenya 2021-09-28 2626 3069
South Africa 2021-10-12 16982 18448
Indonesia 2021-11-29 24621 26843
Malaysia 2021-11-08 19492 22500
Chile 2021-10-26 15670 20899
South Korea 2021-11-24 38081 48601
Slovakia 2021-09-17 21464 34575
Colombia 2021-12-07 5072 5780
Guadeloupe 2021-11-02 493 522
Ecuador 2021-12-02 2839 3215
Argentina 2021-10-27 4640 7978
Austria 2021-09-25 23969 26899
Finland 2021-11-23 13304 16020
New Zealand 2021-12-07 16221 17907
Luxembourg 2021-12-06 25940 28323
Ireland 2021-11-25 39542 44978
Eswatini 2021-11-23 435 443
Vietnam 2021-12-21 3389 3917
Hungary 2021-12-14 36 59
Nigeria 2021-09-07 1104 1982
Russia 2021-12-03 15404 20473
Greece 2021-11-29 8599 9973
Botswana 2021-11-11 1243 1438
Romania 2021-12-01 7914 9748
Peru 2021-11-28 20582 23134
Costa Rica 2021-12-10 5111 5422
Trinidad And Tobago 2021-12-16 1052 1415
Singapore 2021-12-02 14863 15944
Guam 2021-12-20 442 445
Cambodia 2021-12-12 1346 1699
El Salvador 2021-12-05 269 306
Morocco 2021-12-07 850 958
Syria 2022-01-06 62 78
Guatemala 2021-12-13 1112 1202
Brunei 2021-12-16 2123 3596
Pakistan 2021-12-08 1565 2023
Iran 2021-11-26 1144 1360
Georgia 2021-12-14 1281 1493
Malawi 2021-12-02 168 169
Taiwan 2021-12-13 2126 2134
Ghana 2021-11-10 670 747
Ethiopia 2021-12-27 80 82
Mayotte 2021-12-14 317 331
Nepal 2021-11-25 665 1163
Jamaica 2021-12-09 1651 1734
Papua New Guinea 2021-12-26 444 463
Uganda 2021-11-29 225 248
Republic Of Serbia 2021-12-12 1171 1235
Iraq 2021-11-27 222 324
Namibia 2021-12-02 464 468
Latvia 2021-12-07 5037 6249
Laos 2022-02-25 383 430
Cameroon 2021-10-29 409 485
Montenegro 2021-12-04 361 475
Algeria 2021-12-10 165 283
Kosovo 2021-12-16 614 642
Panama 2021-12-11 1648 2644
Guyana 2022-01-02 34 72
Bangladesh 2021-12-06 1459 2012
Saint-Martin 2021-12-14 293 308
Liechtenstein 2021-12-10 546 681
Moldova 2021-12-18 388 421
Curaçao 2021-12-16 1026 1066
British Virgin Islands 2021-12-17 37 57
Zambia 2021-11-30 272 275
Guinea 2021-12-21 250 281
Palestine 2022-01-19 1 1
Iceland 2022-03-14 1722 2056
Belize 2021-12-20 460 552
Sri Lanka 2021-11-24 677 1132
Zimbabwe 2021-11-26 203 214
China 2021-12-09 266 394
Paraguay 2021-10-10 1177 1708
Mongolia 2021-12-12 525 615
Qatar 2021-11-27 414 588
Dominican Republic 2021-12-02 800 946
Aruba 2021-12-16 635 677
Gibraltar 2021-12-07 112 323
Afghanistan 2022-02-13 2 3
Ukraine 2021-12-14 244 589
Tunisia 2021-12-02 198 236
Mozambique 2021-11-26 225 244
Suriname 2021-12-24 127 143
Bahrain 2021-12-05 5659 6357
Kyrgyzstan 2021-12-24 42 49
Kazakhstan 2021-12-10 594 828
Benin 2021-12-14 423 424
Senegal 2021-11-25 599 705
Burundi 2021-12-25 9 9
Democratic Republic Of The Congo 2021-10-26 99 141
Djibouti 2021-12-16 503 504
Andorra 2021-12-17 104 122
Malta 2021-12-13 133 267
Bosnia And Herzegovina 2021-12-08 135 427
Egypt 2021-12-01 324 666
Angola 2021-12-21 71 71
Haiti 2021-12-20 22 61
Saint Lucia 2022-03-26 92 93
South Sudan 2021-12-13 28 28
Kuwait 2022-01-16 204 316
Liberia 2021-12-14 12 12
Jordan 2021-12-07 145 216
North Macedonia 2021-12-28 174 192
Mali 2021-12-23 27 32
Gambia 2021-12-17 153 160
Togo 2021-12-12 103 105
Venezuela 2021-12-11 164 220
Myanmar 2021-11-30 35 50
Saudi Arabia 2021-12-13 119 123
Lebanon 2021-12-03 245 370
Solomon Islands 2022-03-27 121 129
Madagascar 2021-12-12 57 69
Rwanda 2021-12-09 70 71
Republic Of Congo 2021-09-12 63 162
Lesotho 2021-11-12 78 80
Niger 2022-01-06 26 28
Bolivia 2021-12-18 42 52
Sudan 2022-01-05 91 101
Nicaragua 2021-12-23 57 57
Azerbaijan 2022-01-10 20 20
Oman 2021-12-01 80 87
Uruguay 2021-12-27 35 37
Belarus 2022-01-20 16 48
Honduras 2021-12-22 38 47
Cyprus 2021-12-21 395 420
Vanuatu 2022-02-16 87 93
New Caledonia 2021-12-31 6 6
Armenia 2022-01-11 5 7
United Arab Emirates 2022-07-10 1 1
Central African Republic 2022-01-03 8 17
Chad 2021-12-30 4 4
Barbados 2022-05-05 78 96
Ivory Coast 2021-12-03 57 83
Libya 2022-03-23 22 22
Mauritania 2022-05-12 1 1
Tanzania 2021-12-18 2 2
Equatorial Guinea 2022-01-03 2 2
Albania 2022-04-07 1 1
Gabon 2022-06-29 2 2
East Timor 2022-01-31 1 1

Data source and processing

The data on this page is recent as of 2022-11-25, 16:20 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.