B.1.1.529 2022-08-19



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
Luxembourg 2021-12-06 18935 20876
France 2021-11-05 194855 249452
United States Of America 2021-09-02 1359216 2298401
Brazil 2021-11-17 56864 66560
India 2021-10-02 53972 85284
Turkey 2021-12-02 12187 19386
Netherlands 2021-11-13 41192 54076
Spain 2021-11-25 49940 60067
United Kingdom 2021-10-07 1148838 1677446
Mexico 2021-11-16 24755 29533
Australia 2021-10-09 68248 82446
Indonesia 2021-11-29 16597 18229
Italy 2021-10-07 41717 66703
Trinidad And Tobago 2021-12-16 685 925
Germany 2021-11-17 380153 471683
Ireland 2021-11-25 31100 35347
South Korea 2021-11-24 22025 28389
Belgium 2021-10-11 54489 78693
Denmark 2021-11-22 264817 317600
Japan 2021-11-27 165938 169528
Switzerland 2021-11-21 36147 50137
Czech Republic 2021-11-11 20586 28654
Vietnam 2021-12-21 2257 2761
Malaysia 2021-11-08 13010 15643
Peru 2021-11-28 11600 13708
New Zealand 2021-12-07 9144 10328
Lithuania 2021-12-10 8690 11089
Slovakia 2021-10-22 17244 26544
Sweden 2021-11-19 45953 68646
Ukraine 2021-12-14 142 244
Canada 2021-10-29 146306 180218
Slovenia 2021-11-30 20657 26173
Norway 2021-11-24 26859 31008
Jamaica 2021-12-12 1245 1309
Philippines 2021-11-20 6978 7105
Portugal 2021-11-19 15099 17669
Austria 2021-09-25 15396 18082
Namibia 2021-12-02 346 349
Ecuador 2021-12-02 1967 2206
Finland 2021-11-23 10969 13620
Poland 2021-12-10 34423 44754
Greece 2021-11-29 5542 6859
Botswana 2021-11-11 1145 1330
Hong Kong 2021-11-13 5767 6147
Pakistan 2021-12-08 1054 1218
Singapore 2021-12-02 10249 11056
Brunei 2021-12-16 1464 2294
Kenya 2021-11-26 2422 2650
Thailand 2021-09-12 12133 18506
Colombia 2021-12-07 4045 4549
Paraguay 2021-10-10 600 1009
Morocco 2021-12-07 321 399
Israel 2021-09-29 64620 75428
Kosovo 2021-12-16 373 390
Croatia 2021-12-04 14624 20822
Guinea 2021-12-21 124 126
Costa Rica 2021-12-10 3376 3647
Chile 2021-10-26 12784 16872
Sri Lanka 2021-11-24 643 1089
Democratic Republic Of The Congo 2021-10-26 87 127
South Africa 2021-10-12 15032 16223
Puerto Rico 2021-11-29 4385 4616
Guatemala 2021-12-13 687 758
Kuwait 2022-01-16 194 242
Georgia 2021-12-14 977 1152
Panama 2021-12-11 986 1688
Iran 2021-11-26 885 1068
Jordan 2021-12-07 135 205
Estonia 2021-12-15 4402 4805
Honduras 2021-12-22 36 45
Nepal 2021-11-25 540 963
Nigeria 2021-09-07 1050 1856
Barbados 2022-05-05 52 59
Guadeloupe 2021-11-02 402 429
Russia 2021-12-03 3878 6256
Saint-Martin 2021-12-14 284 299
Bangladesh 2021-12-06 1288 1761
Ghana 2021-11-10 623 697
Romania 2021-12-01 5803 6957
Taiwan 2021-12-13 2091 2099
Egypt 2021-12-01 139 235
Argentina 2021-10-27 3437 6745
Moldova 2021-12-18 374 405
Curaçao 2021-12-16 880 906
Liechtenstein 2021-12-10 263 391
Papua New Guinea 2021-12-26 444 463
Djibouti 2021-12-16 335 336
Bulgaria 2021-12-13 5012 6218
Angola 2021-12-21 70 70
Reunion 2021-11-22 5260 6866
Nicaragua 2022-07-01 1 1
Tunisia 2021-12-02 51 56
Mongolia 2021-12-27 127 134
Cambodia 2021-12-12 1071 1409
Guam 2021-12-20 349 352
Malawi 2021-12-02 133 134
Suriname 2021-12-24 127 143
Ethiopia 2021-12-27 80 82
Dominican Republic 2021-12-02 380 519
El Salvador 2021-12-05 176 210
Bosnia And Herzegovina 2021-12-08 135 427
Lebanon 2021-12-03 85 196
Burundi 2021-12-25 9 9
Republic Of Serbia 2021-12-12 759 785
Haiti 2021-12-20 22 61
Mozambique 2021-11-26 157 172
Kazakhstan 2021-12-10 375 592
Andorra 2021-12-17 67 81
Qatar 2021-11-27 344 518
Syria 2022-01-06 49 61
Guyana 2022-01-02 34 72
Iraq 2021-11-27 220 322
Mayotte 2021-12-16 229 237
Belize 2021-12-20 410 456
Republic Of Congo 2021-09-12 58 157
Latvia 2021-12-07 5037 6250
Zambia 2021-11-30 269 272
Cameroon 2021-10-29 388 440
Solomon Islands 2022-03-27 121 129
Eswatini 2021-11-23 361 367
Laos 2022-02-25 338 385
Lesotho 2021-11-12 52 54
Algeria 2021-12-10 90 134
China 2021-12-09 263 379
Malta 2021-12-13 133 267
Zimbabwe 2021-11-26 185 185
North Macedonia 2021-12-28 134 152
Gambia 2021-12-17 82 87
Rwanda 2021-12-09 70 71
Venezuela 2021-12-11 75 113
Oman 2021-12-01 80 87
Montenegro 2021-12-04 209 316
Benin 2021-12-14 36 36
Liberia 2021-12-14 12 12
Bahrain 2021-12-05 3389 4047
Hungary 2021-12-14 28 51
Gibraltar 2021-12-07 112 323
Senegal 2021-11-25 19 26
Myanmar 2021-11-30 35 50
Uganda 2021-11-29 148 166
Aruba 2021-12-16 348 371
Niger 2022-01-06 26 28
British Virgin Islands 2021-12-17 37 57
Saint Lucia 2022-03-26 54 54
Uruguay 2021-12-27 35 37
Togo 2021-12-12 103 106
Iceland 2022-03-14 902 1060
New Caledonia 2021-12-31 6 6
Chad 2021-12-30 4 4
South Sudan 2021-12-13 28 28
Saudi Arabia 2021-12-13 28 32
Central African Republic 2022-01-03 8 17
Belarus 2022-01-20 16 48
Azerbaijan 2022-01-10 12 12
Armenia 2022-01-11 5 7
Ivory Coast 2021-12-03 40 44
Kyrgyzstan 2021-12-24 42 49
Mauritania 2022-05-12 1 1
Libya 2022-03-23 22 22
Tanzania 2021-12-18 2 2
Bolivia 2021-12-18 42 52
Palestine 2022-01-19 1 1
Cyprus 2021-12-21 395 420
Madagascar 2021-12-12 57 69
Gabon 2022-06-29 2 2
Albania 2022-04-07 1 1
Equatorial Guinea 2022-01-03 1 1
United Arab Emirates 2022-07-10 1 1

Data source and processing

The data on this page is recent as of 2022-08-19, 01:14 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.