B.1.1.529 2023-04-02



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 6142
Countries United States of America 2888, Germany 693, Turkey 332, India 296, Italy 210, France 184, Russia 171, Belgium 135, United Kingdom 116, Spain 104, Brazil 92, Czech Republic 81, Argentina 68, Switzerland 58, Thailand 48, Austria 47, Bahrain 46, Poland 43, Mexico 35, Chile 30, Nigeria 26, Iceland 25, Indonesia 22, South Africa 21, Senegal 20, Morocco 20, Saudi Arabia 19, Australia 18, Slovakia 16, Kazakhstan 15, Sweden 14, Paraguay 12, Romania 12, Israel 11, Malaysia 11, Puerto Rico 11, United Arab Emirates 11, Colombia 10, Bangladesh 10, Slovenia 10, Peru 10, Pakistan 9, Philippines 9, Ecuador 8, Canada 7, Botswana 7, Egypt 6, South Korea 6, Lithuania 6, Iran 6, New Zealand 6, Panama 5, Mauritius 5, Sri Lanka 5, Denmark 4, Vietnam 4, Netherlands 3, Japan 3, Ireland 3, Reunion 3, Ghana 3, Qatar 2, Venezuela 2, Ukraine 2, Kenya 2, Republic of Serbia 2, Kuwait 2, Luxembourg 2, Cote d'Ivoire 1, Croatia 1, Portugal 1, Belarus 1, Saint Vincent and the Grenadines 1, Northern Mariana Islands 1, Zambia 1, Saint Lucia 1, Tunisia 1, Guyana 1, Antigua and Barbuda 1, Singapore 1, Hong Kong 1, Guinea 1, Liechtenstein 1, Norway 1, Seychelles 1, Democratic Republic of the Congo 1, Guatemala 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
Germany 2021-11-17 529893 615275
United States Of America 2021-09-02 2034088 3042068
Japan 2021-11-27 389268 394318
United Kingdom 2021-10-07 1282580 1812428
Denmark 2021-11-22 343880 397109
Brazil 2021-10-31 94293 110555
Malaysia 2021-11-08 22732 27173
Thailand 2021-09-12 19918 26191
Vietnam 2021-12-21 4447 4989
Poland 2021-09-21 40446 66509
Australia 2021-10-09 112067 131689
India 2021-09-07 80216 116295
Georgia 2021-12-14 1816 1994
Canada 2021-10-29 246042 287998
South Korea 2021-11-24 69137 75439
Indonesia 2021-11-29 29124 33252
Switzerland 2021-11-21 49071 63117
Spain 2021-09-01 96075 126121
Ireland 2021-11-25 49378 54399
Botswana 2021-11-11 1432 1572
Netherlands 2021-11-13 67480 82359
Czech Republic 2021-11-11 30961 38132
Belgium 2021-10-11 85632 108296
France 2021-11-05 302616 365567
South Africa 2021-10-12 19727 21132
Norway 2021-11-24 32760 37151
Finland 2021-11-23 20019 23121
Sweden 2021-11-19 91380 107806
Italy 2021-10-07 73253 95902
Russia 2021-12-03 36037 43918
Slovakia 2021-09-17 25006 35818
Slovenia 2021-11-30 32215 37783
Bangladesh 2021-11-27 1638 2212
Portugal 2021-11-19 20475 23274
Croatia 2021-12-01 22009 28647
Austria 2021-09-25 43845 50276
Turkey 2021-12-02 20002 25716
Lithuania 2021-12-09 9612 12264
Chile 2021-10-26 21261 25728
Luxembourg 2021-12-06 30011 32766
Estonia 2021-12-15 6148 6518
Israel 2021-09-29 85803 96951
Jamaica 2021-12-09 1852 2008
Hong Kong 2021-11-13 11079 11471
China 2021-12-04 18225 18475
Colombia 2021-12-04 7217 7746
Mexico 2021-11-16 37369 43063
Argentina 2021-10-27 5360 8608
Bulgaria 2021-12-13 6752 8100
Brunei 2021-12-16 3757 5354
Romania 2021-12-01 9469 10156
Egypt 2021-12-01 673 869
Singapore 2021-12-02 16568 20816
Panama 2021-12-11 2515 3093
Latvia 2021-12-07 13585 14966
Pakistan 2021-12-08 2158 2449
Kenya 2021-09-04 3099 3619
Morocco 2021-12-07 1126 1178
Peru 2021-11-28 25468 32622
Costa Rica 2021-12-10 6805 7913
New Zealand 2021-12-07 24709 26828
Reunion 2021-09-24 8801 12160
Curaçao 2021-12-16 1148 1186
Greece 2021-11-29 13778 15317
Republic Of Congo 2021-09-12 68 169
Republic Of Serbia 2021-12-12 1615 1654
Central African Republic 2022-01-03 8 17
Chad 2021-12-30 4 4
Jordan 2021-12-07 199 267
Moldova 2021-12-18 587 642
Suriname 2021-12-24 132 143
Paraguay 2021-12-14 1456 1504
Philippines 2021-11-20 10903 11942
Iran 2021-11-26 1419 1473
Aruba 2021-12-16 935 1005
Cameroon 2021-10-29 517 567
Ghana 2021-11-10 1311 1363
Kosovo 2021-12-16 624 642
Iceland 2021-12-01 9744 11978
Ecuador 2021-12-11 4132 4375
Puerto Rico 2021-11-29 9077 9571
Guinea 2021-12-21 278 280
Guadeloupe 2021-11-02 549 571
Liechtenstein 2021-12-10 661 793
Papua New Guinea 2021-12-26 775 786
Guatemala 2021-12-07 1725 2851
Mayotte 2021-12-14 323 363
Cambodia 2021-12-12 1706 1930
Saint Lucia 2022-01-21 132 145
Bosnia And Herzegovina 2021-12-08 184 478
Qatar 2021-11-27 1362 1538
Nepal 2021-11-25 998 1193
Sri Lanka 2021-11-24 733 1157
Oman 2021-12-01 117 182
Lebanon 2021-12-03 440 561
Honduras 2021-12-14 48 48
Malta 2021-12-13 137 267
Dominican Republic 2021-12-02 947 1549
Syria 2022-01-05 72 80
Zambia 2021-11-30 293 340
Kazakhstan 2021-12-10 900 1111
Nigeria 2021-09-03 1653 2402
Mongolia 2021-12-02 703 736
Montenegro 2021-12-04 402 516
Trinidad And Tobago 2021-12-16 1543 1732
Togo 2021-12-12 171 173
Mozambique 2021-11-26 284 354
Taiwan 2021-12-13 2456 2479
Djibouti 2021-12-16 504 505
Tunisia 2021-12-02 242 287
Bahrain 2021-12-05 6194 7054
Belize 2021-12-20 558 592
Saint-Martin 2021-12-14 295 308
Algeria 2021-12-10 424 470
Guam 2021-12-20 483 489
Barbados 2021-12-16 140 156
Laos 2022-02-25 500 544
Haiti 2021-12-20 295 308
Iraq 2021-11-27 248 357
Ivory Coast 2021-12-03 157 193
Democratic Republic Of The Congo 2021-10-26 117 158
Uganda 2021-11-29 359 404
Uruguay 2021-12-27 198 210
Senegal 2021-11-25 693 705
Namibia 2021-12-02 497 507
Angola 2021-12-21 112 112
Ukraine 2021-12-14 1071 1254
Hungary 2021-12-14 363 391
New Caledonia 2021-12-31 59 60
Gibraltar 2021-12-07 112 323
North Macedonia 2021-12-28 239 256
Belarus 2022-01-20 40 48
Solomon Islands 2022-03-27 218 238
South Sudan 2021-12-13 28 28
Venezuela 2021-12-11 403 433
Saudi Arabia 2021-12-13 568 610
United Arab Emirates 2021-11-10 732 1272
Azerbaijan 2022-01-10 20 20
Guyana 2022-01-02 72 74
Albania 2022-01-20 520 539
Eswatini 2021-11-23 560 563
Burundi 2021-12-25 9 9
Gambia 2021-12-17 159 159
Mauritania 2022-05-12 1 1
Kuwait 2022-01-16 444 473
El Salvador 2021-12-05 294 306
Bolivia 2021-12-18 104 114
Andorra 2021-12-17 138 152
Niger 2022-01-06 28 28
Vanuatu 2022-02-16 93 93
British Virgin Islands 2021-12-17 37 57
Malawi 2021-12-02 174 174
Lesotho 2021-11-12 79 81
Zimbabwe 2021-11-26 230 230
Benin 2021-12-14 450 450
East Timor 2022-01-31 1 1
Equatorial Guinea 2022-01-03 2 2
Rwanda 2021-12-09 70 71
Sudan 2022-01-05 101 107
Cyprus 2021-12-21 396 420
Libya 2022-03-23 22 22
Myanmar 2021-11-30 51 67
Tanzania 2021-12-18 2 2
Kyrgyzstan 2021-12-24 42 49
Ethiopia 2021-12-27 80 82
Mali 2021-12-23 31 32
Burkina Faso 2021-11-03 28 50
Bhutan 2022-04-04 52 57
Gabon 2022-06-29 2 2
Armenia 2022-01-11 5 7
Uzbekistan 2022-05-26 34 36
Liberia 2021-12-14 12 12
Cayman Islands 2022-10-10 210 279
Palestine 2022-01-19 1 1
Afghanistan 2022-02-13 2 3
Nicaragua 2021-12-23 63 142
The Bahamas 2021-12-15 91 96
Madagascar 2021-12-12 57 69

Data source and processing

The data on this page is recent as of 2023-04-02, 14:42 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.