B.1.1.529 2022-05-19



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
Israel 2021-09-29 26486 36133
United States Of America 2021-09-29 879475 1553704
Denmark 2021-11-22 219077 267907
Ireland 2021-11-25 16429 20164
Bulgaria 2021-12-13 2516 3677
Croatia 2021-12-04 11649 17799
United Kingdom 2021-10-07 1046622 1560875
Chile 2021-10-26 5187 8554
Germany 2021-11-17 250024 327589
Gibraltar 2021-12-07 112 323
Italy 2021-10-07 24987 47191
France 2021-11-12 96007 134525
Poland 2021-12-10 32502 42803
Belgium 2021-10-11 30801 50550
Puerto Rico 2021-11-29 3226 3418
Netherlands 2021-11-13 28175 40628
Canada 2021-11-04 97526 125432
Spain 2021-11-25 30471 39796
South Africa 2021-10-12 10926 11792
Turkey 2021-12-02 8760 15719
Georgia 2021-12-14 715 876
Argentina 2021-12-01 2452 3736
Japan 2021-11-27 71958 75413
Slovenia 2021-11-30 16847 21922
Indonesia 2021-11-29 10305 11730
Czech Republic 2021-11-11 15416 22748
Lithuania 2021-12-10 8344 10744
Slovakia 2021-10-22 14264 23217
Mexico 2021-11-16 13577 17788
Austria 2021-09-25 8365 10996
India 2021-10-25 36216 58154
Brazil 2021-11-25 31139 36931
Australia 2021-10-09 39268 51920
Liechtenstein 2021-12-10 247 375
Thailand 2021-09-12 7831 14157
Panama 2021-12-11 559 979
Curaçao 2021-12-16 542 568
Switzerland 2021-11-21 30496 44354
Romania 2021-12-01 4355 5504
Mozambique 2021-11-26 136 148
Greece 2021-11-29 3264 4555
Angola 2022-01-01 25 25
Cameroon 2021-10-29 60 76
Finland 2021-11-23 6371 8892
Reunion 2021-11-22 2016 3617
Sweden 2021-11-19 35562 54811
Malaysia 2021-11-08 6588 8892
Brunei 2021-12-16 851 1402
Singapore 2021-12-02 5373 6174
Luxembourg 2021-12-06 10340 12079
Guadeloupe 2021-12-17 290 298
Hong Kong 2021-11-13 3431 3769
Cambodia 2021-12-12 862 1170
Morocco 2021-12-07 146 213
Iran 2021-11-26 535 676
Senegal 2021-11-25 14 18
Belize 2021-12-20 203 248
Norway 2021-11-24 19720 23562
Moldova 2021-12-18 285 316
Kuwait 2022-01-16 52 57
Kosovo 2021-12-16 284 301
Philippines 2021-11-22 1335 1360
Colombia 2021-12-07 1832 2101
Nigeria 2021-09-07 834 1479
Portugal 2021-11-19 9300 11760
Latvia 2021-12-07 407 1551
China 2021-12-09 93 113
Andorra 2021-12-17 52 66
Bangladesh 2021-12-06 974 1421
Mayotte 2021-12-16 130 136
Ecuador 2021-12-02 1237 1410
Sri Lanka 2021-11-24 606 1052
Russia 2021-12-03 1204 2330
Peru 2021-11-28 4672 6579
Iraq 2021-11-27 204 303
Botswana 2021-11-11 925 1100
Costa Rica 2021-12-10 1608 1753
Guam 2021-12-20 276 279
Kenya 2021-11-26 1794 1874
Vietnam 2021-12-21 1585 2061
Algeria 2021-12-10 64 86
New Zealand 2021-12-07 4512 5560
Jamaica 2021-12-12 615 671
Aruba 2021-12-16 91 114
Nepal 2021-11-25 143 407
Ghana 2021-11-10 532 591
Guatemala 2021-12-13 313 384
Jordan 2021-12-07 73 143
Mongolia 2021-12-27 126 134
Bosnia And Herzegovina 2021-12-08 118 407
Pakistan 2021-12-08 338 420
Saint-Martin 2021-12-14 246 260
Zimbabwe 2021-11-26 185 185
Estonia 2021-12-15 2515 2882
Djibouti 2021-12-16 306 307
Ukraine 2021-12-19 79 96
Zambia 2021-11-30 165 168
Uganda 2021-11-29 12 24
Republic Of Congo 2021-09-12 50 149
South Korea 2021-11-24 10995 16382
Malta 2021-12-13 133 267
El Salvador 2021-12-05 125 158
Namibia 2021-12-02 124 126
Guinea 2021-12-21 124 126
Oman 2021-12-01 64 71
Suriname 2021-12-24 80 92
Qatar 2021-11-27 267 422
Venezuela 2021-12-11 46 80
Dominican Republic 2021-12-02 67 204
Tunisia 2021-12-02 50 56
Guyana 2022-01-02 33 72
Hungary 2021-12-14 28 51
Trinidad And Tobago 2021-12-16 285 411
Malawi 2021-12-02 132 133
Montenegro 2021-12-04 205 312
Eswatini 2021-11-23 124 125
Iceland 2022-04-28 5 5
South Sudan 2021-12-13 28 28
British Virgin Islands 2021-12-17 20 40
Paraguay 2021-12-14 110 155
New Caledonia 2021-12-31 6 6
Gambia 2021-12-17 30 30
Taiwan 2021-12-13 43 45
Benin 2021-12-14 35 35
Ivory Coast 2021-12-03 40 44
Liberia 2021-12-14 12 12
Rwanda 2021-12-09 70 71
Syria 2022-01-06 48 61
Myanmar 2021-11-30 24 39
Saudi Arabia 2021-12-13 28 32
Republic Of Serbia 2021-12-12 103 117
Democratic Republic Of The Congo 2021-10-26 33 72
Kazakhstan 2021-12-10 3 8
Belarus 2022-01-20 15 48
Haiti 2021-12-20 22 61
Lebanon 2021-12-03 82 104
Egypt 2021-12-01 139 235
Albania 2022-04-07 1 1
Azerbaijan 2022-01-10 12 12
North Macedonia 2021-12-28 43 61
Tanzania 2021-12-18 2 2
Papua New Guinea 2021-12-26 444 463
Ethiopia 2021-12-27 80 82
Togo 2021-12-12 103 106
Solomon Islands 2022-03-27 34 39
Armenia 2022-01-11 4 6
Bolivia 2021-12-18 2 3
Honduras 2021-12-22 36 45
Palestine 2022-01-19 1 1
Central African Republic 2022-01-03 8 17
Chad 2021-12-30 4 4
Uruguay 2021-12-27 28 30

Data source and processing

The data on this page is recent as of 2022-05-19, 11:47 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.