B.1.1.529 2023-08-24
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 | 106 |
| Sequence count | 7974 |
| Countries | United States of America 2755, Germany 1082, India 682, Turkey 429, Russia 404, United Kingdom 342, France 237, Italy 173, Spain 130, Belgium 129, Czech Republic 121, Brazil 116, Argentina 71, Switzerland 69, Philippines 69, Poland 68, Iceland 67, Thailand 58, Austria 51, Romania 49, Mexico 48, Paraguay 44, Botswana 41, Nigeria 40, Saudi Arabia 40, Australia 34, Slovakia 33, Chile 32, Bahrain 31, South Africa 26, Ireland 25, Senegal 24, Pakistan 23, Indonesia 23, United Arab Emirates 22, Morocco 21, Kazakhstan 21, Iran 19, Egypt 17, Puerto Rico 16, Israel 16, Sweden 15, Peru 14, Malaysia 13, Canada 13, Colombia 13, Ecuador 13, Bangladesh 12, Slovenia 10, New Zealand 10, South Korea 9, Japan 9, Ghana 9, Vietnam 7, Mauritius 7, Denmark 7, Tunisia 7, Sri Lanka 6, Croatia 6, Lithuania 6, Panama 6, Kuwait 5, Kenya 5, Qatar 5, Netherlands 4, Reunion 4, Singapore 3, Sudan 3, Venezuela 3, Brunei 3, Belarus 3, Cameroon 2, Latvia 2, Guatemala 2, Northern Mariana Islands 2, Ukraine 2, Republic of Serbia 2, Guyana 2, Uruguay 2, Antigua and Barbuda 2, Luxembourg 2, Seychelles 2, Zambia 1, Cambodia 1, Guinea 1, Hong Kong 1, Uganda 1, Democratic Republic of the Congo 1, Saint Vincent and the Grenadines 1, Estonia 1, Portugal 1, Saint Lucia 1, Mali 1, Syria 1, Jordan 1, Cabo Verde 1, Malta 1, Greece 1, Trinidad and Tobago 1, Montenegro 1, Liechtenstein 1, China 1, Norway 1, Grenada 1, Togo 1, Cote d'Ivoire 1 |
| First detected | South Africa and Botswana |
| Earliest sample date | 2021-09-29 |
| 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 | 2058627 | 3171848 |
| Luxembourg | 2021-12-06 | 30232 | 34939 |
| Australia | 2021-10-09 | 118733 | 155860 |
| Indonesia | 2021-11-29 | 29636 | 37318 |
| Brazil | 2021-10-31 | 97725 | 119803 |
| Ireland | 2021-11-25 | 49669 | 57262 |
| Germany | 2021-11-08 | 543771 | 655291 |
| Malaysia | 2021-11-08 | 23557 | 30708 |
| Nigeria | 2021-09-03 | 1666 | 2436 |
| Italy | 2021-10-07 | 75123 | 102619 |
| Japan | 2021-11-27 | 405348 | 428162 |
| Belgium | 2021-10-11 | 86699 | 111955 |
| India | 2021-09-07 | 80807 | 126893 |
| Trinidad And Tobago | 2021-12-16 | 1548 | 1856 |
| Saint Lucia | 2022-01-21 | 136 | 175 |
| Sweden | 2021-11-19 | 99251 | 122131 |
| New Zealand | 2021-12-07 | 25935 | 30192 |
| Republic Of Serbia | 2021-12-12 | 1616 | 1654 |
| France | 2021-11-05 | 304739 | 383660 |
| United Kingdom | 2021-10-07 | 1303243 | 1856026 |
| Argentina | 2021-10-27 | 7867 | 11595 |
| Chile | 2021-10-26 | 21523 | 27835 |
| Norway | 2021-11-24 | 33653 | 39151 |
| Poland | 2021-09-21 | 40754 | 68256 |
| Portugal | 2021-11-19 | 20670 | 25068 |
| Israel | 2021-09-29 | 86059 | 99400 |
| Mexico | 2021-11-16 | 37829 | 44656 |
| Croatia | 2021-12-01 | 22221 | 29896 |
| Netherlands | 2021-11-13 | 68621 | 86583 |
| Denmark | 2021-11-22 | 344639 | 400930 |
| Canada | 2021-10-29 | 250029 | 319977 |
| Turkey | 2021-12-02 | 20035 | 25725 |
| Kazakhstan | 2021-12-10 | 1357 | 1570 |
| Austria | 2021-09-25 | 44842 | 59122 |
| Philippines | 2021-11-20 | 11203 | 12959 |
| Switzerland | 2021-11-21 | 49088 | 64585 |
| Kenya | 2021-09-04 | 3322 | 4010 |
| South Africa | 2021-10-12 | 20143 | 23146 |
| Djibouti | 2021-12-16 | 629 | 632 |
| Puerto Rico | 2021-11-29 | 9616 | 11186 |
| Bulgaria | 2021-12-13 | 7084 | 8747 |
| Ecuador | 2021-12-02 | 4165 | 5084 |
| Andorra | 2021-12-17 | 138 | 152 |
| Brunei | 2021-12-16 | 3761 | 6187 |
| Czech Republic | 2021-11-11 | 31118 | 39158 |
| Peru | 2021-11-28 | 26201 | 36889 |
| Mayotte | 2021-12-14 | 323 | 371 |
| Cambodia | 2021-12-12 | 1702 | 1974 |
| Hong Kong | 2021-11-13 | 12436 | 13453 |
| Singapore | 2021-12-02 | 16827 | 28089 |
| Finland | 2021-11-23 | 20512 | 25453 |
| Spain | 2021-09-01 | 99262 | 142850 |
| Estonia | 2021-12-15 | 6148 | 6518 |
| Thailand | 2021-09-12 | 20418 | 28907 |
| Pakistan | 2021-12-08 | 2157 | 2809 |
| Slovenia | 2021-11-30 | 32608 | 39437 |
| Reunion | 2021-09-24 | 9579 | 13638 |
| Georgia | 2021-12-14 | 1878 | 2216 |
| Lithuania | 2021-12-09 | 9739 | 12647 |
| Curaçao | 2021-12-16 | 1148 | 1227 |
| Guadeloupe | 2021-11-02 | 551 | 631 |
| Moldova | 2021-12-18 | 587 | 685 |
| Paraguay | 2021-10-10 | 1809 | 2164 |
| Russia | 2021-09-29 | 37558 | 54773 |
| Greece | 2021-11-29 | 16644 | 20151 |
| Latvia | 2021-12-07 | 13585 | 14968 |
| Montenegro | 2021-12-04 | 437 | 571 |
| Liechtenstein | 2021-12-10 | 661 | 793 |
| Romania | 2021-12-01 | 10184 | 11305 |
| North Macedonia | 2021-12-28 | 239 | 256 |
| South Korea | 2021-11-24 | 78768 | 106009 |
| Jamaica | 2021-12-09 | 2891 | 3187 |
| Slovakia | 2021-09-17 | 25173 | 36877 |
| Costa Rica | 2021-12-10 | 6836 | 9364 |
| Venezuela | 2021-12-11 | 492 | 574 |
| Uganda | 2021-11-23 | 440 | 581 |
| Kosovo | 2021-12-16 | 643 | 752 |
| Colombia | 2021-10-09 | 7316 | 11121 |
| Syria | 2022-01-05 | 72 | 80 |
| Panama | 2021-12-11 | 2524 | 3347 |
| Bangladesh | 2021-11-27 | 1637 | 2295 |
| China | 2021-12-04 | 29453 | 52185 |
| Taiwan | 2021-12-13 | 2631 | 3264 |
| Mozambique | 2021-11-26 | 306 | 392 |
| Kuwait | 2022-01-16 | 469 | 680 |
| Ghana | 2021-11-10 | 1334 | 1395 |
| Angola | 2021-12-21 | 112 | 112 |
| Jordan | 2021-12-07 | 200 | 267 |
| Iran | 2021-11-26 | 1547 | 1694 |
| Zimbabwe | 2021-11-26 | 249 | 249 |
| Senegal | 2021-11-25 | 714 | 726 |
| Belize | 2021-12-20 | 583 | 642 |
| Vietnam | 2021-12-21 | 4627 | 5802 |
| Dominican Republic | 2021-12-02 | 952 | 2031 |
| Botswana | 2021-11-11 | 1480 | 1616 |
| Sudan | 2022-01-03 | 161 | 183 |
| Algeria | 2021-12-10 | 466 | 550 |
| Morocco | 2021-12-07 | 1164 | 1268 |
| Guinea | 2021-12-21 | 281 | 329 |
| Ukraine | 2021-12-14 | 1275 | 2675 |
| Mongolia | 2021-12-02 | 737 | 933 |
| Nepal | 2021-11-25 | 1000 | 1259 |
| Malta | 2021-12-13 | 138 | 267 |
| Barbados | 2021-12-16 | 149 | 175 |
| Iceland | 2021-12-01 | 9858 | 12459 |
| Myanmar | 2021-11-30 | 61 | 121 |
| Guam | 2021-12-20 | 483 | 489 |
| Saint-Martin | 2021-12-14 | 295 | 313 |
| Nicaragua | 2021-12-23 | 63 | 142 |
| Zambia | 2021-11-30 | 293 | 369 |
| Hungary | 2021-12-14 | 381 | 439 |
| Bosnia And Herzegovina | 2021-12-08 | 194 | 495 |
| Sri Lanka | 2021-11-24 | 741 | 1179 |
| Guatemala | 2021-12-07 | 1736 | 3432 |
| Haiti | 2021-12-20 | 302 | 324 |
| Papua New Guinea | 2021-12-26 | 775 | 786 |
| Laos | 2022-02-25 | 605 | 796 |
| Malawi | 2021-12-02 | 197 | 199 |
| Gibraltar | 2021-12-07 | 112 | 323 |
| Bahrain | 2021-12-05 | 6183 | 7142 |
| Aruba | 2021-12-16 | 945 | 1043 |
| Bolivia | 2021-12-18 | 115 | 173 |
| Iraq | 2021-11-27 | 248 | 357 |
| Ivory Coast | 2021-12-03 | 159 | 195 |
| Egypt | 2021-12-01 | 1157 | 1652 |
| Eswatini | 2021-11-23 | 560 | 563 |
| Palestine | 2022-01-19 | 12 | 25 |
| Qatar | 2021-11-27 | 1364 | 1539 |
| Lebanon | 2021-12-03 | 472 | 604 |
| Oman | 2021-12-01 | 121 | 324 |
| Solomon Islands | 2022-03-27 | 218 | 238 |
| Namibia | 2021-12-02 | 498 | 512 |
| Rwanda | 2021-12-09 | 70 | 71 |
| Democratic Republic Of The Congo | 2021-10-02 | 121 | 174 |
| Cameroon | 2021-10-29 | 988 | 1037 |
| New Caledonia | 2021-12-31 | 59 | 60 |
| Republic Of Congo | 2021-09-12 | 71 | 177 |
| Gambia | 2021-12-17 | 159 | 159 |
| South Sudan | 2021-12-13 | 28 | 28 |
| Lesotho | 2021-11-12 | 79 | 81 |
| Niger | 2022-01-06 | 31 | 31 |
| El Salvador | 2021-12-05 | 302 | 390 |
| Honduras | 2021-12-14 | 60 | 122 |
| Saudi Arabia | 2021-12-13 | 578 | 610 |
| Central African Republic | 2021-12-20 | 39 | 60 |
| Suriname | 2021-12-24 | 132 | 143 |
| Uruguay | 2021-12-27 | 202 | 224 |
| Tunisia | 2021-12-02 | 561 | 634 |
| Kyrgyzstan | 2021-12-24 | 42 | 49 |
| Albania | 2021-10-12 | 767 | 1340 |
| Benin | 2021-12-14 | 454 | 454 |
| British Virgin Islands | 2021-12-17 | 37 | 57 |
| Cyprus | 2021-12-21 | 396 | 420 |
| Mali | 2021-12-23 | 44 | 59 |
| United Arab Emirates | 2021-11-10 | 732 | 1272 |
| Togo | 2021-12-12 | 182 | 208 |
| Ethiopia | 2021-12-27 | 96 | 98 |
| Libya | 2022-03-23 | 22 | 22 |
| Armenia | 2022-01-11 | 5 | 7 |
| Madagascar | 2021-12-12 | 57 | 69 |
| Burkina Faso | 2021-11-03 | 29 | 54 |
| Cayman Islands | 2022-10-10 | 210 | 279 |
| Chad | 2021-12-30 | 4 | 4 |
| Guyana | 2022-01-02 | 72 | 74 |
| Liberia | 2021-12-14 | 12 | 12 |
| The Bahamas | 2021-12-15 | 90 | 96 |
| Mauritania | 2022-05-12 | 1 | 1 |
| Afghanistan | 2022-02-13 | 2 | 3 |
| Bhutan | 2022-01-05 | 82 | 92 |
| Burundi | 2021-12-25 | 9 | 9 |
| Azerbaijan | 2022-01-10 | 20 | 20 |
| Vanuatu | 2022-02-16 | 93 | 93 |
| Belarus | 2022-01-20 | 40 | 48 |
| Tanzania | 2021-12-18 | 2 | 2 |
| Equatorial Guinea | 2022-01-03 | 2 | 2 |
| Uzbekistan | 2022-05-26 | 34 | 36 |
| East Timor | 2022-01-31 | 1 | 1 |
| Gabon | 2022-06-29 | 2 | 2 |
Data source and processing
The data on this page is recent as of 2023-08-24, 10:12 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.