B.1.1.529 2024-10-16
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 | 7656 |
| Countries | United States of America 2598, Germany 1038, India 672, Turkey 416, Russia 403, United Kingdom 339, France 227, Italy 180, Spain 134, Belgium 123, Czech Republic 120, Brazil 110, Argentina 71, Iceland 71, Poland 69, Switzerland 65, Thailand 56, Austria 50, Mexico 48, Paraguay 44, Romania 42, Botswana 41, Saudi Arabia 40, Nigeria 37, Australia 34, South Africa 31, Chile 30, Bahrain 29, Slovakia 27, Ireland 24, Pakistan 23, Senegal 23, Egypt 22, Kazakhstan 21, Morocco 21, Indonesia 20, Iran 18, Sweden 16, New Zealand 16, United Arab Emirates 16, Israel 15, Philippines 14, Bangladesh 13, Puerto Rico 13, Colombia 13, Canada 12, South Korea 12, Ecuador 12, Malaysia 11, Denmark 10, Slovenia 10, Peru 10, Ghana 10, Japan 8, Mauritius 7, Sri Lanka 6, Croatia 6, Vietnam 6, Panama 6, Lithuania 6, Kenya 5, Qatar 5, Finland 5, Kuwait 5, Netherlands 5, Tunisia 5, Reunion 4, Singapore 3, Brunei 3, Sudan 3, Luxembourg 2, Cameroon 2, Seychelles 2, Antigua and Barbuda 2, Latvia 2, China 2, Guatemala 2, Belarus 2, Republic of Serbia 2, Ukraine 2, Venezuela 2, Northern Mariana Islands 2, Guinea 1, Malta 1, Montenegro 1, Saint Vincent and the Grenadines 1, Cabo Verde 1, Cambodia 1, Uganda 1, Liechtenstein 1, Syria 1, Zambia 1, Togo 1, Estonia 1, Trinidad and Tobago 1, Cote d'Ivoire 1, Hong Kong 1, Mali 1, Norway 1, Jordan 1, Grenada 1, Portugal 1, Saint Lucia 1, Democratic Republic of the Congo 1, Uruguay 1, Guyana 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 Kingdom | 2021-10-07 | 1345571 | 1923274 |
| United States Of America | 2021-09-02 | 2204626 | 3473453 |
| Japan | 2021-11-27 | 432045 | 489601 |
| Germany | 2021-11-08 | 550545 | 667190 |
| Vietnam | 2021-12-21 | 4744 | 6112 |
| South Korea | 2021-11-24 | 90844 | 140050 |
| Italy | 2021-10-07 | 81507 | 116985 |
| Canada | 2021-10-29 | 297260 | 412949 |
| Brazil | 2021-10-31 | 104907 | 136812 |
| Sweden | 2021-11-19 | 108681 | 141516 |
| France | 2021-11-05 | 322748 | 422010 |
| Israel | 2021-09-29 | 89670 | 104914 |
| Ireland | 2021-11-25 | 54306 | 64192 |
| Austria | 2021-09-25 | 45959 | 62158 |
| Malaysia | 2021-11-08 | 25878 | 34093 |
| Netherlands | 2021-11-13 | 76641 | 99359 |
| Spain | 2021-09-01 | 125375 | 186071 |
| Peru | 2021-11-28 | 28705 | 42036 |
| Reunion | 2021-09-24 | 9653 | 14407 |
| Singapore | 2021-12-02 | 25151 | 41780 |
| Turkey | 2021-12-02 | 20506 | 27446 |
| Croatia | 2021-12-01 | 22605 | 31900 |
| Taiwan | 2021-12-13 | 4077 | 5596 |
| Colombia | 2021-10-09 | 7511 | 11866 |
| Greece | 2021-11-29 | 18977 | 28014 |
| China | 2021-12-04 | 44774 | 81945 |
| Pakistan | 2021-10-07 | 2381 | 3346 |
| Uruguay | 2021-12-27 | 236 | 336 |
| Australia | 2021-10-09 | 130473 | 176379 |
| Luxembourg | 2021-12-06 | 31834 | 37915 |
| Norway | 2021-11-24 | 34534 | 40799 |
| South Africa | 2021-10-12 | 21536 | 25264 |
| Kenya | 2021-09-04 | 3612 | 4561 |
| India | 2021-09-07 | 83564 | 131390 |
| Switzerland | 2021-11-21 | 51123 | 68990 |
| Poland | 2021-09-21 | 41984 | 71138 |
| Belgium | 2021-10-11 | 88665 | 117416 |
| Denmark | 2021-10-18 | 372119 | 486734 |
| Indonesia | 2021-11-29 | 30784 | 39096 |
| Venezuela | 2021-12-11 | 600 | 715 |
| Cambodia | 2021-12-12 | 1882 | 2183 |
| Algeria | 2021-12-10 | 543 | 665 |
| Sri Lanka | 2021-11-24 | 752 | 1193 |
| Guinea | 2021-12-21 | 287 | 346 |
| New Zealand | 2021-12-07 | 32330 | 42522 |
| Costa Rica | 2021-12-10 | 7920 | 10900 |
| Portugal | 2021-11-19 | 22388 | 27747 |
| Chile | 2021-10-26 | 23329 | 31509 |
| Ukraine | 2021-12-14 | 2204 | 5023 |
| Thailand | 2021-09-12 | 22306 | 32156 |
| Oman | 2021-12-01 | 433 | 761 |
| Hong Kong | 2021-11-13 | 14183 | 16399 |
| Finland | 2021-11-23 | 21711 | 28944 |
| Estonia | 2021-12-15 | 6251 | 6633 |
| Brunei | 2021-12-16 | 3962 | 6597 |
| Russia | 2021-09-29 | 40820 | 64170 |
| Mexico | 2021-11-16 | 40386 | 50967 |
| Slovakia | 2021-09-17 | 25643 | 38344 |
| Puerto Rico | 2021-11-29 | 13101 | 15666 |
| Lithuania | 2021-12-09 | 10245 | 14557 |
| Nepal | 2021-11-25 | 1079 | 1342 |
| Saudi Arabia | 2021-12-13 | 587 | 651 |
| Slovenia | 2021-11-30 | 33321 | 41718 |
| Czech Republic | 2021-11-11 | 31665 | 40471 |
| Senegal | 2021-11-25 | 857 | 907 |
| Gambia | 2021-12-17 | 159 | 159 |
| Georgia | 2021-12-14 | 1947 | 2567 |
| Nigeria | 2021-09-03 | 1929 | 2723 |
| Philippines | 2021-11-20 | 11463 | 13931 |
| Cameroon | 2021-10-29 | 1027 | 1077 |
| Tunisia | 2021-12-02 | 721 | 888 |
| Bahrain | 2021-12-05 | 6202 | 7511 |
| Dominican Republic | 2021-12-02 | 1251 | 2373 |
| Trinidad And Tobago | 2021-12-16 | 1562 | 1988 |
| Zambia | 2021-11-30 | 295 | 371 |
| Iceland | 2021-12-01 | 10691 | 13794 |
| Argentina | 2021-10-27 | 8305 | 12688 |
| North Macedonia | 2021-12-28 | 303 | 439 |
| Guatemala | 2021-12-07 | 2551 | 4527 |
| Romania | 2021-12-01 | 10434 | 12613 |
| Cyprus | 2021-12-04 | 4345 | 4843 |
| Morocco | 2021-12-07 | 1537 | 1708 |
| Uganda | 2021-11-23 | 487 | 783 |
| Ecuador | 2021-12-02 | 4600 | 6140 |
| Panama | 2021-12-11 | 2633 | 3478 |
| Montenegro | 2021-12-04 | 464 | 728 |
| Mozambique | 2021-11-26 | 325 | 413 |
| Kuwait | 2022-01-16 | 525 | 798 |
| Republic Of Serbia | 2021-12-12 | 1618 | 1656 |
| Ghana | 2021-11-10 | 1337 | 1399 |
| Curaçao | 2021-12-16 | 1217 | 1358 |
| Equatorial Guinea | 2022-01-03 | 2 | 2 |
| East Timor | 2022-01-31 | 1 | 1 |
| Angola | 2021-12-21 | 112 | 112 |
| Bulgaria | 2021-12-13 | 7147 | 9220 |
| Eswatini | 2021-11-23 | 583 | 652 |
| Guadeloupe | 2021-11-02 | 597 | 706 |
| Laos | 2022-02-25 | 787 | 1152 |
| Egypt | 2021-12-01 | 1625 | 2370 |
| Qatar | 2021-11-27 | 1428 | 1766 |
| El Salvador | 2021-12-05 | 433 | 677 |
| Belize | 2021-12-20 | 583 | 642 |
| Libya | 2022-03-23 | 22 | 22 |
| Botswana | 2021-11-11 | 1508 | 1644 |
| New Caledonia | 2021-12-31 | 89 | 100 |
| Jamaica | 2021-12-09 | 2899 | 3397 |
| Albania | 2021-10-12 | 776 | 1570 |
| Liechtenstein | 2021-12-10 | 661 | 793 |
| Bangladesh | 2021-11-27 | 1750 | 2561 |
| Kosovo | 2021-12-16 | 731 | 867 |
| Syria | 2022-01-05 | 72 | 83 |
| Zimbabwe | 2021-11-26 | 249 | 249 |
| Bosnia And Herzegovina | 2021-12-08 | 231 | 541 |
| Paraguay | 2021-10-10 | 1934 | 2481 |
| Haiti | 2021-12-20 | 368 | 431 |
| Palestine | 2022-01-19 | 18 | 60 |
| Guam | 2021-12-20 | 514 | 537 |
| Aruba | 2021-12-16 | 945 | 1073 |
| Iran | 2021-11-26 | 1559 | 1785 |
| Kazakhstan | 2021-12-10 | 1836 | 2354 |
| Malta | 2021-12-13 | 138 | 267 |
| Namibia | 2021-12-02 | 499 | 515 |
| Lesotho | 2021-11-12 | 80 | 82 |
| Mayotte | 2021-12-14 | 326 | 374 |
| Malawi | 2021-12-02 | 197 | 199 |
| Honduras | 2021-12-14 | 163 | 305 |
| Azerbaijan | 2022-01-10 | 28 | 36 |
| Togo | 2021-12-12 | 257 | 290 |
| Moldova | 2021-12-18 | 645 | 756 |
| Solomon Islands | 2022-03-27 | 218 | 238 |
| Benin | 2021-12-14 | 454 | 455 |
| Jordan | 2021-12-07 | 248 | 347 |
| South Sudan | 2021-12-13 | 38 | 38 |
| Bolivia | 2021-12-18 | 115 | 173 |
| Latvia | 2021-12-07 | 14126 | 15531 |
| Saint Lucia | 2022-01-21 | 136 | 207 |
| Democratic Republic Of The Congo | 2021-10-02 | 146 | 204 |
| Iraq | 2021-11-27 | 252 | 380 |
| Ethiopia | 2021-12-27 | 246 | 250 |
| Mongolia | 2021-12-02 | 757 | 1085 |
| Andorra | 2021-12-17 | 138 | 152 |
| British Virgin Islands | 2021-12-17 | 37 | 57 |
| Papua New Guinea | 2021-12-26 | 775 | 786 |
| Suriname | 2021-12-24 | 132 | 143 |
| Hungary | 2021-12-14 | 439 | 639 |
| Republic Of Congo | 2021-09-12 | 72 | 178 |
| United Arab Emirates | 2021-11-10 | 732 | 1272 |
| Sudan | 2022-01-03 | 161 | 183 |
| Central African Republic | 2021-12-20 | 41 | 64 |
| Chad | 2021-12-30 | 11 | 11 |
| Rwanda | 2021-12-09 | 70 | 71 |
| Myanmar | 2021-11-30 | 93 | 178 |
| Saint-Martin | 2021-12-14 | 296 | 314 |
| Djibouti | 2021-12-16 | 629 | 632 |
| Afghanistan | 2022-02-13 | 5 | 15 |
| Gibraltar | 2021-12-07 | 112 | 323 |
| Belarus | 2022-01-20 | 40 | 48 |
| Madagascar | 2021-12-12 | 57 | 69 |
| Ivory Coast | 2021-12-03 | 184 | 261 |
| Niger | 2022-01-06 | 31 | 31 |
| Barbados | 2021-12-16 | 214 | 279 |
| Lebanon | 2021-12-03 | 496 | 677 |
| Armenia | 2022-01-11 | 5 | 7 |
| The Bahamas | 2021-12-15 | 101 | 108 |
| Burkina Faso | 2021-11-03 | 37 | 65 |
| Kyrgyzstan | 2021-12-24 | 42 | 49 |
| Vanuatu | 2022-02-16 | 93 | 93 |
| Mali | 2021-12-23 | 44 | 59 |
| Bhutan | 2022-01-05 | 86 | 103 |
| Liberia | 2021-12-14 | 16 | 17 |
| Cayman Islands | 2022-10-10 | 210 | 279 |
| Guyana | 2022-01-02 | 72 | 74 |
| Uzbekistan | 2022-05-26 | 34 | 36 |
| Tanzania | 2021-12-18 | 2 | 2 |
| Mauritania | 2022-05-12 | 11 | 14 |
| Nicaragua | 2021-12-23 | 63 | 142 |
| Burundi | 2021-12-25 | 9 | 9 |
| Gabon | 2022-06-29 | 2 | 2 |
Data source and processing
The data on this page is recent as of 2024-10-16, 14:27 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.