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.