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.