B.1.617.2 2023-04-02



Description

A lineage circulating with variants of biological significance S:P681R and S:L452R, first detected in India and international cases with travel history from India. Designated through GitHub issues https://github.com/cov-lineages/pango-designation/issues/38 and https://github.com/cov-lineages/pango-designation/issues/49
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.

Table 1 | Summary of B.1.617.2 data

Statistic Information
Countries with sequences 182
Sequence count 276632
Countries India 61608, Turkey 43795, United States of America 39224, Germany 19378, United Kingdom 18231, France 11591, Denmark 10516, Netherlands 4533, Sweden 4316, Belgium 4126, Italy 4061, Canada 3448, Switzerland 3033, Spain 2874, Poland 2815, Croatia 2791, United Arab Emirates 2601, Slovenia 2174, Bulgaria 2141, Bangladesh 2072, Philippines 1781, Israel 1704, Nepal 1566, Czech Republic 1412, Norway 1120, Singapore 1086, Bahrain 1076, Latvia 1024, Portugal 941, Russia 927, Slovakia 916, Qatar 912, Luxembourg 902, Pakistan 826, Finland 817, Ireland 764, Thailand 744, Japan 694, China 627, South Africa 610, Indonesia 487, South Korea 474, Austria 435, Romania 387, Australia 370, Mexico 364, Reunion 343, Malawi 315, Malaysia 298, Kenya 288, Iceland 274, Greece 267, Lithuania 251, Ghana 233, Iraq 214, Egypt 211, Brazil 204, Cameroon 202, Mongolia 191, Maldives 177, Lebanon 165, Cambodia 156, Sri Lanka 155, Hong Kong 140, Ethiopia 134, Georgia 133, Kuwait 129, Puerto Rico 128, Aruba 126, Chile 121, Iran 118, Jordan 117, Guadeloupe 112, Estonia 108, Togo 99, Gambia 98, Kyrgyzstan 98, Botswana 93, Nigeria 92, Panama 87, Senegal 83, Bosnia and Herzegovina 81, Mauritius 81, Democratic Republic of the Congo 81, Algeria 78, Peru 77, Belize 77, Rwanda 76, Oman 74, Canary Islands 70, Argentina 69, Benin 67, Cote d'Ivoire 65, Zambia 63, Colombia 61, Sudan 59, Morocco 58, Zimbabwe 57, Cyprus 56, Guinea 53, Montenegro 51, French Guiana 47, Uganda 45, Mozambique 44, New Zealand 43, Angola 41, Ukraine 38, Kazakhstan 37, Sierra Leone 37, Sint Maarten 35, Seychelles 34, Kosovo 32, Burkina Faso 30, Uzbekistan 29, Myanmar 26, Burundi 26, Bhutan 25, Ecuador 24, Fiji 23, Republic of Serbia 20, Paraguay 19, Afghanistan 18, Martinique 18, Guyana 16, Vietnam 16, Saudi Arabia 14, Malta 14, Republic of the Congo 13, Gibraltar 13, Jamaica 11, Syria 11, Curaçao 10, Chad 9, Taiwan 9, U.S. Virgin Islands 8, Eswatini 8, Costa Rica 8, Papua New Guinea 8, Tunisia 8, Crimea 7, North Macedonia 7, Laos 7, Venezuela 6, Belarus 6, South Sudan 6, Antigua and Barbuda 6, Djibouti 6, Cayman Islands 6, Liberia 5, Dominican Republic 5, Guatemala 5, Niger 5, Northern Mariana Islands 5, Brunei 5, Grenada 5, Azerbaijan 5, Cabo Verde 4, Albania 4, Sao Tome and Principe 4, Liechtenstein 4, Bonaire 4, Turks and Caicos Islands 3, Lesotho 3, Gabon 3, Barbados 3, Hungary 3, The Bahamas 3, Armenia 3, Comoros 2, Mauritania 2, Moldova 2, Madagascar 2, Montserrat 2, Suriname 1, Mayotte 1, Monaco 1, Trinidad and Tobago 1, Tanzania 1, Guam 1, Uruguay 1, East Timor 1, British Virgin Islands 1
First detected India
Earliest sample date 2021-03-01
Defining SNPs S:T19R
S:L452R
S:T478K
S:P681R
S:D950N
ORF3a:S26L
M:I82T
ORF7a:V82A
ORF7a:T120I
N:D63G
N:R203M
N:D377Y

Figure 1 | Cumulative sequence count over time B.1.617.2

Bars show the number of new sequences on GISAID over time, binned by epi-week. The line shows the cumulative number of sequences over time.


Figure 2 | Date of earliest_B.1.617.2 detected

Schematic map showing the date of the first sequence sample date in each country containing the lineage. Darker countries have earlier first sample dates.


Figure 3 | Map of B.1.617.2 sequence counts

Map showing the logged number of sequences of the variant in each country. Countries with more sequences are shown in darker colours.


Figure 4 | Sequence count per country B.1.617.2

The number of sequences of the lineage recorded in each country. The height of the bar is the logged number and the numbers above the bar are the raw counts.


Figure 5 | Frequency B.1.617.2 in sequences produced since first new variant reported per country

The overall frequency of the lineage, defined as the number of sequences assigned the lineage divided by the total number of sequences from that country in the time since the variant was first sequenced in that country.


Figure 6 | B.1.617.2 count per continent

Seven day rolling average of sequence counts per continent. Please note that recent declines may be due to delay in reporting rather than reflecting a change in the underlying virus population.


Figure 7 | Rolling average B.1.617.2 frequency per continent

Seven day rolling average of frequency of sequences of the lineage of interest. Frequency is calculated by dividing the number of sequences of the lineage of interest by the total sequences for each continent for each day.



Table 3 | Raw data for figures




Country Earliest sequence Number of variant sequences Total sequences since first variant sequence
United States Of America 2021-03-03 1430273 3943755
United Kingdom 2021-03-09 1101502 2518995
Germany 2021-03-09 211805 852992
France 2021-03-17 151395 484158
Australia 2021-03-18 30347 150284
Netherlands 2021-03-07 44845 141392
Sweden 2021-04-01 57701 184879
Switzerland 2021-04-07 56625 119397
India 2021-03-01 77454 171556
Indonesia 2021-03-09 8302 42196
Mexico 2021-03-02 25413 78085
Japan 2021-03-28 96330 542660
Italy 2021-03-16 44797 142426
Croatia 2021-04-25 13862 37891
Russia 2021-03-01 14990 53439
Czech Republic 2021-03-03 18084 53189
Belgium 2021-04-06 48051 149793
Israel 2021-04-08 18282 107004
Poland 2021-04-22 29145 77157
Ireland 2021-04-03 26697 85878
Denmark 2021-03-29 159366 554573
Chile 2021-06-13 8663 36116
Latvia 2021-03-25 5527 23036
Spain 2021-03-08 52699 179817
Brazil 2021-04-06 45529 187994
Reunion 2021-05-04 5612 17107
Bosnia And Herzegovina 2021-06-08 1079 1290
Canada 2021-03-06 104391 422571
Argentina 2021-04-24 4040 13747
Norway 2021-04-15 22933 63605
Slovenia 2021-03-01 27710 70899
Republic Of Serbia 2021-06-26 175 1823
South Korea 2021-04-19 16971 89932
Puerto Rico 2021-06-03 3740 13274
Turkey 2021-03-09 59887 96495
Peru 2021-05-15 7103 42467
Tunisia 2021-04-05 549 1323
Qatar 2021-04-17 1686 3433
Singapore 2021-04-01 8746 29145
Portugal 2021-04-18 14560 37299
Romania 2021-03-28 6046 16554
Bulgaria 2021-04-05 10242 18041
Malaysia 2021-03-09 7258 33098
Lithuania 2021-05-26 14794 26555
Thailand 2021-03-06 8143 30360
Colombia 2021-03-11 3832 15857
Guam 2021-04-26 279 861
Nepal 2021-04-12 1848 2862
Gabon 2021-07-06 109 122
Brunei 2021-07-21 603 5809
Luxembourg 2021-04-01 9016 44345
Saint-Martin 2021-11-24 27 322
Slovakia 2021-03-09 13948 43078
Paraguay 2021-03-01 419 2268
Dominican Republic 2021-03-11 619 2293
Bangladesh 2021-04-23 2876 4869
Finland 2021-04-17 13314 36005
Liechtenstein 2021-06-18 383 1054
China 2021-04-21 1358 19729
Belize 2021-03-07 220 904
New Zealand 2021-03-15 4792 30715
Hong Kong 2021-03-25 757 12084
Cyprus 2021-04-25 825 1470
Vietnam 2021-04-20 2524 7062
Eswatini 2021-06-08 272 862
Guatemala 2021-04-24 698 3832
Gambia 2021-04-08 307 483
Kenya 2021-03-15 2197 6208
Senegal 2021-04-02 617 1784
Saudi Arabia 2021-05-12 22 657
South Africa 2021-03-17 10989 34705
Botswana 2021-05-09 994 2638
Kosovo 2021-04-30 914 1562
Philippines 2021-04-13 3300 19174
Bahrain 2021-04-05 3537 10355
Georgia 2021-05-11 766 2723
Greece 2021-03-23 4953 23194
British Virgin Islands 2021-07-27 31 86
Uganda 2021-04-20 385 822
Cambodia 2021-05-25 1209 3540
Austria 2021-04-17 6157 55643
Papua New Guinea 2021-07-07 1498 2289
Pakistan 2021-04-08 1495 4305
Nicaragua 2021-06-23 156 426
Nigeria 2021-04-10 2070 3841
Panama 2021-04-29 895 4897
Trinidad And Tobago 2021-08-03 412 2221
Gibraltar 2021-06-03 1739 1872
Aruba 2021-04-10 1856 3418
Montenegro 2021-06-18 437 871
Malta 2021-05-19 399 566
Ecuador 2021-06-22 1195 6949
Bolivia 2021-06-14 49 195
Democratic Republic Of The Congo 2021-03-03 252 481
Ukraine 2021-06-17 449 1578
Guadeloupe 2021-05-25 1398 2028
Kyrgyzstan 2021-06-08 134 186
Chad 2021-07-05 33 38
Jordan 2021-04-26 498 749
Iran 2021-04-18 249 1816
Jamaica 2021-04-11 391 2429
Laos 2021-08-04 472 974
Ghana 2021-03-05 882 2732
Mozambique 2021-03-15 522 967
Zimbabwe 2021-06-23 135 367
Guyana 2021-09-06 48 124
Iraq 2021-03-01 503 826
Kazakhstan 2021-07-25 464 1436
Sri Lanka 2021-03-11 1388 2578
Egypt 2021-06-22 284 1026
Estonia 2021-06-10 4228 10495
North Macedonia 2021-06-14 122 371
Oman 2021-03-05 111 420
Costa Rica 2021-06-13 1282 9355
Armenia 2021-06-17 39 45
Mayotte 2021-07-28 146 501
Mongolia 2021-03-08 321 1567
Ethiopia 2021-03-15 368 485
Angola 2021-04-18 232 451
Malawi 2021-03-17 384 608
Algeria 2021-05-10 80 542
Iceland 2021-05-07 5673 15809
Togo 2021-04-12 337 537
Venezuela 2021-07-07 176 686
Suriname 2021-07-12 266 499
Saint Lucia 2021-07-14 11 160
Cameroon 2021-04-01 328 909
United Arab Emirates 2021-05-28 3877 4620
Uruguay 2021-09-03 64 267
Albania 2021-06-16 559 1080
Curaçao 2021-06-28 599 1768
Kuwait 2021-05-24 144 639
Belarus 2021-05-24 232 275
Liberia 2021-03-09 56 89
The Bahamas 2021-05-17 141 285
Andorra 2021-07-08 51 189
Rwanda 2021-03-22 214 358
Mauritania 2021-03-16 20 49
Moldova 2021-06-17 167 782
Lebanon 2021-06-07 631 1074
Honduras 2021-07-30 64 114
Morocco 2021-04-22 204 1369
Benin 2021-05-27 168 663
Solomon Islands 2022-01-26 77 307
El Salvador 2021-08-02 79 389
Ivory Coast 2021-03-01 83 529
Lesotho 2021-04-30 41 128
Burkina Faso 2021-03-18 58 104
Central African Republic 2021-12-12 2 18
Taiwan 2021-03-22 39 2683
Fiji 2021-04-14 469 470
Myanmar 2021-05-28 40 98
Barbados 2021-04-25 12 178
Namibia 2021-03-08 79 633
Afghanistan 2021-04-26 18 63
Hungary 2021-11-15 85 453
Guinea 2021-05-17 115 409
Zambia 2021-03-26 335 698
Sierra Leone 2021-05-07 39 43
Sudan 2021-05-07 60 194
Cayman Islands 2021-07-19 37 316
Niger 2021-07-01 8 38
Republic Of Congo 2021-03-12 91 307
South Sudan 2021-04-27 83 117
Syria 2021-12-01 32 106
Uzbekistan 2021-06-25 51 92
Libya 2021-12-29 3 25
Vanuatu 2021-10-24 2 95
Equatorial Guinea 2021-07-17 12 15
Burundi 2021-05-27 57 72
Bhutan 2021-04-12 26 84
Djibouti 2021-06-30 64 568
Mali 2021-04-08 6 49
Somalia 2021-08-31 2 2
Azerbaijan 2021-07-14 33 53
Haiti 2021-10-21 12 318
East Timor 2021-03-08 23 271
Madagascar 2021-09-27 29 86
Tanzania 2021-05-03 1 3

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.1.617.2 to sequences with at least 5 of the 15 defining B.1.617.2 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.