B.1.617.2 2024-05-24



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 184
Sequence count 278666
Countries India 61854, Turkey 43803, United States of America 39482, Germany 19791, United Kingdom 18218, France 11633, Denmark 10735, Netherlands 4607, Italy 4408, Sweden 4356, Belgium 4148, Canada 3452, Spain 3040, Switzerland 3035, Poland 2818, Croatia 2784, United Arab Emirates 2606, Slovenia 2158, Bulgaria 2153, Bangladesh 2092, Israel 1740, Philippines 1632, Nepal 1569, Czech Republic 1394, Norway 1118, Singapore 1086, Bahrain 1083, Russia 1075, Latvia 1007, Pakistan 982, Portugal 941, Slovakia 915, Qatar 908, Luxembourg 906, Finland 792, Ireland 762, Japan 729, South Africa 712, China 628, Indonesia 494, South Korea 483, Austria 432, Romania 395, Mexico 373, Thailand 360, Reunion 358, Australia 355, Malawi 315, Malaysia 294, Kenya 289, Mongolia 279, Iceland 275, Greece 267, Lithuania 262, Ghana 234, Lebanon 223, Iraq 214, Egypt 212, Cameroon 202, Brazil 184, Maldives 177, Sri Lanka 175, Chile 145, Sudan 141, Hong Kong 139, Georgia 133, Ethiopia 133, Kuwait 130, Puerto Rico 129, Aruba 126, Iran 124, Jordan 118, Estonia 113, Guadeloupe 112, Botswana 107, Cyprus 102, Gambia 99, Togo 99, Kyrgyzstan 98, Nigeria 96, Panama 87, Senegal 83, Mauritius 81, Democratic Republic of the Congo 81, Bosnia and Herzegovina 80, Algeria 78, Rwanda 76, Belize 76, Peru 74, Oman 74, Kazakhstan 73, Benin 71, Canary Islands 70, Cambodia 69, Argentina 68, Cote d'Ivoire 68, Morocco 67, Colombia 58, Guinea 56, Zimbabwe 56, Montenegro 51, French Guiana 47, Mozambique 46, Uganda 45, New Zealand 43, Angola 41, Ukraine 38, Sierra Leone 37, Seychelles 34, Sint Maarten 34, Kosovo 30, Burkina Faso 30, Bhutan 30, Uzbekistan 29, Zambia 28, Burundi 26, Ecuador 26, Myanmar 26, Paraguay 21, Republic of Serbia 20, Martinique 18, Afghanistan 18, Vietnam 16, Guyana 16, Malta 15, Saudi Arabia 14, Gibraltar 14, Republic of the Congo 13, Syria 12, Jamaica 11, Curaçao 11, Chad 10, U.S. Virgin Islands 10, Taiwan 9, Tunisia 9, Papua New Guinea 8, Eswatini 8, Laos 8, Costa Rica 8, Northern Mariana Islands 7, Niger 7, Venezuela 7, Crimea 7, Grenada 7, North Macedonia 7, Guatemala 7, Antigua and Barbuda 6, South Sudan 6, Djibouti 6, Cayman Islands 6, Cabo Verde 6, Liberia 5, Azerbaijan 5, Liechtenstein 4, Brunei 4, Albania 4, Dominican Republic 4, Hungary 4, Belarus 4, Bonaire 4, Sao Tome and Principe 4, Gabon 3, Barbados 3, Turks and Caicos Islands 3, Armenia 3, The Bahamas 3, Uruguay 3, Moldova 2, Mauritania 2, Madagascar 2, Lesotho 2, Fiji 2, Montserrat 2, Central African Republic 1, Suriname 1, Namibia 1, East Timor 1, Guam 1, Mayotte 1, British Virgin Islands 1, Monaco 1, Comoros 1, Tanzania 1, Trinidad and Tobago 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
France 2021-03-17 151396 532569
Netherlands 2021-03-07 44926 154552
Czech Republic 2021-03-03 18447 55717
Germany 2021-03-09 215277 890707
United States Of America 2021-03-03 1435010 4309834
Australia 2021-03-18 30444 189343
United Kingdom 2021-03-09 1101958 2615892
Spain 2021-03-08 54600 224655
Italy 2021-03-16 47944 162912
Brazil 2021-04-06 46258 213370
Malaysia 2021-03-09 7315 39507
Suriname 2021-07-12 266 499
Indonesia 2021-03-09 8311 47862
Switzerland 2021-04-07 56697 124755
Canada 2021-03-06 105109 523187
Ireland 2021-04-03 26697 92923
Slovakia 2021-03-09 13952 45602
Bulgaria 2021-04-05 10279 19175
Belgium 2021-04-06 48058 158456
Israel 2021-04-08 18296 113411
Norway 2021-04-15 22933 66971
Slovenia 2021-03-01 27712 74452
South Africa 2021-03-17 11175 38610
Mexico 2021-03-02 25451 85574
Jordan 2021-04-26 499 801
Croatia 2021-04-25 13866 41028
Latvia 2021-03-25 5528 23599
Reunion 2021-05-04 5612 19353
Colombia 2021-03-11 3923 18082
Montenegro 2021-06-18 437 1050
Vanuatu 2021-10-24 2 95
India 2021-03-01 77834 186343
Puerto Rico 2021-06-03 3740 17304
Vietnam 2021-04-20 2594 8255
Japan 2021-03-28 97051 623622
Greece 2021-03-23 4954 35023
Poland 2021-04-22 29148 81294
Sweden 2021-04-01 57776 215286
New Zealand 2021-03-15 4797 43756
Singapore 2021-04-01 8746 45741
Costa Rica 2021-06-13 1282 11671
Peru 2021-05-15 7112 50944
Kuwait 2021-05-24 144 911
Lithuania 2021-05-26 14796 28845
Denmark 2021-03-29 162710 593799
Turkey 2021-03-09 59904 98218
Egypt 2021-06-22 287 2504
Finland 2021-04-17 13316 41542
Luxembourg 2021-04-01 9016 48764
Mozambique 2021-03-15 522 1018
Romania 2021-03-28 6048 18918
Thailand 2021-03-06 8148 35448
Gabon 2021-07-06 109 122
Trinidad And Tobago 2021-08-03 413 2477
Austria 2021-04-17 6158 67319
Estonia 2021-06-10 4233 10589
Guadeloupe 2021-05-25 1398 2122
South Korea 2021-04-19 17153 152368
Chile 2021-06-13 8669 41688
Portugal 2021-04-18 14590 40656
Russia 2021-03-01 18864 71417
Gambia 2021-04-08 307 483
Brunei 2021-07-21 603 7011
Moldova 2021-06-17 167 829
Guatemala 2021-04-24 698 5051
Kenya 2021-03-15 2205 7156
Bosnia And Herzegovina 2021-06-08 1079 1353
Belarus 2021-05-24 232 275
Bahrain 2021-04-05 3537 10810
Bangladesh 2021-04-23 2899 5176
Hungary 2021-05-27 86 697
Honduras 2021-07-30 64 329
Dominican Republic 2021-03-11 620 2961
Argentina 2021-04-24 4041 17684
Papua New Guinea 2021-07-07 1498 2289
Jamaica 2021-04-11 391 3818
Nepal 2021-04-12 1850 2943
North Macedonia 2021-06-14 122 554
Botswana 2021-05-09 1005 2703
Saudi Arabia 2021-05-12 22 695
Kosovo 2021-04-30 914 1714
Cyprus 2021-04-25 1563 6168
Ethiopia 2021-03-15 370 650
Curaçao 2021-06-28 599 1901
Aruba 2021-04-10 1856 3486
Nigeria 2021-04-10 2085 4115
Philippines 2021-04-13 3308 21087
Cambodia 2021-05-25 1209 3666
Sri Lanka 2021-03-11 1445 2731
Liechtenstein 2021-06-18 383 1054
Mayotte 2021-07-28 146 511
Ghana 2021-03-05 889 2778
Pakistan 2021-04-08 1751 5200
Guam 2021-04-26 279 881
Gibraltar 2021-06-03 1740 1872
Uzbekistan 2021-06-25 51 92
Ukraine 2021-06-17 448 4939
Zambia 2021-03-26 335 729
Ecuador 2021-06-22 1196 8394
China 2021-04-21 1397 76788
Iran 2021-04-18 256 2129
Tunisia 2021-04-05 641 2017
Haiti 2021-10-21 12 399
Mongolia 2021-03-08 435 2403
Iraq 2021-03-01 503 849
Andorra 2021-07-08 51 189
Rwanda 2021-03-22 214 358
Hong Kong 2021-03-25 757 14468
Chad 2021-07-05 47 59
Bolivia 2021-06-14 49 257
Angola 2021-04-18 232 451
Malta 2021-05-19 400 566
Republic Of Serbia 2021-06-26 180 1830
Armenia 2021-06-17 39 45
Paraguay 2021-03-01 421 3017
Eswatini 2021-06-08 272 951
Guinea 2021-05-17 119 478
Ivory Coast 2021-03-01 86 611
Democratic Republic Of The Congo 2021-03-03 268 543
British Virgin Islands 2021-07-27 31 86
Cameroon 2021-04-01 328 1411
Zimbabwe 2021-06-23 135 386
Morocco 2021-04-22 222 1587
Taiwan 2021-03-22 43 5122
Belize 2021-03-07 259 995
Burundi 2021-05-27 57 72
Senegal 2021-04-02 617 1877
Fiji 2021-04-14 469 470
Qatar 2021-04-17 1687 3626
Malawi 2021-03-17 384 633
Albania 2021-06-16 589 1589
Republic Of Congo 2021-03-12 92 316
Benin 2021-05-27 176 676
Burkina Faso 2021-03-18 61 119
El Salvador 2021-08-02 86 714
Nicaragua 2021-06-23 156 426
Kyrgyzstan 2021-06-08 134 186
United Arab Emirates 2021-05-28 3878 4620
South Sudan 2021-04-27 83 117
Niger 2021-07-01 10 43
Algeria 2021-05-10 80 655
Uganda 2021-04-20 452 1241
Panama 2021-04-29 895 5266
Georgia 2021-05-11 766 3264
Central African Republic 2021-11-25 5 82
Iceland 2021-05-07 5674 17265
Sudan 2021-03-01 156 428
Guyana 2021-09-06 48 124
Solomon Islands 2022-01-26 77 307
Togo 2021-04-12 337 654
Oman 2021-03-05 111 922
Venezuela 2021-07-07 176 853
Azerbaijan 2021-07-14 33 53
Lebanon 2021-06-07 639 1195
The Bahamas 2021-05-17 141 297
Barbados 2021-04-25 12 252
East Timor 2021-03-08 23 271
Uruguay 2021-09-03 68 349
Mauritania 2021-03-16 20 49
Kazakhstan 2021-07-25 721 2935
Mali 2021-04-08 6 76
Saint Lucia 2021-07-14 11 222
Laos 2021-07-27 1169 2139
Syria 2021-12-01 32 109
Namibia 2021-03-08 79 641
Afghanistan 2021-04-26 18 75
Sierra Leone 2021-05-07 39 43
Djibouti 2021-06-30 64 695
Myanmar 2021-05-28 40 209
Somalia 2021-08-31 2 10
Libya 2021-12-29 3 25
Liberia 2021-03-09 61 99
Cayman Islands 2021-07-19 37 316
Saint-Martin 2021-11-24 27 328
Equatorial Guinea 2021-07-17 12 15
Bhutan 2021-04-12 31 132
Madagascar 2021-09-27 29 86
Lesotho 2021-04-30 41 129
Tanzania 2021-05-03 1 3

Data source and processing

The data on this page is recent as of 2024-05-24, 18:05 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.