B.1.617.2 2024-05-13



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 278593
Countries India 61854, Turkey 43803, United States of America 39482, Germany 19791, United Kingdom 18218, France 11633, Denmark 10665, 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 1738, 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 132, 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, Cote d'Ivoire 68, Argentina 68, Morocco 67, Colombia 58, Zimbabwe 56, Guinea 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, Myanmar 26, Ecuador 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, Curaçao 11, Jamaica 11, Chad 10, U.S. Virgin Islands 10, Tunisia 9, Taiwan 9, Costa Rica 8, Eswatini 8, Papua New Guinea 8, Laos 8, North Macedonia 7, Guatemala 7, Crimea 7, Niger 7, Grenada 7, Northern Mariana Islands 7, Venezuela 7, Cabo Verde 6, Cayman Islands 6, South Sudan 6, Antigua and Barbuda 6, Djibouti 6, Liberia 5, Azerbaijan 5, Liechtenstein 4, Hungary 4, Belarus 4, Sao Tome and Principe 4, Albania 4, Dominican Republic 4, Bonaire 4, Brunei 4, Turks and Caicos Islands 3, Barbados 3, Gabon 3, Armenia 3, The Bahamas 3, Uruguay 3, Lesotho 2, Moldova 2, Fiji 2, Mauritania 2, Montserrat 2, Madagascar 2, Mayotte 1, Monaco 1, Tanzania 1, Suriname 1, British Virgin Islands 1, East Timor 1, Guam 1, Trinidad and Tobago 1, Comoros 1, Namibia 1, Central African Republic 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 Kingdom 2021-03-09 1101958 2614556
Czech Republic 2021-03-03 18447 55717
Cambodia 2021-05-25 1209 3646
United States Of America 2021-03-03 1434928 4304716
Mexico 2021-03-02 25451 85305
Bosnia And Herzegovina 2021-06-08 1079 1353
Norway 2021-04-15 22933 66946
South Africa 2021-03-17 11175 38497
Guam 2021-04-26 279 881
Thailand 2021-03-06 8148 35321
Germany 2021-03-09 215277 890679
Poland 2021-04-22 29148 81294
Philippines 2021-04-13 3308 21087
India 2021-03-01 77834 186136
Turkey 2021-03-09 59904 98218
Brazil 2021-04-06 46258 212632
Sri Lanka 2021-03-11 1445 2731
Zambia 2021-03-26 335 729
Chile 2021-06-13 8669 41676
Switzerland 2021-04-07 56697 124755
Bangladesh 2021-04-23 2899 5176
Ireland 2021-04-03 26697 92808
Japan 2021-03-28 97051 621633
Portugal 2021-04-18 14590 40622
France 2021-03-17 151398 532446
Spain 2021-03-08 54600 223858
Malaysia 2021-03-09 7315 39471
Israel 2021-04-08 18291 113403
Finland 2021-04-17 13316 41458
Russia 2021-03-01 18864 71417
Romania 2021-03-28 6048 18904
Sweden 2021-04-01 57776 215210
Canada 2021-03-06 105109 521476
Netherlands 2021-03-07 44926 154527
Indonesia 2021-03-09 8311 47592
Vietnam 2021-04-20 2594 8255
Italy 2021-03-16 47944 162886
Denmark 2021-03-29 161462 580056
Bulgaria 2021-04-05 10279 19175
Jordan 2021-04-26 499 766
Austria 2021-04-17 6158 67319
Australia 2021-03-18 30444 188472
Curaçao 2021-06-28 599 1901
Slovakia 2021-03-09 13952 45602
North Macedonia 2021-06-14 122 554
Belgium 2021-04-06 48058 158438
Greece 2021-03-23 4954 35023
Belarus 2021-05-24 232 275
Liechtenstein 2021-06-18 383 1054
Reunion 2021-05-04 5612 19353
Slovenia 2021-03-01 27712 74444
Colombia 2021-03-11 3923 18082
South Korea 2021-04-19 17153 151717
Estonia 2021-06-10 4233 10589
Puerto Rico 2021-06-03 3740 17189
Lithuania 2021-05-26 14796 28845
Belize 2021-03-07 259 995
Pakistan 2021-04-08 1751 5191
Zimbabwe 2021-06-23 135 386
Malawi 2021-03-17 384 633
Cameroon 2021-04-01 328 1411
Rwanda 2021-03-22 214 358
Peru 2021-05-15 7112 50758
Montenegro 2021-06-18 437 1050
Mongolia 2021-03-08 435 2403
Bahrain 2021-04-05 3537 10810
Hong Kong 2021-03-25 757 14428
Panama 2021-04-29 895 5266
Singapore 2021-04-01 8746 45741
British Virgin Islands 2021-07-27 31 86
Saint Lucia 2021-07-14 11 222
Uganda 2021-04-20 452 1095
Argentina 2021-04-24 4041 17647
Ukraine 2021-06-17 448 4855
Syria 2021-12-01 32 109
Croatia 2021-04-25 13866 41028
Nigeria 2021-04-10 2085 4115
Ecuador 2021-06-22 1196 8386
Kenya 2021-03-15 2205 7132
Gibraltar 2021-06-03 1740 1872
New Zealand 2021-03-15 4797 43010
Nicaragua 2021-06-23 156 426
Luxembourg 2021-04-01 9016 48764
Georgia 2021-05-11 766 3249
Brunei 2021-07-21 603 7011
Dominican Republic 2021-03-11 620 2961
Latvia 2021-03-25 5528 23599
Jamaica 2021-04-11 391 3818
Costa Rica 2021-06-13 1282 11671
Malta 2021-05-19 400 566
Nepal 2021-04-12 1850 2943
Aruba 2021-04-10 1856 3486
Ghana 2021-03-05 889 2778
Egypt 2021-06-22 287 2504
Ethiopia 2021-03-15 368 587
Papua New Guinea 2021-07-07 1498 2289
Guadeloupe 2021-05-25 1398 2122
Saudi Arabia 2021-05-12 22 695
Mozambique 2021-03-15 522 1018
Moldova 2021-06-17 167 829
Angola 2021-04-18 232 451
Paraguay 2021-03-01 421 3017
Eswatini 2021-06-08 272 862
Algeria 2021-05-10 80 655
Kyrgyzstan 2021-06-08 134 186
Trinidad And Tobago 2021-08-03 413 2477
Guatemala 2021-04-24 698 5051
Gambia 2021-04-08 307 483
Kosovo 2021-04-30 914 1714
Republic Of Serbia 2021-06-26 180 1830
Gabon 2021-07-06 109 122
Tunisia 2021-04-05 641 2008
Morocco 2021-04-22 222 1587
Albania 2021-06-16 589 1589
Guinea 2021-05-17 119 478
Ivory Coast 2021-03-01 86 611
Qatar 2021-04-17 1687 3626
China 2021-04-21 1397 75779
Iran 2021-04-18 256 2129
Solomon Islands 2022-01-26 77 307
Venezuela 2021-07-07 176 853
Mayotte 2021-07-28 146 511
Taiwan 2021-03-22 43 5039
Chad 2021-07-05 47 59
Andorra 2021-07-08 51 189
Botswana 2021-05-09 1005 2703
United Arab Emirates 2021-05-28 3878 4620
Suriname 2021-07-12 266 499
Republic Of Congo 2021-03-12 92 316
Sudan 2021-03-01 156 428
Myanmar 2021-05-28 40 184
Hungary 2021-05-27 86 697
Fiji 2021-04-14 469 470
Kazakhstan 2021-07-25 721 2935
Senegal 2021-04-02 617 1877
Lebanon 2021-06-07 639 1155
Democratic Republic Of The Congo 2021-03-03 268 543
Barbados 2021-04-25 12 252
Niger 2021-07-01 10 43
Armenia 2021-06-17 39 45
Honduras 2021-07-30 64 329
Burkina Faso 2021-03-18 61 119
Benin 2021-05-27 176 676
South Sudan 2021-04-27 83 117
Iraq 2021-03-01 503 849
Iceland 2021-05-07 5674 17265
Kuwait 2021-05-24 144 911
Laos 2021-07-27 1169 2139
Burundi 2021-05-27 57 72
Oman 2021-03-05 111 871
East Timor 2021-03-08 23 271
Liberia 2021-03-09 61 99
Cayman Islands 2021-07-19 37 316
The Bahamas 2021-05-17 141 297
Sierra Leone 2021-05-07 39 43
El Salvador 2021-08-02 86 714
Togo 2021-04-12 337 654
Bhutan 2021-04-12 31 132
Bolivia 2021-06-14 49 257
Djibouti 2021-06-30 64 695
Uzbekistan 2021-06-25 51 92
Haiti 2021-10-21 12 399
Cyprus 2021-04-25 1563 6168
Mali 2021-04-08 6 76
Mauritania 2021-03-16 20 49
Somalia 2021-08-31 2 10
Tanzania 2021-05-03 1 3
Afghanistan 2021-04-26 18 75
Equatorial Guinea 2021-07-17 12 15
Saint-Martin 2021-11-24 27 328
Vanuatu 2021-10-24 2 95
Guyana 2021-09-06 48 124
Lesotho 2021-04-30 41 129
Namibia 2021-03-08 79 641
Central African Republic 2021-11-25 5 82
Azerbaijan 2021-07-14 33 53
Libya 2021-12-29 3 25
Uruguay 2021-09-03 68 349
Madagascar 2021-09-27 29 86

Data source and processing

The data on this page is recent as of 2024-05-13, 13:58 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.