B.1.617.2 2024-09-27



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 278786
Countries India 61898, Turkey 43803, United States of America 39486, Germany 19791, United Kingdom 18218, France 11633, Denmark 10735, Netherlands 4607, Italy 4408, Sweden 4356, Belgium 4148, Canada 3452, Spain 3064, Switzerland 3035, Poland 2818, Croatia 2784, United Arab Emirates 2606, Slovenia 2158, Bulgaria 2153, Bangladesh 2092, Israel 1739, 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 731, South Africa 715, China 635, Indonesia 494, South Korea 483, Austria 432, Romania 395, Mexico 373, Thailand 360, Reunion 358, Australia 355, Malawi 315, Malaysia 295, 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, Algeria 81, Democratic Republic of the Congo 81, Bosnia and Herzegovina 80, Rwanda 76, Belize 76, Peru 74, Oman 74, Kazakhstan 73, Benin 71, Morocco 70, Canary Islands 70, Cambodia 69, Cote d'Ivoire 68, Argentina 68, 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, Sint Maarten 34, Seychelles 34, Burkina Faso 30, Kosovo 30, Bhutan 30, Uzbekistan 29, Zambia 28, Ecuador 26, Myanmar 26, Burundi 26, Uruguay 24, Paraguay 21, Republic of Serbia 20, Martinique 18, Afghanistan 18, Vietnam 16, Guyana 16, Malta 15, Gibraltar 14, Saudi Arabia 14, Republic of the Congo 13, Syria 12, Curaçao 11, Jamaica 11, Chad 10, Mauritania 10, U.S. Virgin Islands 10, Taiwan 9, Tunisia 9, Eswatini 8, Guatemala 8, Laos 8, Papua New Guinea 8, Costa Rica 8, Grenada 7, North Macedonia 7, Crimea 7, Northern Mariana Islands 7, Niger 7, Venezuela 7, Cabo Verde 6, Antigua and Barbuda 6, South Sudan 6, Djibouti 6, Cayman Islands 6, Azerbaijan 5, Liberia 5, Bonaire 4, Liechtenstein 4, Hungary 4, Sao Tome and Principe 4, Albania 4, Belarus 4, Dominican Republic 4, Brunei 4, Gabon 3, Barbados 3, The Bahamas 3, Armenia 3, Turks and Caicos Islands 3, Montserrat 2, Madagascar 2, Fiji 2, Moldova 2, Lesotho 2, Trinidad and Tobago 1, Mayotte 1, Comoros 1, Tanzania 1, British Virgin Islands 1, Guam 1, Namibia 1, Suriname 1, Monaco 1, East Timor 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
Denmark 2021-03-29 162710 595765
United Kingdom 2021-03-09 1101958 2628877
South Korea 2021-04-19 17153 154326
United States Of America 2021-03-03 1435317 4368988
Germany 2021-03-09 215278 893056
France 2021-03-17 151396 539283
Brazil 2021-04-06 46266 215469
Belize 2021-03-07 259 995
Japan 2021-03-28 97156 637987
Malaysia 2021-03-09 7318 39859
Czech Republic 2021-03-03 18447 55841
Italy 2021-03-16 47944 165076
Norway 2021-04-15 22933 67217
Netherlands 2021-03-07 44926 157909
Australia 2021-03-18 30444 194083
Belgium 2021-04-06 48058 158883
Croatia 2021-04-25 13866 41147
Slovakia 2021-03-09 13952 45604
Austria 2021-04-17 6158 67414
Hungary 2021-05-27 86 700
Ireland 2021-04-03 26697 95330
Dominican Republic 2021-03-11 620 3117
Poland 2021-04-22 29148 81590
Reunion 2021-05-04 5612 19354
India 2021-03-01 77887 186980
Lithuania 2021-05-26 14796 28848
Israel 2021-04-08 18294 114918
Georgia 2021-05-11 766 3296
Spain 2021-03-08 55168 240289
Slovenia 2021-03-01 27712 74729
Latvia 2021-03-25 5528 23599
Bangladesh 2021-04-23 2899 5241
Peru 2021-05-15 7112 51656
Chile 2021-06-13 8670 41833
Canada 2021-03-06 105109 542809
Switzerland 2021-04-07 56697 125362
Thailand 2021-03-06 8148 36267
Puerto Rico 2021-06-03 3740 19248
Ivory Coast 2021-03-01 86 611
Portugal 2021-04-18 14590 41697
Greece 2021-03-23 4954 35327
Turkey 2021-03-09 59904 98223
Russia 2021-03-01 18868 73754
Nepal 2021-04-12 1850 3013
Bulgaria 2021-04-05 10279 19176
Mongolia 2021-03-08 435 2403
Honduras 2021-07-30 64 371
Mexico 2021-03-02 25451 86040
Argentina 2021-04-24 4054 17900
Finland 2021-04-17 13316 41828
Indonesia 2021-03-09 8311 48049
Kenya 2021-03-15 2205 7156
South Africa 2021-03-17 11263 39021
Vietnam 2021-04-20 2594 8255
Sweden 2021-04-01 57776 217667
Cambodia 2021-05-25 1209 3793
Singapore 2021-04-01 8746 49894
Estonia 2021-06-10 4233 10589
Liechtenstein 2021-06-18 383 1054
Brunei 2021-07-21 603 7052
Jordan 2021-04-26 499 830
Hong Kong 2021-03-25 757 16932
New Zealand 2021-03-15 4797 46223
Bahrain 2021-04-05 3537 10810
Guatemala 2021-04-24 836 5767
Botswana 2021-05-09 1005 2710
Gibraltar 2021-06-03 1740 1872
Moldova 2021-06-17 167 896
Qatar 2021-04-17 1687 3626
Rwanda 2021-03-22 214 358
Luxembourg 2021-04-01 9016 49494
Iraq 2021-03-01 503 849
Tunisia 2021-04-05 646 2040
Romania 2021-03-28 6048 19008
Costa Rica 2021-06-13 1282 11940
Kosovo 2021-04-30 914 1714
Ecuador 2021-06-22 1196 8629
Uruguay 2021-07-05 304 713
Trinidad And Tobago 2021-08-03 413 2477
Gabon 2021-07-06 109 122
Panama 2021-04-29 895 5283
Colombia 2021-03-11 3931 18176
Zimbabwe 2021-06-23 135 386
Bosnia And Herzegovina 2021-06-08 1079 1353
Belarus 2021-05-24 232 275
Ukraine 2021-06-17 448 5269
Kazakhstan 2021-07-25 721 2935
Guinea 2021-05-17 119 478
Saint-Martin 2021-11-24 27 328
Nigeria 2021-04-10 2085 4172
Fiji 2021-04-14 469 470
Jamaica 2021-04-11 391 3818
Philippines 2021-04-13 3309 21169
Chad 2021-07-05 47 59
Venezuela 2021-07-07 176 968
Gambia 2021-04-08 307 483
Aruba 2021-04-10 1856 3486
Morocco 2021-04-22 239 1954
Ghana 2021-03-05 889 2778
Curaçao 2021-06-28 599 1939
Lebanon 2021-06-07 639 1195
Burkina Faso 2021-03-18 61 119
Malawi 2021-03-17 384 633
China 2021-04-21 1438 82774
Republic Of Serbia 2021-06-26 180 1830
Senegal 2021-04-02 617 1986
Angola 2021-04-18 232 451
Eswatini 2021-06-08 272 951
Laos 2021-07-04 1179 2260
Montenegro 2021-06-18 437 1083
Syria 2021-12-01 32 109
Malta 2021-05-19 400 566
Iceland 2021-05-07 5674 17625
Taiwan 2021-03-22 43 5813
Iran 2021-04-18 256 2129
Egypt 2021-06-22 287 2529
Ethiopia 2021-03-15 370 653
Pakistan 2021-04-08 1751 5258
Sri Lanka 2021-03-11 1445 2731
Myanmar 2021-05-28 40 209
Kyrgyzstan 2021-06-08 134 186
Sierra Leone 2021-05-07 39 43
Mozambique 2021-03-15 522 1026
Solomon Islands 2022-01-26 77 307
Guam 2021-04-26 279 909
Uganda 2021-04-20 452 1268
Cameroon 2021-04-01 328 1419
Papua New Guinea 2021-07-07 1498 2289
Oman 2021-03-05 111 999
Zambia 2021-03-26 335 729
Saudi Arabia 2021-05-12 22 698
Nicaragua 2021-06-23 156 426
Kuwait 2021-05-24 144 964
Guadeloupe 2021-05-25 1398 2157
Mayotte 2021-07-28 146 511
Paraguay 2021-03-01 421 3041
Uzbekistan 2021-06-25 51 92
United Arab Emirates 2021-05-28 3878 4620
Algeria 2021-05-10 83 746
Bolivia 2021-06-14 49 257
El Salvador 2021-08-02 86 767
Suriname 2021-07-12 266 499
Democratic Republic Of The Congo 2021-03-03 268 543
Benin 2021-05-27 176 676
Republic Of Congo 2021-03-12 92 316
Central African Republic 2021-11-25 5 82
East Timor 2021-03-08 23 271
Liberia 2021-03-09 61 99
Guyana 2021-09-06 48 124
North Macedonia 2021-06-14 122 554
Madagascar 2021-09-27 29 86
Cayman Islands 2021-07-19 37 316
Mauritania 2021-03-08 53 113
Somalia 2021-08-31 2 10
Andorra 2021-07-08 51 189
Albania 2021-06-16 589 1589
Libya 2021-12-29 3 25
The Bahamas 2021-05-17 141 297
Barbados 2021-04-25 12 301
Azerbaijan 2021-07-14 33 69
Djibouti 2021-06-30 64 695
Cyprus 2021-04-25 1563 6168
Saint Lucia 2021-07-14 11 222
Mali 2021-04-08 6 76
British Virgin Islands 2021-07-27 31 86
Namibia 2021-03-08 79 641
South Sudan 2021-04-27 83 127
Sudan 2021-03-01 156 428
Haiti 2021-10-21 12 432
Niger 2021-07-01 10 43
Togo 2021-04-12 337 654
Equatorial Guinea 2021-07-17 12 15
Tanzania 2021-05-03 1 3
Afghanistan 2021-04-26 18 75
Lesotho 2021-04-30 41 129
Armenia 2021-06-17 39 45
Bhutan 2021-04-12 31 135
Vanuatu 2021-10-24 2 95
Burundi 2021-05-27 57 72

Data source and processing

The data on this page is recent as of 2024-09-27, 08:42 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.