B.1.617.2 2024-02-22



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 183
Sequence count 278665
Countries India 61564, Turkey 43816, United States of America 39224, Germany 19863, United Kingdom 18614, France 11624, Denmark 10665, Netherlands 4603, Italy 4467, Sweden 4355, Belgium 4086, Canada 3461, Spain 3042, Switzerland 3037, Poland 2835, Croatia 2795, United Arab Emirates 2607, Slovenia 2173, Bulgaria 2141, Bangladesh 2093, Israel 1739, Philippines 1651, Nepal 1568, Czech Republic 1426, Norway 1133, Singapore 1086, Bahrain 1085, Russia 1073, Latvia 1019, Pakistan 984, Portugal 942, Slovakia 920, Qatar 914, Luxembourg 902, Finland 789, Ireland 762, Japan 721, South Africa 682, China 627, Indonesia 492, South Korea 485, Austria 433, Romania 385, Mexico 374, Thailand 359, Reunion 357, Australia 356, Malawi 315, Malaysia 300, Kenya 290, Iceland 281, Mongolia 279, Greece 267, Lithuania 262, Ghana 232, Lebanon 225, Iraq 213, Egypt 213, Brazil 212, Cameroon 202, Maldives 177, Sri Lanka 174, Chile 142, Hong Kong 139, Sudan 138, Georgia 133, Ethiopia 133, Puerto Rico 130, Kuwait 130, Aruba 126, Botswana 122, Jordan 120, Iran 120, Estonia 113, Guadeloupe 112, Cyprus 102, Canary Islands 100, Gambia 99, Togo 99, Kyrgyzstan 98, Nigeria 95, Panama 87, Senegal 83, Mauritius 81, Bosnia and Herzegovina 81, Democratic Republic of the Congo 81, Kazakhstan 78, Algeria 78, Belize 76, Rwanda 76, Oman 74, Peru 73, Benin 71, Argentina 70, Cote d'Ivoire 68, Morocco 67, Cambodia 66, Colombia 58, Guinea 56, Zimbabwe 56, Montenegro 51, French Guiana 47, Mozambique 45, Uganda 45, New Zealand 43, Angola 39, Ukraine 38, Sierra Leone 37, Seychelles 35, 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, Afghanistan 18, Martinique 18, Guyana 16, Malta 15, Vietnam 15, Gibraltar 15, Saudi Arabia 14, Republic of the Congo 13, Syria 12, Curaçao 11, Chad 10, Jamaica 10, U.S. Virgin Islands 10, Taiwan 9, Tunisia 9, Papua New Guinea 8, Costa Rica 8, Eswatini 8, Laos 8, Crimea 7, Venezuela 7, Niger 7, Guatemala 7, Northern Mariana Islands 7, North Macedonia 7, South Sudan 6, Cabo Verde 6, Antigua and Barbuda 6, Cayman Islands 6, Djibouti 6, Liberia 5, Azerbaijan 5, Belarus 4, Uruguay 4, Brunei 4, Liechtenstein 4, Sao Tome and Principe 4, Hungary 4, Dominican Republic 4, Albania 4, Bonaire 4, Gabon 3, Armenia 3, Barbados 3, Turks and Caicos Islands 3, The Bahamas 3, Madagascar 2, Moldova 2, Lesotho 2, Fiji 2, Montserrat 2, Mauritania 2, Suriname 1, Tanzania 1, Monaco 1, Comoros 1, Guam 1, Mayotte 1, East Timor 1, Namibia 1, Trinidad and Tobago 1, British Virgin Islands 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 2606620
United States Of America 2021-03-03 1434095 4255831
Switzerland 2021-04-07 56696 124572
Australia 2021-03-18 30444 185183
Belgium 2021-04-06 48058 158344
Japan 2021-03-28 96892 608506
South Africa 2021-03-17 11175 38233
Morocco 2021-04-22 222 1582
Turkey 2021-03-09 59909 97541
India 2021-03-01 77527 184703
Puerto Rico 2021-06-03 3740 16039
Nigeria 2021-04-10 2085 3907
Philippines 2021-04-13 3309 20997
Germany 2021-03-09 215277 889517
Netherlands 2021-03-07 44926 153791
Italy 2021-03-16 47945 162114
Lithuania 2021-05-26 14796 28220
Botswana 2021-05-09 1005 2703
Mexico 2021-03-02 25428 83900
Gambia 2021-04-08 307 483
Brazil 2021-04-06 46236 208776
Cambodia 2021-05-25 1209 3646
Denmark 2021-03-29 161462 579854
Sweden 2021-04-01 57776 214607
Croatia 2021-04-25 13866 40851
Czech Republic 2021-03-03 18447 55551
New Zealand 2021-03-15 4797 41877
Argentina 2021-04-24 4041 17354
Belize 2021-03-07 259 995
France 2021-03-17 151400 531223
Reunion 2021-05-04 5612 19353
Qatar 2021-04-17 1687 3600
Poland 2021-04-22 29148 81099
Slovakia 2021-03-09 13952 45514
South Korea 2021-04-19 17153 145075
Djibouti 2021-06-30 64 695
Hong Kong 2021-03-25 757 14347
Finland 2021-04-17 13316 41228
Belarus 2021-05-24 232 275
Albania 2021-06-16 589 1589
Canada 2021-03-06 104861 511620
Singapore 2021-04-01 8746 44949
Georgia 2021-05-11 766 3249
Greece 2021-03-23 4954 34298
Bulgaria 2021-04-05 10279 19105
Norway 2021-04-15 22933 66604
Portugal 2021-04-18 14590 40569
Malaysia 2021-03-09 7315 38945
Slovenia 2021-03-01 27712 74384
Russia 2021-03-01 18864 69980
Austria 2021-04-17 6158 67243
Nepal 2021-04-12 1850 2943
Ireland 2021-04-03 26697 92166
Republic Of Serbia 2021-06-26 175 1825
Ecuador 2021-06-22 1196 8240
Vietnam 2021-04-20 2594 8119
Colombia 2021-03-11 3833 17734
Peru 2021-05-15 7112 49890
Thailand 2021-03-06 8148 34699
Israel 2021-04-08 18296 112927
Spain 2021-03-08 54599 220416
Kyrgyzstan 2021-06-08 134 186
Romania 2021-03-28 6048 18793
Latvia 2021-03-25 5528 23599
Jordan 2021-04-26 499 766
Montenegro 2021-06-18 437 1049
Chile 2021-06-13 8669 40262
Nicaragua 2021-06-23 156 426
Liechtenstein 2021-06-18 383 1054
Iran 2021-04-18 252 2115
Kenya 2021-03-15 2204 6986
Uganda 2021-04-20 452 1082
Pakistan 2021-04-08 1751 5097
Gibraltar 2021-06-03 1740 1872
Sri Lanka 2021-03-11 1445 2731
Indonesia 2021-03-09 8311 47481
Ghana 2021-03-05 886 2771
Estonia 2021-06-10 4233 10495
Suriname 2021-07-12 266 499
Luxembourg 2021-04-01 9016 48355
Brunei 2021-07-21 603 6905
Curaçao 2021-06-28 599 1896
Malta 2021-05-19 400 566
Bosnia And Herzegovina 2021-06-08 1079 1353
Costa Rica 2021-06-13 1282 11347
Guam 2021-04-26 279 878
South Sudan 2021-04-27 83 117
Burundi 2021-05-27 57 72
Guatemala 2021-04-24 698 4741
Senegal 2021-04-02 617 1870
Bangladesh 2021-04-23 2899 5176
Kazakhstan 2021-07-25 721 2935
Papua New Guinea 2021-07-07 1498 2289
Ukraine 2021-06-17 448 4149
Laos 2021-07-27 1169 2093
Guadeloupe 2021-05-25 1398 2120
Aruba 2021-04-10 1856 3486
Oman 2021-03-05 111 751
Jamaica 2021-04-11 391 3818
Mongolia 2021-03-08 435 2379
United Arab Emirates 2021-05-28 3878 4620
Mozambique 2021-03-15 522 1017
Andorra 2021-07-08 51 189
Angola 2021-04-18 232 451
Malawi 2021-03-17 384 633
Mayotte 2021-07-28 146 511
Bahrain 2021-04-05 3537 10810
Uruguay 2021-09-03 69 351
China 2021-04-21 1395 67355
The Bahamas 2021-05-17 141 285
Liberia 2021-03-09 56 89
Trinidad And Tobago 2021-08-03 413 2469
Dominican Republic 2021-03-11 620 2930
Cameroon 2021-04-01 328 1411
Ethiopia 2021-03-15 368 570
Kosovo 2021-04-30 914 1714
Republic Of Congo 2021-03-12 92 316
Ivory Coast 2021-03-01 86 563
Hungary 2021-05-27 86 655
Venezuela 2021-07-07 176 853
Iraq 2021-03-01 503 849
Tunisia 2021-04-05 712 2127
Kuwait 2021-05-24 144 911
Rwanda 2021-03-22 214 358
Zambia 2021-03-26 335 727
Egypt 2021-06-22 288 2504
Paraguay 2021-03-01 421 2941
Fiji 2021-04-14 469 470
British Virgin Islands 2021-07-27 31 86
Moldova 2021-06-17 167 829
Saint-Martin 2021-11-24 27 327
Democratic Republic Of The Congo 2021-03-03 268 518
Myanmar 2021-05-28 40 184
Guinea 2021-05-17 119 478
Solomon Islands 2022-01-26 77 307
Madagascar 2021-09-27 29 86
Cyprus 2021-04-25 1563 6168
Bolivia 2021-06-14 49 257
Sudan 2021-03-01 156 428
Eswatini 2021-06-08 272 862
Algeria 2021-05-10 80 655
Panama 2021-04-29 895 5257
El Salvador 2021-08-02 79 677
Cayman Islands 2021-07-19 37 316
Iceland 2021-05-07 5674 17096
Equatorial Guinea 2021-07-17 12 15
Chad 2021-07-05 47 59
Gabon 2021-07-06 109 122
Benin 2021-05-27 176 676
Syria 2021-12-01 32 107
Taiwan 2021-03-22 43 4634
Zimbabwe 2021-06-23 135 386
North Macedonia 2021-06-14 122 528
Mauritania 2021-03-16 20 49
Saint Lucia 2021-07-14 11 222
Afghanistan 2021-04-26 18 63
Togo 2021-04-12 337 635
Honduras 2021-07-30 64 286
Armenia 2021-06-17 39 45
Saudi Arabia 2021-05-12 22 695
Barbados 2021-04-25 12 252
Somalia 2021-08-31 2 10
Sierra Leone 2021-05-07 39 43
Guyana 2021-09-06 48 124
Azerbaijan 2021-07-14 33 53
Burkina Faso 2021-03-18 61 112
Lebanon 2021-06-07 639 1149
Niger 2021-07-01 10 43
Namibia 2021-03-08 79 641
Uzbekistan 2021-06-25 51 92
Vanuatu 2021-10-24 2 95
Tanzania 2021-05-03 1 3
Lesotho 2021-04-30 41 129
Libya 2021-12-29 3 25
Central African Republic 2021-11-25 5 80
Bhutan 2021-04-12 31 132
Mali 2021-04-08 6 76
Haiti 2021-10-21 12 367
East Timor 2021-03-08 23 271

Data source and processing

The data on this page is recent as of 2024-02-22, 22:41 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.