B.1.617.2 2023-08-24



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 283463
Countries India 61627, Turkey 43919, United States of America 43397, Germany 19929, United Kingdom 18479, France 11663, Denmark 10463, Netherlands 4625, Sweden 4295, Italy 4254, Belgium 4177, Canada 3465, Switzerland 3096, Spain 2957, Poland 2844, Croatia 2795, United Arab Emirates 2629, Israel 2327, Slovenia 2186, Bulgaria 2138, Bangladesh 2079, Philippines 1649, Nepal 1569, Czech Republic 1476, Russia 1144, Norway 1136, Singapore 1086, Bahrain 1082, Latvia 1031, Slovakia 955, Pakistan 941, Portugal 939, Qatar 914, Luxembourg 903, Finland 866, Japan 781, Ireland 776, China 628, South Africa 623, Indonesia 495, South Korea 486, Austria 440, Romania 399, Australia 385, Mexico 374, Reunion 361, Thailand 341, Malawi 316, Malaysia 306, Kenya 295, Iceland 283, Greece 270, Lithuania 263, Ghana 243, Lebanon 228, Iraq 216, Egypt 212, Cameroon 202, Mongolia 193, Brazil 192, Maldives 177, Sri Lanka 161, Chile 147, Hong Kong 139, Ethiopia 139, Sudan 139, Puerto Rico 134, Jordan 134, Georgia 133, Kuwait 130, Aruba 126, Botswana 123, Iran 122, Estonia 113, Guadeloupe 112, Togo 102, Canary Islands 99, Nigeria 98, Kyrgyzstan 98, Gambia 98, Panama 87, Senegal 84, Argentina 83, Democratic Republic of the Congo 82, Bosnia and Herzegovina 81, Mauritius 81, Peru 78, Algeria 78, Belize 76, Rwanda 76, Oman 76, Benin 71, Cote d'Ivoire 68, Zambia 63, Zimbabwe 62, Colombia 61, Morocco 61, Cambodia 60, Cyprus 56, Guinea 55, Mozambique 54, Kazakhstan 54, Montenegro 51, Uganda 50, French Guiana 47, New Zealand 43, Angola 41, Ukraine 40, Sierra Leone 37, Seychelles 35, Sint Maarten 35, Paraguay 33, Burkina Faso 30, Kosovo 30, Bhutan 30, Uzbekistan 29, Ecuador 28, Myanmar 26, Burundi 26, Fiji 23, Republic of Serbia 20, Martinique 18, Afghanistan 18, Guyana 16, Malta 15, Vietnam 15, Republic of the Congo 14, Saudi Arabia 14, Gibraltar 13, Syria 12, Curaçao 11, Jamaica 11, U.S. Virgin Islands 10, Guatemala 10, Chad 9, Taiwan 9, Venezuela 9, Laos 8, Eswatini 8, Papua New Guinea 8, North Macedonia 8, Tunisia 8, Costa Rica 8, Northern Mariana Islands 7, Crimea 7, Niger 7, Grenada 7, South Sudan 7, Cabo Verde 6, Antigua and Barbuda 6, Cayman Islands 6, Djibouti 6, Belarus 5, Brunei 5, Azerbaijan 5, Liberia 5, Hungary 4, Bonaire 4, Liechtenstein 4, Dominican Republic 4, Sao Tome and Principe 4, Albania 4, Gabon 3, Armenia 3, Barbados 3, Turks and Caicos Islands 3, The Bahamas 3, Uruguay 3, Namibia 2, Moldova 2, Montserrat 2, Lesotho 2, Madagascar 2, Mauritania 2, Comoros 1, British Virgin Islands 1, Trinidad and Tobago 1, Suriname 1, Mayotte 1, Central African Republic 1, Tanzania 1, Guam 1, Monaco 1, East Timor 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 159366 558394
United States Of America 2021-03-03 1432792 4076678
France 2021-03-17 151401 502254
Brazil 2021-04-06 45841 197978
Netherlands 2021-03-07 44919 145690
United Kingdom 2021-03-09 1101960 2563086
Turkey 2021-03-09 59914 96504
Switzerland 2021-04-07 56606 120808
Japan 2021-03-28 96888 577268
Germany 2021-03-09 214403 880738
India 2021-03-01 77540 182190
Singapore 2021-04-01 8746 36418
Canada 2021-03-06 104393 454549
Norway 2021-04-15 22934 65605
Ireland 2021-04-03 26698 88741
Spain 2021-03-08 52815 196927
Italy 2021-03-16 45036 149378
Sweden 2021-04-01 57710 199204
Pakistan 2021-04-08 1686 4867
Austria 2021-04-17 6158 64489
Poland 2021-04-22 29150 78905
Slovenia 2021-03-01 27712 72553
Czech Republic 2021-03-03 18082 54215
Belgium 2021-04-06 48057 153453
Costa Rica 2021-06-13 1282 10806
Romania 2021-03-28 6047 17703
Eswatini 2021-06-08 272 862
Estonia 2021-06-10 4233 10495
Croatia 2021-04-25 13864 39141
Mexico 2021-03-02 25430 79703
Bulgaria 2021-04-05 10266 18697
Latvia 2021-03-25 5527 23036
Angola 2021-04-18 232 451
Republic Of Serbia 2021-06-26 175 1823
Slovakia 2021-03-09 13952 44137
Thailand 2021-03-06 8148 33076
Bosnia And Herzegovina 2021-06-08 1079 1307
Lithuania 2021-05-26 14797 26938
Luxembourg 2021-04-01 9016 46518
Indonesia 2021-03-09 8310 46271
Australia 2021-03-18 30445 174502
South Africa 2021-03-17 11130 36915
Finland 2021-04-17 13316 38337
Chile 2021-06-13 8667 38226
Malaysia 2021-03-09 7280 36634
Colombia 2021-03-11 3835 17315
South Korea 2021-04-19 17153 120833
Peru 2021-05-15 7105 46736
Vietnam 2021-04-20 2594 7945
New Zealand 2021-03-15 4792 34079
Portugal 2021-04-18 14560 39093
Argentina 2021-04-24 4048 16775
Nepal 2021-04-12 1850 2930
Liechtenstein 2021-06-18 383 1054
Israel 2021-04-08 18288 109451
Reunion 2021-05-04 5613 18585
Brunei 2021-07-21 603 6642
Cambodia 2021-05-25 1209 3584
Bangladesh 2021-04-23 2877 4953
Honduras 2021-07-30 64 188
Equatorial Guinea 2021-07-17 12 15
Mozambique 2021-03-15 522 1005
Bolivia 2021-06-14 49 254
Iceland 2021-05-07 5674 16290
Kenya 2021-03-15 2204 6605
Guadeloupe 2021-05-25 1398 2088
Puerto Rico 2021-06-03 3740 14889
Greece 2021-03-23 4954 28028
Gibraltar 2021-06-03 1740 1872
British Virgin Islands 2021-07-27 31 86
Sri Lanka 2021-03-11 1402 2628
Chad 2021-07-05 33 38
Democratic Republic Of The Congo 2021-03-03 264 505
Ivory Coast 2021-03-01 86 534
Belarus 2021-05-24 232 275
Dominican Republic 2021-03-11 620 2775
Moldova 2021-06-17 167 825
Guam 2021-04-26 279 861
Burkina Faso 2021-03-18 58 108
Nicaragua 2021-06-23 156 426
Hong Kong 2021-03-25 757 14066
Russia 2021-03-01 18846 64471
Fiji 2021-04-14 469 470
Nigeria 2021-04-10 2083 3885
Qatar 2021-04-17 1687 3434
Curaçao 2021-06-28 599 1809
Uganda 2021-04-20 452 1066
Ecuador 2021-06-22 1196 7590
Aruba 2021-04-10 1856 3456
Jordan 2021-04-26 499 749
Philippines 2021-04-13 3308 20197
Republic Of Congo 2021-03-12 92 315
Jamaica 2021-04-11 391 3608
Ghana 2021-03-05 882 2764
Montenegro 2021-06-18 437 926
Bahrain 2021-04-05 3537 10443
Senegal 2021-04-02 617 1805
Malta 2021-05-19 400 566
Ukraine 2021-06-17 449 2999
Guatemala 2021-04-24 698 4413
Sierra Leone 2021-05-07 39 43
Mongolia 2021-03-08 323 1765
Kuwait 2021-05-24 144 846
Belize 2021-03-07 259 995
Tunisia 2021-04-05 552 1670
Algeria 2021-05-10 80 622
Kyrgyzstan 2021-06-08 134 186
Myanmar 2021-05-28 40 152
Rwanda 2021-03-22 214 358
Papua New Guinea 2021-07-07 1498 2289
Gabon 2021-07-06 109 122
Taiwan 2021-03-22 40 3468
Iran 2021-04-18 253 2037
Oman 2021-03-05 111 562
Somalia 2021-08-31 2 10
North Macedonia 2021-06-14 122 371
Cameroon 2021-04-01 328 1379
Botswana 2021-05-09 1006 2682
Trinidad And Tobago 2021-08-03 412 2345
Paraguay 2021-03-01 421 2724
Egypt 2021-06-22 287 1811
Saudi Arabia 2021-05-12 22 657
Georgia 2021-05-11 766 2945
Gambia 2021-04-08 307 483
Guyana 2021-09-06 48 124
Ethiopia 2021-03-15 368 501
Kosovo 2021-04-30 914 1672
China 2021-04-21 1395 53477
Hungary 2021-05-27 86 502
Guinea 2021-05-17 117 459
Saint Lucia 2021-07-14 11 190
Laos 2021-07-27 1169 1926
Zambia 2021-03-26 335 727
Syria 2021-12-01 32 106
Venezuela 2021-07-07 176 827
Iraq 2021-03-01 503 826
Saint-Martin 2021-11-24 27 327
Uzbekistan 2021-06-25 51 92
Armenia 2021-06-17 39 45
The Bahamas 2021-05-17 141 285
Suriname 2021-07-12 266 499
Lebanon 2021-06-07 639 1122
Mayotte 2021-07-28 146 509
Panama 2021-04-29 895 5152
Solomon Islands 2022-01-26 77 307
Kazakhstan 2021-07-25 530 1960
Morocco 2021-04-22 206 1465
Malawi 2021-03-17 384 633
El Salvador 2021-08-02 79 473
Barbados 2021-04-25 12 197
Benin 2021-05-27 176 675
Namibia 2021-03-08 79 638
Niger 2021-07-01 10 43
East Timor 2021-03-08 23 271
United Arab Emirates 2021-05-28 3878 4620
Togo 2021-04-12 337 572
Albania 2021-06-16 589 1359
Zimbabwe 2021-06-23 135 386
Liberia 2021-03-09 56 89
Cyprus 2021-04-25 825 1470
Sudan 2021-03-01 156 428
Burundi 2021-05-27 57 72
Cayman Islands 2021-07-19 37 316
Andorra 2021-07-08 51 189
South Sudan 2021-04-27 83 117
Central African Republic 2021-11-25 5 78
Lesotho 2021-04-30 41 128
Mali 2021-04-08 6 76
Djibouti 2021-06-30 64 695
Afghanistan 2021-04-26 18 63
Madagascar 2021-09-27 29 86
Azerbaijan 2021-07-14 33 53
Uruguay 2021-09-03 65 281
Mauritania 2021-03-16 20 49
Tanzania 2021-05-03 1 3
Vanuatu 2021-10-24 2 95
Haiti 2021-10-21 12 334
Bhutan 2021-04-12 31 124
Libya 2021-12-29 3 25

Data source and processing

The data on this page is recent as of 2023-08-24, 10:12 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.