B.1.617.2 2022-09-13



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 180
Sequence count 179814
Countries United States of America 38361, India 31668, United Kingdom 22704, Turkey 20913, Germany 8600, France 6580, Denmark 5102, Netherlands 3834, Canada 3033, Sweden 2639, Croatia 2619, Belgium 2468, Poland 2350, Italy 2152, Bulgaria 1982, Philippines 1905, Spain 1600, Bangladesh 1384, Nepal 1294, Switzerland 1154, Singapore 1069, Norway 1024, Slovenia 922, Luxembourg 824, Latvia 790, Japan 744, Czech Republic 710, Ireland 699, Israel 584, South Africa 533, Qatar 510, Slovakia 401, Pakistan 396, Portugal 355, South Korea 325, Indonesia 317, Austria 301, Australia 288, Thailand 284, Finland 282, Reunion 263, Russia 255, Romania 247, Bahrain 246, China 234, Malaysia 192, Lithuania 190, Mongolia 180, Iraq 171, Malawi 171, Sri Lanka 139, Lebanon 136, Greece 134, Ghana 132, Kenya 129, Hong Kong 128, Aruba 127, Mexico 122, Puerto Rico 117, Georgia 103, Guadeloupe 97, Estonia 95, Kuwait 95, Iceland 92, Gambia 90, Panama 83, Togo 76, Rwanda 76, Belize 70, Mauritius 67, Jordan 67, Ethiopia 66, Bosnia and Herzegovina 64, Oman 63, Cameroon 61, Senegal 59, Cote d'Ivoire 59, Kyrgyzstan 58, Peru 53, Sudan 53, Chile 51, Brazil 44, Zambia 44, Benin 42, Canary Islands 40, Ecuador 37, Angola 37, Gibraltar 35, Guinea 35, New Zealand 35, Uganda 34, Colombia 33, Egypt 30, Sint Maarten 29, Kosovo 27, Vietnam 27, Nigeria 27, Cambodia 26, Papua New Guinea 25, Ukraine 23, Iran 22, United Arab Emirates 22, Mozambique 21, Myanmar 21, Zimbabwe 20, Montenegro 19, Burundi 19, Democratic Republic of the Congo 19, Afghanistan 18, Morocco 17, Northern Mariana Islands 17, Botswana 17, Argentina 16, Uzbekistan 16, Guyana 16, Martinique 14, Kazakhstan 12, Maldives 12, Saudi Arabia 11, French Guiana 10, Burkina Faso 10, Republic of the Congo 10, Sierra Leone 9, Algeria 8, Seychelles 8, Curaçao 8, Costa Rica 8, Jamaica 8, U.S. Virgin Islands 8, Malta 7, Fiji 7, Paraguay 7, Crimea 7, Eswatini 6, South Sudan 6, Grenada 6, Cayman Islands 6, Djibouti 6, Taiwan 5, Guam 5, Chad 5, Republic of Serbia 5, Liberia 5, North Macedonia 4, Tunisia 4, Bonaire 4, Sao Tome and Principe 4, Cyprus 4, The Bahamas 3, Guatemala 3, Gabon 3, Liechtenstein 3, Brunei 3, Barbados 2, Trinidad and Tobago 2, Comoros 2, Venezuela 2, Cabo Verde 2, Montserrat 2, Moldova 2, Belarus 2, Lesotho 2, British Virgin Islands 2, Syria 2, Hungary 2, Nicaragua 1, Dominican Republic 1, Uruguay 1, Monaco 1, East Timor 1, Laos 1, Mayotte 1, Suriname 1, Albania 1, Niger 1, Antigua and Barbuda 1, Mauritania 1, Madagascar 1, Namibia 1, Turks and Caicos Islands 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 States Of America 2021-03-03 1409012 3310716
Norway 2021-04-15 22083 57977
India 2021-03-01 76828 155904
United Kingdom 2021-03-09 1101264 2400308
Spain 2021-03-30 44463 121899
Germany 2021-03-09 206308 720564
Ireland 2021-04-03 26690 70642
Canada 2021-03-06 104163 327594
Denmark 2021-03-29 159229 487122
France 2021-03-17 151177 412071
Poland 2021-04-22 29140 72533
Estonia 2021-06-10 4238 8782
Peru 2021-05-15 6639 25698
Malaysia 2021-03-09 7254 23227
Jamaica 2021-04-11 382 2067
Gabon 2021-07-06 109 122
Vietnam 2021-04-20 2421 5079
Australia 2021-03-18 30349 107991
Switzerland 2021-04-07 56640 108422
Turkey 2021-03-09 60216 91138
Brazil 2021-04-06 43551 149701
Slovenia 2021-03-01 27710 60608
Sweden 2021-04-01 57527 152554
South Africa 2021-03-17 10706 29849
Guatemala 2021-04-24 699 1942
Venezuela 2021-07-07 167 392
Russia 2021-03-01 6773 14595
Italy 2021-03-16 44125 116077
Colombia 2021-03-11 3766 13059
Slovakia 2021-03-09 13952 39508
Croatia 2021-04-25 13859 32242
Portugal 2021-04-18 14554 32674
Belgium 2021-04-06 48043 134615
Romania 2021-03-28 6042 14144
The Bahamas 2021-05-17 141 191
Israel 2021-04-08 18301 90636
Japan 2021-03-28 96254 350166
Panama 2021-04-29 886 4052
Bolivia 2021-06-14 49 132
Thailand 2021-03-06 8049 23408
South Korea 2021-04-19 16891 49246
Luxembourg 2021-04-01 9008 35407
Bulgaria 2021-04-05 10240 16304
Senegal 2021-04-02 618 1747
Czech Republic 2021-03-03 18085 45583
Montenegro 2021-06-18 437 823
Finland 2021-04-17 13318 27203
Indonesia 2021-03-09 8283 29985
Reunion 2021-05-04 5615 13939
Netherlands 2021-03-07 44820 116790
Ukraine 2021-06-17 421 745
Fiji 2021-04-14 469 470
Latvia 2021-03-25 5527 14319
Democratic Republic Of The Congo 2021-03-03 184 387
Austria 2021-04-17 6158 28037
Bangladesh 2021-04-23 2843 4535
Belarus 2021-05-24 232 275
Brunei 2021-07-21 603 3089
Kuwait 2021-05-24 144 409
Mexico 2021-03-02 25212 67186
Bosnia And Herzegovina 2021-06-08 1079 1239
Lithuania 2021-05-26 14794 25516
Kyrgyzstan 2021-06-08 134 186
Liechtenstein 2021-06-18 383 753
Argentina 2021-04-24 4102 12030
British Virgin Islands 2021-07-27 30 83
Uganda 2021-04-20 375 558
Morocco 2021-04-22 203 633
Chile 2021-06-13 8519 28517
Puerto Rico 2021-06-03 3312 8703
Sri Lanka 2021-03-11 1387 2542
Singapore 2021-04-01 8746 20684
Greece 2021-03-23 4954 15826
Tunisia 2021-05-25 489 620
Nepal 2021-04-12 1848 2737
New Zealand 2021-03-15 4792 18818
Suriname 2021-07-12 266 499
Eswatini 2021-06-08 269 742
Trinidad And Tobago 2021-08-03 405 1664
Aruba 2021-04-10 1856 2900
Costa Rica 2021-06-13 1282 5847
Pakistan 2021-04-08 1093 2966
Mongolia 2021-03-08 321 1304
South Sudan 2021-04-27 83 117
Togo 2021-04-12 336 470
China 2021-04-21 724 1042
Cameroon 2021-04-01 327 782
Iraq 2021-04-27 479 762
Solomon Islands 2022-01-26 77 198
Kenya 2021-03-15 2113 5628
Lebanon 2021-06-07 631 883
Papua New Guinea 2021-07-07 1498 1966
Hong Kong 2021-03-25 737 6888
Georgia 2021-05-11 752 1989
Philippines 2021-04-09 3290 14822
Saint-Martin 2021-11-24 27 319
Ghana 2021-04-20 857 1794
Guam 2021-04-26 279 724
Mozambique 2021-05-04 376 609
Zambia 2021-03-26 335 630
Cambodia 2021-05-25 1208 3166
Republic Of Serbia 2021-06-26 175 1142
Jordan 2021-04-26 499 689
Dominican Republic 2021-03-11 552 1341
Paraguay 2021-03-01 420 1645
Honduras 2021-07-30 64 112
Guadeloupe 2021-05-25 1398 1947
Algeria 2021-05-10 62 242
Malta 2021-05-19 400 566
Gambia 2021-04-08 307 448
Curaçao 2021-06-28 599 1546
Chad 2021-07-05 33 38
Hungary 2021-11-15 85 113
Gibraltar 2021-06-03 1740 1872
Nicaragua 2021-06-23 122 229
Mayotte 2021-07-28 146 451
Ecuador 2021-06-22 1198 5313
Malawi 2021-03-17 312 494
Nigeria 2021-04-10 2045 3428
Albania 2021-06-16 25 27
Ivory Coast 2021-03-01 81 376
Laos 2021-12-08 56 398
Mauritania 2021-03-16 20 49
Kosovo 2021-04-30 914 1403
Rwanda 2021-03-22 214 358
Iran 2021-04-18 66 1267
Guinea 2021-05-17 116 353
Belize 2021-03-07 220 796
Botswana 2021-05-09 1004 2407
North Macedonia 2021-06-14 122 267
Qatar 2021-04-17 1681 2458
Central African Republic 2021-12-12 2 18
Kazakhstan 2021-07-25 385 854
Bahrain 2021-04-05 3536 7348
Moldova 2021-06-17 167 545
El Salvador 2021-08-02 79 293
Egypt 2021-06-22 280 598
Burkina Faso 2021-03-18 23 39
Angola 2021-04-18 232 410
Armenia 2021-06-17 39 45
Uzbekistan 2021-06-25 49 56
Andorra 2021-07-08 51 132
Ethiopia 2021-03-15 368 485
Sierra Leone 2021-05-07 10 10
Syria 2021-12-01 32 89
Zimbabwe 2021-06-23 135 322
Namibia 2021-03-08 79 594
Oman 2021-03-05 111 325
Barbados 2021-04-25 12 109
Republic Of Congo 2021-03-12 90 295
Uruguay 2021-09-03 58 93
Lesotho 2021-04-30 41 101
Myanmar 2021-05-28 40 81
Taiwan 2021-03-22 36 2309
Burundi 2021-05-27 57 72
Saint Lucia 2021-07-14 11 89
Niger 2021-07-01 8 38
United Arab Emirates 2021-06-12 22 23
Benin 2021-05-27 168 637
Saudi Arabia 2021-05-12 20 78
Cyprus 2021-08-28 137 533
Madagascar 2021-09-27 29 86
Haiti 2021-10-21 11 71
Iceland 2021-05-07 3668 4981
Djibouti 2021-06-30 64 399
Liberia 2021-03-09 56 89
Cayman Islands 2021-07-19 37 37
Guyana 2021-09-06 48 122
East Timor 2021-03-08 23 271
Equatorial Guinea 2021-07-17 12 15
Afghanistan 2021-04-26 18 60
Libya 2021-12-29 3 25
Mali 2021-08-10 3 5
Somalia 2021-08-31 2 2
Azerbaijan 2021-07-14 1 13
Sudan 2021-05-07 59 188

Data source and processing

The data on this page is recent as of 2022-09-13, 04:50 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 3.1.20, pangoLEARN version 2022-02-02.

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.