B.1.617.2 2022-05-19



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 174
Sequence count 170623
Countries United States of America 38464, India 28966, United Kingdom 22860, Turkey 16374, Germany 9028, Denmark 5288, France 4998, Netherlands 3965, Canada 2756, Sweden 2721, Croatia 2644, Belgium 2454, Poland 2410, Italy 2029, Bulgaria 1885, Spain 1630, Philippines 1516, Slovenia 1496, Switzerland 1377, Bangladesh 1376, Singapore 1062, Norway 1003, Luxembourg 819, Czech Republic 768, Latvia 767, Japan 689, Nepal 679, Ireland 632, Israel 603, Qatar 516, Portugal 436, South Africa 401, Pakistan 396, Slovakia 370, Austria 336, Indonesia 324, Australia 292, Finland 289, Thailand 271, South Korea 269, Romania 266, Russia 258, Reunion 220, Lithuania 215, Mongolia 184, Malaysia 178, Malawi 178, Iraq 157, Greece 140, Sri Lanka 140, Bahrain 139, Aruba 126, Kenya 126, Ghana 119, Hong Kong 117, Puerto Rico 115, Mexico 114, China 108, Cameroon 103, Georgia 100, Kuwait 99, Estonia 98, Iceland 90, Rwanda 76, Panama 76, Togo 74, Jordan 71, Gambia 69, Mauritius 68, Ethiopia 66, Belize 63, Bosnia and Herzegovina 60, Oman 59, Cote d'Ivoire 58, Kyrgyzstan 57, Senegal 55, Chile 54, Zambia 51, Peru 46, Brazil 45, Colombia 40, Gibraltar 38, Uganda 38, Ecuador 36, New Zealand 35, Angola 32, Benin 31, Sint Maarten 30, Kosovo 28, Guadeloupe 27, Nigeria 27, Zimbabwe 23, Iran 22, United Arab Emirates 22, Egypt 22, Myanmar 21, Mozambique 20, Papua New Guinea 20, Ukraine 19, Maldives 19, Burundi 19, Democratic Republic of the Congo 18, Afghanistan 18, Botswana 17, Montenegro 17, Cambodia 16, Northern Mariana Islands 16, Guyana 16, Uzbekistan 16, Vietnam 15, Seychelles 15, Morocco 14, Argentina 14, Saudi Arabia 12, Paraguay 11, Jamaica 10, Curaçao 10, Lebanon 10, Republic of the Congo 10, Sierra Leone 9, Canary Islands 9, U.S. Virgin Islands 8, Guinea 8, Kazakhstan 7, Malta 7, Algeria 6, South Sudan 6, Martinique 6, Grenada 6, Chad 6, Djibouti 6, Crimea 6, Cayman Islands 6, Guam 5, Costa Rica 5, Guatemala 5, Liberia 5, North Macedonia 4, Antigua and Barbuda 4, Burkina Faso 4, Tunisia 4, Sao Tome and Principe 4, Bonaire 4, French Guiana 4, Republic of Serbia 4, Brunei 4, Barbados 3, Gabon 3, Syria 3, Venezuela 3, Liechtenstein 3, Eswatini 3, The Bahamas 3, British Virgin Islands 2, Taiwan 2, Moldova 2, Comoros 2, Trinidad and Tobago 2, Montserrat 2, Hungary 2, Belarus 2, Monaco 1, Turks and Caicos Islands 1, Namibia 1, Mauritania 1, Nicaragua 1, Mayotte 1, Suriname 1, Cabo Verde 1, Armenia 1, Dominican Republic 1, Uruguay 1, Albania 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
Luxembourg 2021-04-01 9008 23658
United Kingdom 2021-03-09 1099281 2265520
Germany 2021-03-09 206147 561426
Canada 2021-03-06 100476 260042
United States Of America 2021-03-03 1393350 2675416
Slovenia 2021-03-01 27312 54628
Croatia 2021-04-25 13857 27277
Italy 2021-03-16 42815 92539
Brazil 2021-04-12 41103 114031
Gibraltar 2021-06-03 1740 1872
Denmark 2021-03-29 158884 425260
Czech Republic 2021-03-03 18072 37805
Singapore 2021-04-01 8746 14503
Finland 2021-04-02 13318 22584
South Korea 2021-04-19 16890 30777
France 2021-03-17 116269 240104
Malaysia 2021-03-09 7122 14683
Sweden 2021-04-01 57374 131797
Israel 2021-04-08 18288 46192
Belgium 2021-04-06 45580 91807
Netherlands 2021-03-07 44808 99608
Ireland 2021-04-03 26694 51637
Japan 2021-03-28 95071 222227
Switzerland 2021-04-07 56615 100632
Mexico 2021-03-27 24765 50059
Papua New Guinea 2021-07-07 1498 1966
Latvia 2021-03-25 5476 9613
India 2021-03-01 72341 124212
North Macedonia 2021-06-14 122 176
Slovakia 2021-03-09 13952 33735
Belize 2021-03-07 213 554
Spain 2021-03-30 44356 95394
Peru 2021-05-15 6589 16101
Vietnam 2021-04-20 2400 4001
Thailand 2021-03-06 8022 18257
Australia 2021-03-18 30278 70478
Aruba 2021-04-10 1856 2527
Curaçao 2021-06-28 599 1150
Guam 2021-04-26 279 651
Greece 2021-03-23 4954 12432
Reunion 2021-05-04 5297 9635
Turkey 2021-03-09 59947 86463
Indonesia 2021-03-09 8265 20639
Jordan 2021-04-26 496 622
South Africa 2021-03-17 10532 24765
Nigeria 2021-04-10 1981 3010
Mali 2021-08-10 3 5
Cameroon 2021-04-01 301 418
Portugal 2021-04-18 14550 25783
Hungary 2021-11-15 85 113
Austria 2021-04-17 6144 16363
Lithuania 2021-05-26 14794 25171
Chile 2021-06-13 8521 18775
Bulgaria 2021-04-05 9766 13326
Uganda 2021-04-20 366 411
Tunisia 2021-05-25 489 620
Eswatini 2021-06-08 212 362
Poland 2021-04-22 28973 68969
Mongolia 2021-03-08 312 978
New Zealand 2021-03-15 4792 9447
Romania 2021-03-28 6039 11896
Cambodia 2021-05-25 1197 2780
Hong Kong 2021-03-25 720 4334
Puerto Rico 2021-06-03 3284 6798
Liechtenstein 2021-06-18 383 636
China 2021-04-21 455 596
Colombia 2021-03-11 3626 9920
Iraq 2021-04-27 437 683
Jamaica 2021-04-11 380 1100
Morocco 2021-04-22 195 398
Bosnia And Herzegovina 2021-06-08 1079 1219
Dominican Republic 2021-03-11 552 948
Philippines 2021-04-09 3266 8607
Kyrgyzstan 2021-06-14 85 90
Qatar 2021-04-17 1676 2316
Russia 2021-03-01 6690 9791
Montenegro 2021-06-18 437 667
Costa Rica 2021-06-13 1282 3195
Senegal 2021-04-02 608 1058
Liberia 2021-03-09 56 89
Bahrain 2021-04-05 1986 2069
Kenya 2021-03-15 2009 4682
Norway 2021-04-15 21818 49245
Ukraine 2021-06-17 348 446
Trinidad And Tobago 2021-08-03 404 894
Barbados 2021-04-25 12 23
British Virgin Islands 2021-07-27 30 66
Bangladesh 2021-04-23 2814 4109
Togo 2021-04-12 336 471
Sierra Leone 2021-05-07 10 10
Argentina 2021-03-04 3879 11453
Taiwan 2021-03-22 23 142
Zambia 2021-03-26 335 526
Kosovo 2021-04-30 914 1221
Sri Lanka 2021-03-11 1386 2473
Nepal 2021-04-12 1113 1391
Gambia 2021-04-08 307 354
Mayotte 2021-07-28 101 234
Ecuador 2021-06-22 1116 3620
Brunei 2021-07-21 603 1857
Estonia 2021-06-10 4232 6859
Democratic Republic Of The Congo 2021-03-03 184 322
Malta 2021-05-19 400 566
Kuwait 2021-05-24 144 223
Georgia 2021-05-11 728 1572
Moldova 2021-06-17 167 456
Niger 2021-07-01 6 8
Algeria 2021-05-10 54 143
Kazakhstan 2021-07-25 184 193
Iran 2021-04-18 67 787
Guadeloupe 2021-05-25 317 682
Pakistan 2021-04-08 1063 1847
Rwanda 2021-03-22 214 358
Nicaragua 2021-06-23 121 224
Panama 2021-04-29 824 2708
Ghana 2021-04-20 835 1668
El Salvador 2021-08-02 79 241
Guatemala 2021-04-24 698 1377
Saudi Arabia 2021-05-12 19 77
Burkina Faso 2021-03-18 10 25
Uzbekistan 2021-06-25 48 56
Myanmar 2021-05-28 40 70
Oman 2021-03-05 111 309
Botswana 2021-05-09 1008 2143
Fiji 2021-04-14 469 470
Lebanon 2021-07-01 129 214
Afghanistan 2021-04-26 18 60
Egypt 2021-06-22 234 392
The Bahamas 2021-05-17 141 191
Guinea 2021-05-17 91 232
Iceland 2021-05-07 3668 3801
Uruguay 2021-09-03 58 86
Suriname 2021-07-12 266 448
Malawi 2021-03-17 313 493
East Timor 2021-03-08 23 270
Laos 2021-12-08 6 6
Saint-Martin 2021-11-24 27 274
Venezuela 2021-07-07 167 319
Ethiopia 2021-03-15 367 485
Belarus 2021-05-24 232 275
Gabon 2021-07-06 108 119
Djibouti 2021-06-30 64 370
Paraguay 2021-04-09 380 719
Honduras 2021-07-30 64 112
Haiti 2021-10-21 11 71
Guyana 2021-09-06 48 122
Angola 2021-04-18 231 364
Andorra 2021-07-08 51 103
Zimbabwe 2021-06-23 135 322
Equatorial Guinea 2021-07-17 12 13
South Sudan 2021-04-27 83 117
Republic Of Congo 2021-03-12 90 287
Mozambique 2021-05-04 373 540
Saint Lucia 2021-07-14 11 16
Republic Of Serbia 2021-06-26 174 285
Solomon Islands 2022-01-26 74 108
United Arab Emirates 2021-06-12 22 22
Namibia 2021-04-26 51 195
Syria 2021-12-01 32 89
Ivory Coast 2021-03-01 81 376
Albania 2021-06-16 25 27
Chad 2021-07-05 33 38
Azerbaijan 2021-07-14 1 13
Benin 2021-05-27 168 248
Central African Republic 2021-12-12 2 18
Bolivia 2021-06-14 40 83
Burundi 2021-05-27 57 63
Mauritania 2021-03-16 20 48
Armenia 2021-06-17 39 44
Lesotho 2021-08-18 5 5
Cayman Islands 2021-07-19 37 37
Cyprus 2021-08-28 1 1

Data source and processing

The data on this page is recent as of 2022-05-19, 11:47 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.