B.1.617.2 2023-01-31



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 181
Sequence count 272143
Countries India 61522, Turkey 43784, United States of America 38251, Germany 19450, United Kingdom 17974, France 11419, Denmark 10544, Netherlands 4603, Sweden 4336, Belgium 4148, Italy 4074, Canada 3455, Switzerland 3055, Spain 2865, Poland 2816, Croatia 2791, Slovenia 2171, Bulgaria 2140, Bangladesh 2058, Israel 1713, Philippines 1633, Nepal 1565, Czech Republic 1426, Norway 1103, Singapore 1086, Bahrain 1083, Latvia 1000, Portugal 942, Slovakia 915, Qatar 914, Luxembourg 913, Russia 884, Pakistan 822, Finland 794, Ireland 781, Japan 715, Thailand 664, China 626, South Africa 606, Indonesia 487, South Korea 469, Austria 433, Romania 390, Australia 355, Reunion 324, Malawi 315, Kenya 294, Malaysia 275, Greece 269, Lithuania 253, Ghana 236, Brazil 224, Lebanon 224, Mexico 222, Iraq 215, Egypt 212, Cameroon 202, Mongolia 190, Maldives 176, Iceland 162, Sri Lanka 155, Hong Kong 138, Cambodia 138, Ethiopia 134, Georgia 132, Kuwait 129, Puerto Rico 129, Aruba 126, Chile 122, Iran 119, Jordan 115, Estonia 108, Togo 99, Gambia 98, Kyrgyzstan 97, Canary Islands 96, Botswana 95, Nigeria 94, Panama 85, Senegal 83, Bosnia and Herzegovina 81, Mauritius 81, Democratic Republic of the Congo 80, Algeria 78, Belize 78, Rwanda 76, Oman 74, Peru 73, Argentina 69, Benin 67, Cote d'Ivoire 65, Morocco 59, Sudan 59, Colombia 58, Zimbabwe 57, Cyprus 56, Guinea 53, Guadeloupe 53, Montenegro 51, French Guiana 47, Uganda 45, New Zealand 43, Zambia 42, Angola 41, Ukraine 38, Sierra Leone 37, Seychelles 34, Sint Maarten 34, Kazakhstan 31, Kosovo 30, Mozambique 30, Uzbekistan 29, Myanmar 26, Burundi 26, Ecuador 24, Fiji 23, Republic of Serbia 20, United Arab Emirates 20, Paraguay 19, Martinique 18, Afghanistan 18, Guyana 16, Vietnam 15, Saudi Arabia 14, Malta 14, Burkina Faso 13, Gibraltar 13, Republic of the Congo 12, Syria 11, Curaçao 11, Chad 9, Jamaica 9, U.S. Virgin Islands 9, Eswatini 8, Papua New Guinea 8, Costa Rica 8, Venezuela 7, Laos 7, Crimea 7, Tunisia 7, North Macedonia 7, Grenada 7, Taiwan 6, Antigua and Barbuda 6, Northern Mariana Islands 6, Belarus 6, Cayman Islands 6, Guatemala 6, South Sudan 6, Djibouti 6, Azerbaijan 5, Liechtenstein 5, Liberia 5, Dominican Republic 5, Niger 5, Cabo Verde 4, Bonaire 4, Sao Tome and Principe 4, Brunei 4, The Bahamas 3, Gabon 3, Lesotho 3, Turks and Caicos Islands 3, Barbados 3, Armenia 3, Hungary 3, Madagascar 2, Moldova 2, Mauritania 2, Comoros 1, Albania 1, Montserrat 1, Monaco 1, Guam 1, Uruguay 1, East Timor 1, Trinidad and Tobago 1, Mayotte 1, British Virgin Islands 1, Suriname 1, Tanzania 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
Germany 2021-03-09 211803 824366
Netherlands 2021-03-07 44827 136502
France 2021-03-17 151373 475026
Lithuania 2021-05-26 14794 26036
United States Of America 2021-03-03 1421474 3790001
Denmark 2021-03-29 159363 550431
Belgium 2021-04-06 48052 147558
Canada 2021-03-06 104391 398629
Botswana 2021-05-09 994 2634
Japan 2021-03-28 96283 499602
Czech Republic 2021-03-03 18084 52583
Malaysia 2021-03-09 7258 32464
Sweden 2021-04-01 57700 176426
Iraq 2021-03-01 503 826
Bulgaria 2021-04-05 10242 18041
United Kingdom 2021-03-09 1101443 2488788
Italy 2021-03-16 44798 136766
Indonesia 2021-03-09 8293 41246
New Zealand 2021-03-15 4792 28152
Austria 2021-04-17 6158 49213
Ireland 2021-04-03 26697 83451
India 2021-03-01 77449 170671
Turkey 2021-03-09 59887 96448
Brazil 2021-04-06 45138 178794
South Africa 2021-03-17 10985 32996
Australia 2021-03-18 30347 143586
Israel 2021-04-08 18283 104312
Mexico 2021-03-02 25206 73752
Ghana 2021-03-05 882 2499
Kazakhstan 2021-07-25 385 1168
Burkina Faso 2021-03-18 24 40
Spain 2021-03-08 52688 172578
Romania 2021-03-28 6046 16363
Slovakia 2021-03-09 13948 42529
Slovenia 2021-03-01 27710 69989
Norway 2021-04-15 22103 61656
Republic Of Serbia 2021-06-26 175 1673
Portugal 2021-04-18 14560 36418
Kosovo 2021-04-30 914 1562
Bangladesh 2021-04-23 2864 4856
Switzerland 2021-04-07 56634 118501
Puerto Rico 2021-06-03 3740 11738
Guam 2021-04-26 279 851
Albania 2021-06-16 25 27
Nepal 2021-04-12 1848 2862
Cambodia 2021-05-25 1209 3519
Montenegro 2021-06-18 437 830
Vietnam 2021-04-20 2497 6839
Russia 2021-03-01 14970 52327
South Korea 2021-04-19 16970 77471
Kuwait 2021-05-24 144 624
Greece 2021-03-23 4953 22892
Poland 2021-04-22 29145 75674
Andorra 2021-07-08 51 189
Thailand 2021-03-06 8128 28431
Chile 2021-06-13 8518 33810
Bosnia And Herzegovina 2021-06-08 1079 1239
Qatar 2021-04-17 1686 3433
Ecuador 2021-06-22 1195 6773
Jordan 2021-04-26 498 707
Singapore 2021-04-01 8746 27561
Tunisia 2021-05-25 533 836
Croatia 2021-04-25 13862 36898
Peru 2021-05-15 7103 39073
Paraguay 2021-03-01 419 2268
Taiwan 2021-03-22 39 2470
Nigeria 2021-04-10 2070 3831
Latvia 2021-03-25 5527 23036
Argentina 2021-04-24 4040 13618
Moldova 2021-06-17 167 717
Estonia 2021-06-10 4228 10495
Reunion 2021-05-04 5612 16391
Colombia 2021-03-11 3832 15459
Saint Lucia 2021-07-14 11 144
Ukraine 2021-06-17 449 1146
Republic Of Congo 2021-03-12 91 307
Finland 2021-04-17 13314 34708
Kenya 2021-03-15 2196 6069
Luxembourg 2021-04-01 9016 42692
Guinea 2021-05-17 115 409
Liechtenstein 2021-06-18 383 1054
Malta 2021-05-19 399 566
Philippines 2021-04-13 3298 18237
Hong Kong 2021-03-25 756 11835
Sri Lanka 2021-03-11 1388 2569
Venezuela 2021-07-07 176 570
China 2021-04-21 1358 10358
Gabon 2021-07-06 109 122
Trinidad And Tobago 2021-08-03 412 2094
Brunei 2021-07-21 603 4933
Georgia 2021-05-11 752 2547
Mongolia 2021-03-08 321 1567
Hungary 2021-11-15 85 222
Gambia 2021-04-08 307 483
Bahrain 2021-04-05 3537 9658
Angola 2021-04-18 232 451
Mauritania 2021-03-16 20 49
Costa Rica 2021-06-13 1282 8282
Dominican Republic 2021-03-11 619 2240
Belarus 2021-05-24 232 275
Pakistan 2021-04-08 1470 4146
Panama 2021-04-29 895 4822
Gibraltar 2021-06-03 1739 1872
Mozambique 2021-05-04 377 702
Laos 2021-08-04 394 890
Suriname 2021-07-12 266 499
Belize 2021-03-07 220 864
Uganda 2021-04-20 385 755
Mayotte 2021-07-28 146 501
Cyprus 2021-04-25 825 1470
Lebanon 2021-06-07 631 1039
Algeria 2021-05-10 80 499
Democratic Republic Of The Congo 2021-03-03 252 464
Guadeloupe 2021-05-25 1398 2018
Senegal 2021-04-02 617 1780
Fiji 2021-04-14 469 470
Papua New Guinea 2021-07-07 1498 2289
Curaçao 2021-06-28 599 1730
Egypt 2021-06-22 284 1026
Aruba 2021-04-10 1856 3302
Syria 2021-12-01 32 106
Saudi Arabia 2021-05-12 22 591
Zimbabwe 2021-06-23 135 351
Eswatini 2021-06-08 270 742
Solomon Islands 2022-01-26 77 307
Jamaica 2021-04-11 391 2155
Ivory Coast 2021-03-01 83 492
Morocco 2021-04-22 204 1366
Nicaragua 2021-06-23 152 334
Togo 2021-04-12 337 469
United Arab Emirates 2021-06-12 22 23
Guatemala 2021-04-24 698 3573
Rwanda 2021-03-22 214 358
Malawi 2021-03-17 384 603
Kyrgyzstan 2021-06-08 134 186
Iceland 2021-05-07 3669 6856
Zambia 2021-03-26 335 633
Chad 2021-07-05 33 38
British Virgin Islands 2021-07-27 31 86
El Salvador 2021-08-02 79 389
Libya 2021-12-29 3 25
Cameroon 2021-04-01 328 827
Honduras 2021-07-30 64 114
Cayman Islands 2021-07-19 37 37
Iran 2021-04-18 249 1815
Namibia 2021-03-08 79 607
Central African Republic 2021-12-12 2 18
The Bahamas 2021-05-17 141 191
Bolivia 2021-06-14 49 132
Mali 2021-04-08 6 49
Azerbaijan 2021-07-14 33 53
South Sudan 2021-04-27 83 117
Djibouti 2021-06-30 64 568
Ethiopia 2021-03-15 368 485
Lesotho 2021-04-30 41 128
Uruguay 2021-09-03 64 235
Liberia 2021-03-09 56 89
Myanmar 2021-05-28 40 81
North Macedonia 2021-06-14 122 371
Benin 2021-05-27 168 663
Barbados 2021-04-25 12 139
Oman 2021-03-05 111 387
Guyana 2021-09-06 48 124
Armenia 2021-06-17 39 45
East Timor 2021-03-08 23 271
Uzbekistan 2021-06-25 51 92
Sudan 2021-05-07 59 188
Burundi 2021-05-27 57 72
Saint-Martin 2021-11-24 27 322
Niger 2021-07-01 8 38
Sierra Leone 2021-05-07 39 43
Equatorial Guinea 2021-07-17 12 15
Afghanistan 2021-04-26 18 63
Madagascar 2021-09-27 29 86
Haiti 2021-10-21 12 173
Somalia 2021-08-31 2 2
Vanuatu 2021-10-24 2 95
Tanzania 2021-05-03 1 3

Data source and processing

The data on this page is recent as of 2023-01-31, 22:14 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.