B.1.617.2 2021-05-19



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 141
Sequence count 367377
Countries United States of America 155360, Turkey 37826, United Kingdom 37712, India 14702, Germany 13583, Denmark 13028, Sweden 12437, France 10123, Netherlands 8845, Italy 7200, Belgium 6132, Spain 5565, Brazil 3910, Norway 3606, Switzerland 3407, Canada 3395, South Korea 2383, Ireland 2378, South Africa 2002, Russia 1597, Czech Republic 1487, Australia 1478, Finland 1224, Singapore 1165, Croatia 1155, Estonia 1057, Japan 1039, New Zealand 938, Mexico 912, Luxembourg 815, Slovenia 721, Slovakia 671, Poland 603, Malaysia 529, Portugal 476, Iceland 469, Bangladesh 444, Bulgaria 439, Reunion 400, Sint Maarten 396, Lithuania 362, Austria 359, Greece 324, Aruba 297, Israel 274, Botswana 248, Puerto Rico 218, Uganda 162, Maldives 156, Costa Rica 143, Romania 135, Hong Kong 129, Sri Lanka 125, Togo 118, Gibraltar 115, Bahrain 107, Peru 106, Kuwait 104, Pakistan 103, Rwanda 89, Oman 88, Thailand 87, China 85, Qatar 82, Zambia 82, Montenegro 80, Ghana 77, Guadeloupe 76, Guatemala 69, Curaçao 64, Nepal 58, Chile 55, Liberia 55, Vietnam 53, Bosnia and Herzegovina 51, Indonesia 51, Martinique 49, Kenya 49, Malawi 47, U.S. Virgin Islands 46, Nigeria 43, Gambia 36, Bonaire 35, French Guiana 33, Uzbekistan 31, North Macedonia 31, Eswatini 29, Paraguay 29, South Sudan 25, Bahamas 23, Georgia 23, Crimea 23, United Arab Emirates 22, Cambodia 22, Latvia 22, Zimbabwe 21, Belize 19, Kosovo 18, Monaco 18, Ecuador 18, Northern Mariana Islands 16, Andorra 15, Argentina 15, Mozambique 15, Suriname 14, Ukraine 13, Angola 13, Parana 13, Democratic Republic of the Congo 12, Moldova 11, Iran 11, Jordan 11, Philippines 10, Senegal 9, Cayman Islands 8, Ethiopia 8, Republic of the Congo 7, Colombia 7, Mauritius 5, Republic of Serbia 5, Morocco 5, Myanmar 5, Rio de Janeiro 5, Mayotte 4, Guam 4, Albania 4, Malta 3, Burundi 3, Taiwan 3, Barbados 2, Mali 2, Honduras 2, Lebanon 1, Algeria 1, Burkina Faso 1, Anguilla 1, Jamaica 1, Guinea 1, Slovak Republic 1, Antigua and Barbuda 1, British Virgin Islands 1
First detected India
Earliest sample date 2020-09-22
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 2021-03-18 37712 519756
United States Of America 2020-12-16 155360 831787
Switzerland 2021-04-07 3407 29762
Italy 2021-01-07 7200 45385
Sweden 2020-11-19 12437 99957
Portugal 2021-04-18 476 8552
South Africa 2021-04-24 2002 7570
Ireland 2021-04-07 2378 18931
Belgium 2021-04-06 6132 27698
Spain 2021-01-29 5565 46266
Australia 2021-02-07 1478 10466
Poland 2021-04-22 603 8349
Gibraltar 2021-07-12 115 725
France 2021-02-27 10123 65027
Mayotte 2021-08-02 4 10
Guadeloupe 2021-05-25 76 227
Brazil 2021-04-26 3910 20053
Lithuania 2021-05-26 362 5355
India 2020-10-30 14702 35258
Norway 2021-04-15 3606 12436
Croatia 2021-04-25 1155 3091
Slovenia 2021-05-27 721 6137
Netherlands 2021-04-13 8845 31694
Singapore 2021-02-06 1165 5522
Czech Republic 2021-02-11 1487 6491
Turkey 2021-03-09 37826 58446
Moldova 2021-06-17 11 13
Mexico 2020-09-22 912 25144
Kuwait 2021-05-24 104 150
Germany 2021-02-07 13583 166339
Malaysia 2021-03-17 529 1480
Japan 2021-03-28 1039 58363
Estonia 2021-06-10 1057 1282
Kosovo 2021-04-30 18 49
Canada 2021-01-26 3395 66652
Guatemala 2021-06-24 69 249
Reunion 2021-05-18 400 1766
New Zealand 2021-03-30 938 1115
Hong Kong 2021-03-25 129 389
Denmark 2021-03-29 13028 91821
China 2021-04-21 85 114
Bangladesh 2021-04-27 444 909
Thailand 2021-05-02 87 1887
Luxembourg 2021-04-02 815 5310
Chile 2021-06-13 55 3408
Romania 2021-03-28 135 1522
Puerto Rico 2021-06-03 218 1022
Bulgaria 2021-04-05 439 1811
Austria 2021-04-17 359 4506
Kenya 2021-04-07 49 933
Bahrain 2021-04-05 107 694
Togo 2021-04-12 118 158
Russia 2021-04-07 1597 3036
Iran 2021-04-26 11 13
Malta 2021-05-19 3 69
Curaçao 2021-06-28 64 240
Aruba 2021-01-08 297 2507
Bosnia And Herzegovina 2021-06-08 51 75
Andorra 2021-07-08 15 15
Slovakia 2021-04-01 671 4468
Indonesia 2021-01-07 51 5325
Ukraine 2021-06-17 13 17
Democratic Republic Of The Congo 2021-04-20 12 25
South Korea 2021-04-22 2383 5436
Ghana 2021-01-06 77 869
Barbados 2021-05-04 2 16
Israel 2021-04-10 274 4119
Nigeria 2021-05-02 43 433
Iceland 2021-05-07 469 3796
United Arab Emirates 2021-06-12 22 22
Qatar 2021-04-17 82 451
Liberia 2021-03-09 55 77
Finland 2021-04-17 1224 7641
Pakistan 2021-04-12 103 527
Malawi 2021-03-17 47 104
Argentina 2021-04-24 15 1621
Guam 2021-04-26 4 98
Nepal 2021-04-20 58 138
Rwanda 2021-06-08 89 116
Botswana 2021-05-10 248 583
Senegal 2021-06-01 9 14
Georgia 2021-05-11 23 119
Republic Of Congo 2021-06-26 7 22
Lebanon 2021-07-02 1 22
Burundi 2021-05-27 3 9
South Sudan 2021-04-27 25 35
Republic Of Serbia 2021-06-29 5 6
Jordan 2021-04-26 11 27
Sri Lanka 2021-06-05 125 598
Uganda 2021-04-20 162 193
Colombia 2021-07-26 7 82
Uzbekistan 2021-06-25 31 56
Greece 2021-03-23 324 4970
Costa Rica 2021-06-13 143 445
Cambodia 2021-07-06 22 507
North Macedonia 2021-06-14 31 43
Gambia 2021-05-17 36 45
Cayman Islands 2021-07-19 8 13
Montenegro 2021-06-18 80 109
Peru 2021-05-15 106 2607
Ecuador 2021-07-05 18 567
Algeria 2021-05-10 1 20
Latvia 2021-05-05 22 829
Morocco 2021-04-22 5 19
Vietnam 2021-04-21 53 62
Angola 2021-04-18 13 108
Zambia 2021-05-24 82 82
Myanmar 2021-05-28 5 10
Zimbabwe 2021-06-28 21 82
Taiwan 2021-06-22 3 14
Ethiopia 2021-07-18 8 8
Oman 2021-01-06 88 269
Philippines 2021-04-24 10 195
Burkina Faso 2021-03-18 1 17
Suriname 2021-07-29 14 57
Jamaica 2021-07-22 1 3
Mali 2021-08-10 2 3
Belize 2021-01-07 19 125
Guinea 2021-05-17 1 14
Albania 2021-06-16 4 12
Eswatini 2021-06-23 29 67
Paraguay 2021-07-30 29 55
British Virgin Islands 2021-07-27 1 1
Mozambique 2021-06-30 15 53
Honduras 2021-07-30 2 2

Data source and processing

The data on this page is recent as of 2021-05-19, 10:13 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 2.3.9, pangoLEARN version 2021-04-21.

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 pre-print up on virological here describing this web tracker.