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 145
Sequence count 158619
Countries United States of America 55048, United Kingdom 22629, India 17343, Germany 8435, Denmark 8091, Turkey 7410, France 4371, Netherlands 4154, Sweden 3050, Belgium 2759, Canada 2334, Switzerland 1894, Croatia 1772, Italy 1577, Norway 1489, Spain 1294, Bulgaria 1293, Poland 1239, Singapore 955, Japan 875, Philippines 811, Bangladesh 622, Czech Republic 613, Ireland 602, Luxembourg 568, Slovenia 461, Qatar 411, Portugal 367, Israel 338, Romania 329, Slovakia 301, South Africa 254, Mexico 236, Australia 231, Finland 212, South Korea 197, Austria 181, Russia 175, Thailand 147, Bahrain 143, Aruba 140, Pakistan 140, Guadeloupe 139, Lithuania 130, Greece 130, Estonia 118, Kosovo 116, Sri Lanka 106, Indonesia 105, Hong Kong 96, Iceland 93, Georgia 82, Cameroon 82, China 81, Malaysia 75, Cambodia 69, Kenya 64, Oman 61, Nepal 58, Gambia 58, Puerto Rico 55, Angola 53, Rwanda 51, Malawi 49, Belize 47, Kuwait 45, Zambia 45, Djibouti 44, Sint Maarten 43, New Zealand 42, Togo 42, Brazil 40, Bosnia and Herzegovina 40, Ghana 38, Gibraltar 36, Zimbabwe 35, Chile 34, Guatemala 34, Botswana 33, Martinique 31, Uganda 30, Colombia 30, Ethiopia 27, Jordan 24, North Macedonia 22, United Arab Emirates 22, Argentina 21, Mauritius 20, Costa Rica 19, Seychelles 19, Ukraine 18, Uzbekistan 18, Vietnam 17, Ecuador 17, Burundi 17, Reunion 16, Peru 16, Afghanistan 16, Montenegro 15, Guyana 15, Nigeria 14, Maldives 13, Mozambique 11, Democratic Republic of the Congo 11, Iran 11, Morocco 11, Algeria 11, Curaçao 9, Kazakhstan 9, Republic of the Congo 9, Papua New Guinea 8, Bonaire 7, Canary Islands 7, Myanmar 7, Egypt 7, Sierra Leone 6, Iraq 6, Jamaica 6, Benin 6, Liechtenstein 5, Cayman Islands 5, Liberia 5, Andorra 4, Republic of Serbia 4, Saudi Arabia 4, French Guiana 4, Crimea 3, Mayotte 3, Comoros 2, Guinea 2, South Sudan 2, Latvia 2, Senegal 2, Antigua and Barbuda 2, Venezuela 1, Taiwan 1, Mongolia 1, Albania 1, Paraguay 1, Lebanon 1, Panama 1, Guam 1, The Bahamas 1, U.S. Virgin Islands 1, East Timor 1
First detected India
Earliest sample date 2020-09-11
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
Sweden 2021-04-01 3050 72622
Turkey 2021-02-08 7410 69944
United States Of America 2020-10-28 55048 1512934
Belgium 2021-04-06 2759 45818
Netherlands 2021-04-13 4154 43345
Aruba 2021-04-16 140 2083
Poland 2021-04-26 1239 17098
Curaçao 2021-07-14 9 421
Switzerland 2021-04-07 1894 49858
Norway 2021-04-15 1489 20110
Japan 2021-03-28 875 121479
Spain 2021-02-03 1294 57533
Germany 2020-09-11 8435 252145
Ireland 2021-04-03 602 28393
Argentina 2021-04-24 21 4033
Puerto Rico 2021-06-14 55 1452
United Kingdom 2021-02-09 22629 972362
Malaysia 2021-04-09 75 4138
Canada 2021-01-26 2334 118102
Russia 2021-04-07 175 4828
Italy 2021-03-16 1577 49238
Czech Republic 2021-03-07 613 12278
South Africa 2021-04-24 254 11422
Malawi 2021-03-17 49 179
Zimbabwe 2021-06-23 35 130
Singapore 2021-04-01 955 7875
Croatia 2021-04-25 1772 7816
Denmark 2021-03-29 8091 140821
Chile 2021-07-13 34 9331
Sierra Leone 2021-07-06 6 7
Georgia 2021-05-15 82 350
Philippines 2021-04-10 811 7010
Bahrain 2021-04-09 143 2052
Ukraine 2021-06-17 18 199
Rwanda 2021-02-24 51 299
South Korea 2021-04-22 197 9055
Bulgaria 2021-06-07 1293 4897
Romania 2021-03-29 329 5606
Slovenia 2021-05-27 461 14156
Bangladesh 2021-04-27 622 1364
Vietnam 2021-04-21 17 1267
Estonia 2021-06-30 118 2900
Mexico 2021-04-19 236 26515
France 2021-04-06 4371 77320
Brazil 2021-04-20 40 52481
Thailand 2021-05-02 147 5986
Indonesia 2021-01-07 105 7670
India 2020-11-03 17343 54508
Slovakia 2021-01-09 301 12012
Bosnia And Herzegovina 2021-06-08 40 377
Kenya 2021-01-21 64 2214
Qatar 2021-04-17 411 1610
Ecuador 2021-08-10 17 1046
Lithuania 2021-05-26 130 9896
Austria 2021-04-17 181 6281
Australia 2021-03-18 231 21202
Angola 2021-05-04 53 234
China 2021-04-21 81 117
Mozambique 2021-05-20 11 300
Israel 2021-04-11 338 12572
Democratic Republic Of The Congo 2021-05-03 11 24
Ghana 2021-05-12 38 486
Finland 2021-04-17 212 10798
Oman 2021-01-06 61 270
Reunion 2021-05-04 16 2265
Hong Kong 2021-03-25 96 522
Portugal 2021-04-18 367 13374
Andorra 2021-07-09 4 22
Papua New Guinea 2021-08-17 8 541
Jordan 2021-04-26 24 334
Venezuela 2021-07-07 1 1
Sri Lanka 2021-03-11 106 1244
Greece 2021-04-24 130 5583
Uganda 2021-04-20 30 322
Pakistan 2021-05-17 140 764
New Zealand 2021-03-30 42 2577
Taiwan 2021-07-12 1 9
North Macedonia 2021-07-01 22 87
Kuwait 2021-06-21 45 100
Ethiopia 2021-05-25 27 392
Liechtenstein 2021-10-02 5 53
Cambodia 2021-06-29 69 1125
Colombia 2021-07-14 30 2587
Kazakhstan 2021-08-17 9 89
Nepal 2021-04-19 58 185
Gambia 2021-04-08 58 209
Republic Of Congo 2021-06-26 9 92
Luxembourg 2021-04-02 568 9423
United Arab Emirates 2021-06-12 22 22
Guadeloupe 2021-05-25 139 368
Guatemala 2021-06-22 34 484
Kosovo 2021-04-30 116 815
Iran 2021-04-26 11 62
Costa Rica 2021-06-17 19 918
Iraq 2021-07-20 6 10
Cayman Islands 2021-07-23 5 32
Montenegro 2021-07-10 15 167
Mongolia 2021-09-23 1 1
Myanmar 2021-05-28 7 25
Albania 2021-06-16 1 12
Iceland 2021-05-23 93 3751
Republic Of Serbia 2021-07-13 4 45
Nigeria 2021-05-02 14 1573
Morocco 2021-04-22 11 147
Botswana 2021-05-09 33 1000
Peru 2021-08-17 16 3798
Gibraltar 2021-07-12 36 725
Uzbekistan 2021-06-25 18 56
Belize 2021-01-07 47 266
Guinea 2021-06-28 2 9
Djibouti 2021-08-25 44 56
Saudi Arabia 2021-05-21 4 22
Paraguay 2021-08-19 1 14
Lebanon 2021-07-14 1 1
Panama 2021-04-29 1 15
Guam 2021-04-26 1 98
Cameroon 2021-08-11 82 264
Algeria 2021-05-10 11 29
Guyana 2021-09-06 15 49
Jamaica 2021-07-19 6 56
South Sudan 2021-04-27 2 35
Togo 2021-04-26 42 149
Latvia 2021-02-08 2 4710
Liberia 2021-04-06 5 69
The Bahamas 2021-08-07 1 13
Benin 2021-05-27 6 87
Afghanistan 2021-05-08 16 47
Zambia 2021-05-24 45 302
Senegal 2021-06-05 2 8
Mayotte 2021-08-02 3 44
Burundi 2021-07-28 17 54
Egypt 2021-10-18 7 63
East Timor 2021-04-22 1 226

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.