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 158
Sequence count 851391
Countries United States of America 351089, United Kingdom 101459, Germany 62822, Turkey 43450, Denmark 32930, France 30506, India 26076, Switzerland 19396, Sweden 18795, Spain 17889, Belgium 15936, Italy 14679, Netherlands 12621, Brazil 8940, Slovenia 7657, Canada 7458, Norway 6911, South Africa 5270, Finland 5267, Portugal 5024, Ireland 4318, South Korea 4233, Poland 3191, Czech Republic 2957, Russia 2870, Luxembourg 2718, Austria 2706, Slovakia 2504, Croatia 2122, Mexico 2025, Romania 1752, Estonia 1497, Japan 1426, Israel 1359, Malaysia 1349, Chile 1265, Bulgaria 1249, Greece 1216, Singapore 1192, Iceland 1067, Lithuania 975, Bangladesh 890, Sint Maarten 556, Peru 540, Thailand 468, Fiji 467, Puerto Rico 460, Kosovo 449, Vietnam 422, Pakistan 419, Australia 390, Aruba 353, Botswana 337, Kenya 323, Bahrain 301, Nigeria 299, Zambia 299, Sri Lanka 265, Costa Rica 259, Gibraltar 245, Guadeloupe 219, Maldives 213, Uganda 208, Indonesia 204, Rwanda 198, French Guiana 188, Hong Kong 180, Argentina 178, Bonaire 167, Ghana 166, Ecuador 158, Montenegro 151, Ethiopia 143, Reunion 127, Cambodia 127, Nepal 127, Guatemala 114, New Zealand 112, Togo 103, Kuwait 101, Curaçao 100, Jordan 99, Qatar 96, Malawi 94, Oman 93, U.S. Virgin Islands 90, Colombia 87, China 86, Suriname 77, Mozambique 76, Zimbabwe 73, Georgia 72, Latvia 70, Philippines 65, Burundi 57, Seychelles 56, Canary Islands 54, Bosnia and Herzegovina 52, Namibia 50, Monaco 47, Kazakhstan 46, Eswatini 44, Malta 37, Uzbekistan 37, Angola 37, The Bahamas 34, Republic of Serbia 32, Martinique 32, Gambia 31, North Macedonia 31, Benin 27, South Sudan 25, Ukraine 25, Republic of the Congo 23, Crimea 22, United Arab Emirates 22, Morocco 21, Belize 20, Mayotte 18, Afghanistan 18, Andorra 17, Algeria 15, Paraguay 15, Iran 13, Myanmar 13, Moldova 11, Liechtenstein 10, Democratic Republic of the Congo 10, Mauritius 10, Cayman Islands 10, Taiwan 9, Sierra Leone 9, Equatorial Guinea 9, Gabon 7, Senegal 7, Armenia 6, Liberia 5, Northern Mariana Islands 5, Albania 4, Saint Barthelemy 4, Guam 4, Dominican Republic 4, Lebanon 3, Barbados 3, Antigua and Barbuda 3, Papua New Guinea 3, Guinea 2, Honduras 2, Iraq 1, Panama 1, Anguilla 1, Mongolia 1, El Salvador 1, Grenada 1, Slovak Republic 1, Egypt 1, East Timor 1, Venezuela 1
First detected India
Earliest sample date 2020-09-07
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
Canada 2021-01-26 7458 98366
United States Of America 2020-12-16 351089 1149471
Ireland 2021-04-07 4318 23886
Belgium 2021-04-06 15936 39149
Switzerland 2021-01-08 19396 55881
Poland 2021-01-09 3191 22288
Mexico 2020-09-22 2025 30228
Brazil 2021-04-26 8940 29793
Bangladesh 2021-04-27 890 1236
France 2021-01-16 30506 80327
Denmark 2021-03-29 32930 104660
United Kingdom 2021-01-09 101459 837667
Spain 2020-11-03 17889 59406
Italy 2021-01-07 14679 52800
India 2020-09-07 26076 46176
Bahrain 2021-04-05 301 787
Pakistan 2021-04-12 419 736
Suriname 2021-07-29 77 140
Lithuania 2021-05-26 975 8193
Costa Rica 2021-06-13 259 618
Sweden 2020-11-19 18795 108500
Slovenia 2020-11-13 7657 26605
Slovakia 2021-01-09 2504 8251
Germany 2021-02-07 62822 208654
Malaysia 2021-03-09 1349 3045
Norway 2021-04-15 6911 16673
Burundi 2021-05-27 57 63
South Sudan 2021-04-27 25 35
Russia 2021-04-07 2870 3953
Japan 2021-03-28 1426 91902
Iraq 2021-04-27 1 16
China 2021-04-21 86 116
Czech Republic 2021-01-28 2957 9325
Hong Kong 2021-03-25 180 448
Romania 2021-03-28 1752 3602
Republic Of Serbia 2021-06-26 32 36
Jordan 2021-04-26 99 119
Netherlands 2021-04-13 12621 37939
Ukraine 2021-06-17 25 42
Liechtenstein 2021-06-18 10 18
Australia 2021-03-18 390 16031
Singapore 2021-02-06 1192 6914
New Zealand 2021-03-30 112 1628
Rwanda 2020-09-10 198 489
Albania 2021-06-16 4 12
Puerto Rico 2021-06-03 460 1419
Kosovo 2021-04-30 449 742
Guatemala 2021-06-24 114 299
Taiwan 2021-06-14 9 27
South Africa 2021-01-19 5270 11269
Austria 2021-04-17 2706 5243
Argentina 2021-04-24 178 2711
Portugal 2021-04-18 5024 11054
Guadeloupe 2021-05-25 219 342
Finland 2021-04-17 5267 8346
Croatia 2021-04-25 2122 4621
Israel 2021-04-08 1359 4198
Kazakhstan 2021-08-17 46 89
Colombia 2021-01-20 87 3203
Iran 2021-04-26 13 19
Morocco 2021-04-22 21 85
Montenegro 2021-06-18 151 191
Greece 2021-03-23 1216 6387
Chile 2021-01-10 1265 9835
Panama 2021-04-29 1 15
Peru 2021-05-15 540 4485
Kenya 2021-04-29 323 887
Sierra Leone 2021-05-07 9 9
Georgia 2021-05-11 72 163
Nigeria 2021-05-02 299 1180
Bulgaria 2021-04-05 1249 3315
Malta 2021-05-19 37 69
Luxembourg 2021-04-02 2718 8030
Turkey 2021-03-09 43450 62657
Qatar 2021-04-18 96 441
Ghana 2021-04-20 166 489
Gabon 2021-08-13 7 19
Republic Of Congo 2021-06-26 23 45
Vietnam 2021-04-21 422 438
Bosnia And Herzegovina 2021-06-08 52 80
Philippines 2021-04-15 65 1655
Indonesia 2021-01-07 204 6846
Reunion 2021-05-04 127 2230
Fiji 2021-04-14 467 470
Liberia 2021-04-06 5 69
Thailand 2021-01-09 468 3931
The Bahamas 2021-07-08 34 62
Democratic Republic Of The Congo 2021-04-20 10 25
South Korea 2021-04-22 4233 7090
Gibraltar 2021-07-12 245 725
Botswana 2021-06-01 337 674
Senegal 2021-06-01 7 15
Estonia 2021-06-10 1497 1819
Mongolia 2021-09-23 1 1
Lebanon 2021-07-02 3 22
Cambodia 2021-06-23 127 812
Uzbekistan 2021-06-25 37 56
Sri Lanka 2021-03-11 265 1050
El Salvador 2021-08-02 1 17
Kuwait 2021-06-01 101 143
Aruba 2021-04-10 353 2127
Curaçao 2021-06-28 100 370
Gambia 2021-05-17 31 45
Algeria 2021-05-10 15 29
Belize 2021-01-07 20 125
Nepal 2021-04-15 127 184
Malawi 2021-03-17 94 154
Mayotte 2021-07-28 18 22
Namibia 2021-04-26 50 65
Ecuador 2021-06-22 158 1141
Paraguay 2021-08-05 15 52
Iceland 2021-05-07 1067 3796
Andorra 2021-07-08 17 18
Ethiopia 2021-03-31 143 197
Cayman Islands 2021-07-19 10 24
Myanmar 2021-05-28 13 25
Guam 2021-04-26 4 98
Benin 2021-05-27 27 87
Moldova 2021-06-17 11 13
Zambia 2021-05-24 299 302
Angola 2021-04-18 37 151
Egypt 2021-09-04 1 20
East Timor 2021-04-22 1 226
Uganda 2021-04-20 208 246
Latvia 2021-05-05 70 934
Oman 2021-01-06 93 269
Afghanistan 2021-04-26 18 60
Zimbabwe 2021-06-23 73 85
Mozambique 2021-06-25 76 115
United Arab Emirates 2021-06-12 22 22
Barbados 2021-05-04 3 16
Equatorial Guinea 2021-07-17 9 10
North Macedonia 2021-06-14 31 43
Armenia 2021-06-29 6 24
Venezuela 2021-07-07 1 1
Eswatini 2021-06-23 44 67
Togo 2021-04-12 103 158
Papua New Guinea 2021-08-17 3 122
Guinea 2021-05-17 2 14
Dominican Republic 2021-07-27 4 16
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.