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 104
Sequence count 232721
Countries United Kingdom 151363, United States of America 18272, India 13176, Denmark 9092, Germany 4620, Spain 3211, Italy 2760, Sweden 2451, Netherlands 2372, Belgium 2320, France 2308, Portugal 2291, Israel 1803, Ireland 1777, Singapore 1428, Mexico 1275, Switzerland 1190, South Africa 1172, Russia 1001, Indonesia 811, Australia 746, Turkey 693, Austria 669, Canada 557, Norway 508, South Korea 494, Japan 485, Finland 382, Kenya 265, Croatia 240, Botswana 208, Bangladesh 197, Poland 180, Czech Republic 171, Slovenia 168, Thailand 148, Hong Kong 140, Qatar 125, Lithuania 117, Bahrain 108, Brazil 103, Romania 93, Rwanda 91, Kuwait 87, Cambodia 85, Zambia 82, China 73, Bulgaria 70, Malaysia 59, Vietnam 54, Luxembourg 48, Nepal 47, New Zealand 44, Malta 42, Uganda 38, Monaco 34, Sri Lanka 34, Slovakia 28, Pakistan 26, Angola 23, Latvia 22, Democratic Republic of the Congo 17, Greece 17, Ghana 16, Sint Maarten 15, Bosnia and Herzegovina 14, Costa Rica 12, Philippines 11, Iran 11, Aruba 9, Ecuador 9, Oman 8, Mauritius 6, Lebanon 6, North Macedonia 6, Republic of the Congo 6, Malawi 6, Jordan 5, Myanmar 5, Curaçao 5, Senegal 5, Guadeloupe 5, Nigeria 4, Chile 4, Georgia 4, Burundi 3, South Sudan 3, Dominican Republic 3, Taiwan 3, Republic of Serbia 3, Ukraine 3, Reunion 2, Iraq 2, Peru 2, United Arab Emirates 2, Barbados 2, Gambia 2, Kosovo 2, Morocco 1, kuwait 1, Martinique 1, Argentina 1, Guam 1, French Guiana 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
Netherlands 2021-03-07 2372 27121
United States Of America 2021-02-25 18272 349938
Belgium 2021-04-06 2320 16373
Spain 2021-04-22 3211 14440
Canada 2021-03-21 557 20620
Austria 2021-04-17 669 2182
United Kingdom 2020-11-04 151363 467189
Mexico 2020-09-22 1275 15832
Switzerland 2021-03-10 1190 18583
Ireland 2021-04-07 1777 9471
Norway 2021-04-15 508 4113
India 2020-09-07 13176 27558
Italy 2021-01-07 2760 30748
Czech Republic 2021-03-07 171 3051
Australia 2021-02-07 746 1495
China 2021-04-21 73 99
Oman 2021-04-18 8 11
France 2021-04-13 2308 16443
Russia 2021-04-07 1001 1721
Romania 2021-03-28 93 671
Aruba 2021-04-16 9 493
Hong Kong 2021-03-25 140 260
Indonesia 2021-01-07 811 2495
Israel 2021-04-08 1803 2762
Malaysia 2021-04-28 59 250
Finland 2021-04-17 382 2137
Denmark 2021-03-29 9092 51319
Malta 2021-05-19 42 69
Singapore 2021-02-06 1428 2037
Sweden 2021-04-01 2451 25773
Germany 2021-02-07 4620 123540
Poland 2021-04-22 180 6459
Portugal 2021-04-18 2291 4208
Pakistan 2021-05-16 26 55
Japan 2021-03-28 485 25923
South Africa 2021-04-24 1172 2443
Reunion 2021-05-04 2 385
Thailand 2021-05-02 148 749
Bangladesh 2021-04-27 197 301
Vietnam 2021-04-21 54 63
Burundi 2021-05-27 3 9
South Sudan 2021-04-27 3 8
Iraq 2021-04-27 2 6
Botswana 2021-05-09 208 350
New Zealand 2021-03-30 44 116
Peru 2021-05-15 2 131
Slovakia 2021-06-02 28 482
Bahrain 2021-04-05 108 183
Latvia 2021-05-05 22 829
Lithuania 2021-05-26 117 1380
Jordan 2021-04-26 5 9
Morocco 2021-04-22 1 4
Philippines 2021-04-15 11 240
Brazil 2021-04-26 103 7554
Slovenia 2021-04-20 168 4541
Nigeria 2021-06-20 4 4
Kuwait 2021-05-24 88 106
Turkey 2021-03-31 693 2288
Sri Lanka 2021-04-07 34 333
Chile 2021-06-13 4 631
Lebanon 2021-07-01 6 6
Ecuador 2021-06-22 9 177
Costa Rica 2021-06-17 12 40
South Korea 2021-04-11 494 2709
Kenya 2021-04-07 265 593
Cambodia 2021-04-05 85 489
North Macedonia 2021-07-01 6 6
Myanmar 2021-05-28 5 10
Angola 2020-12-07 23 432
Nepal 2021-04-12 47 52
Luxembourg 2021-04-14 48 1947
Qatar 2021-04-17 125 447
Rwanda 2021-06-08 91 116
United Arab Emirates 2021-06-23 2 2
Curaçao 2021-06-29 5 5
Senegal 2021-05-05 5 7
Barbados 2021-04-25 2 5
Republic Of Congo 2021-06-26 6 21
Argentina 2021-04-24 1 221
Uganda 2021-04-20 38 63
Malawi 2021-04-22 6 13
Bosnia And Herzegovina 2021-06-08 14 34
Zambia 2021-05-24 82 82
Democratic Republic Of The Congo 2021-04-20 17 23
Greece 2021-03-23 17 4006
Croatia 2021-04-25 240 1864
Guadeloupe 2021-05-25 5 47
Georgia 2021-05-11 4 10
Iran 2021-04-26 11 13
Ghana 2021-04-20 16 117
Bulgaria 2021-04-05 70 1018
Guam 2021-04-26 1 20
Gambia 2021-05-17 2 4
Dominican Republic 2021-05-20 3 38
Taiwan 2021-06-14 3 13
Republic Of Serbia 2021-06-29 3 3
Kosovo 2021-04-30 2 21
Ukraine 2021-06-18 3 3

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.