B.1.617.2 2022-01-22



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 160
Sequence count 133726
Countries United States of America 37088, India 21986, United Kingdom 20272, Turkey 7508, Germany 6782, Denmark 4517, Netherlands 3473, France 2972, Croatia 2239, Canada 2189, Sweden 2150, Belgium 1964, Poland 1896, Spain 1465, Italy 1420, Bulgaria 1403, Singapore 1036, Switzerland 929, Bangladesh 890, Norway 820, Slovenia 733, Japan 663, Czech Republic 534, Ireland 512, Luxembourg 470, Qatar 457, Israel 395, Portugal 315, South Korea 305, Nepal 293, Slovakia 290, Philippines 277, Australia 271, South Africa 262, Russia 244, Indonesia 235, Romania 215, Austria 206, Finland 203, Thailand 202, Pakistan 177, Sri Lanka 177, Malaysia 173, Puerto Rico 146, Lithuania 139, Bahrain 138, Aruba 121, Malawi 107, Mexico 106, Greece 101, China 94, Hong Kong 92, Ghana 89, Mongolia 84, Estonia 76, Kenya 71, Iceland 71, Chile 65, Reunion 65, Brazil 64, Georgia 60, Bosnia and Herzegovina 57, Zambia 55, Oman 51, Mauritius 51, Latvia 48, Kuwait 46, Rwanda 46, Ethiopia 44, Togo 42, Cambodia 37, Colombia 35, Jordan 35, New Zealand 35, Belize 30, Gibraltar 28, Cameroon 28, Sint Maarten 27, Uganda 27, Egypt 27, Benin 24, Vietnam 23, Peru 23, Mozambique 23, Ecuador 23, Angola 23, Kosovo 23, United Arab Emirates 22, Argentina 20, Maldives 19, Nigeria 16, Iran 16, Algeria 16, Afghanistan 16, Burundi 16, Guyana 16, Northern Mariana Islands 15, Senegal 15, Papua New Guinea 15, Uzbekistan 14, Botswana 14, Montenegro 13, Morocco 11, Guadeloupe 10, Costa Rica 10, Democratic Republic of the Congo 10, Ukraine 10, Fiji 10, Iraq 10, Sierra Leone 9, Jamaica 9, Curaçao 9, Canary Islands 9, Republic of the Congo 9, Myanmar 9, Brunei 9, Saudi Arabia 8, Kazakhstan 7, Grenada 7, Djibouti 6, Crimea 6, Republic of Serbia 6, Martinique 6, Zimbabwe 6, Cayman Islands 6, Bonaire 5, Liechtenstein 5, Cote d'Ivoire 5, Guam 5, Liberia 5, Seychelles 4, Mayotte 4, Antigua and Barbuda 3, Malta 3, Gambia 3, Paraguay 3, French Guiana 3, Moldova 3, North Macedonia 3, British Virgin Islands 2, South Sudan 2, Trinidad and Tobago 2, Montserrat 2, Dominican Republic 2, U.S. Virgin Islands 2, Guinea 2, Tunisia 2, Guatemala 1, Barbados 1, Monaco 1, Panama 1, Eswatini 1, Suriname 1, Albania 1, Syria 1, East Timor 1, Lebanon 1, Venezuela 1, Saint Vincent and the Grenadines 1, Taiwan 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
France 2021-04-13 2972 117632
United States Of America 2021-03-16 37088 1798768
United Kingdom 2021-03-18 20272 1340309
Germany 2021-03-18 6782 297578
Switzerland 2021-04-07 929 74286
Australia 2021-03-18 271 34625
Netherlands 2021-03-11 3473 70460
Denmark 2021-03-29 4517 233650
Poland 2021-04-26 1896 33490
Italy 2021-03-16 1420 65899
Mexico 2021-04-21 106 34796
Turkey 2021-03-09 7508 77608
India 2021-03-01 21986 65356
Belgium 2021-04-06 1964 61123
Norway 2021-04-15 820 28858
Bahrain 2021-04-06 138 2058
Croatia 2021-04-25 2239 13753
Sweden 2021-04-01 2150 85356
Spain 2021-04-27 1465 57994
Bulgaria 2021-06-07 1403 8888
Japan 2021-03-28 663 145082
Vietnam 2021-04-20 23 1841
Aruba 2021-04-16 121 2371
Russia 2021-04-07 244 6738
Romania 2021-03-29 215 7116
Sierra Leone 2021-05-07 9 10
Thailand 2021-05-02 202 9562
Chile 2021-06-13 65 13055
Singapore 2021-04-01 1036 10085
Cambodia 2021-06-29 37 1731
Uzbekistan 2021-06-25 14 56
Lithuania 2021-05-26 139 15948
Qatar 2021-04-17 457 1897
Canada 2021-03-21 2189 152403
Ireland 2021-04-07 512 34987
British Virgin Islands 2021-07-27 2 23
South Africa 2021-04-24 262 14888
Finland 2021-04-17 203 14338
Israel 2021-04-11 395 21408
Pakistan 2021-05-16 177 948
Bosnia And Herzegovina 2021-06-08 57 1008
Slovenia 2021-05-27 733 28109
Brazil 2021-04-26 64 73458
Czech Republic 2021-03-07 534 21506
Indonesia 2021-03-19 235 10391
Peru 2021-08-17 23 7103
Philippines 2021-04-15 277 6969
Ethiopia 2021-05-25 44 392
Oman 2021-03-05 51 247
Georgia 2021-06-21 60 875
Portugal 2021-04-18 315 17338
Bangladesh 2021-04-27 890 2298
Slovakia 2021-06-02 290 13712
Gibraltar 2021-07-12 28 1871
Guadeloupe 2021-05-25 10 401
Jamaica 2021-07-22 9 108
Nigeria 2021-07-19 16 1918
Luxembourg 2021-04-14 470 13398
Colombia 2021-07-25 35 5269
Malaysia 2021-04-28 173 6643
South Korea 2021-04-22 305 18488
Greece 2021-04-24 101 7633
South Sudan 2021-04-27 2 35
Austria 2021-04-17 206 6909
Jordan 2021-04-26 35 457
Kenya 2021-04-29 71 1739
Costa Rica 2021-09-10 10 1046
New Zealand 2021-03-30 35 5004
Belize 2021-05-07 30 261
Curaçao 2021-07-14 9 569
Nepal 2021-05-04 293 671
Mozambique 2021-05-04 23 409
China 2021-04-21 94 398
Sri Lanka 2021-03-11 177 2017
Latvia 2021-05-26 48 1218
Malta 2021-12-17 3 205
Estonia 2021-06-30 76 4070
Malawi 2021-03-18 107 360
Montenegro 2021-07-10 13 434
Zambia 2021-05-24 55 373
Puerto Rico 2021-05-08 146 3910
Kuwait 2021-06-21 46 110
Liechtenstein 2021-10-02 5 408
Togo 2021-04-26 42 149
Botswana 2021-05-10 14 1832
Gambia 2021-07-09 3 243
Guatemala 2021-07-11 1 677
Hong Kong 2021-03-25 92 717
Kazakhstan 2021-08-17 7 192
Reunion 2021-05-04 65 3822
Argentina 2021-04-24 20 6645
Rwanda 2021-06-08 46 247
United Arab Emirates 2021-06-12 22 22
Iran 2021-04-26 16 99
Trinidad And Tobago 2021-09-06 2 332
Barbados 2021-07-29 1 5
Paraguay 2021-08-18 3 141
Democratic Republic Of The Congo 2021-05-03 10 24
Ukraine 2021-06-17 10 276
Djibouti 2021-08-25 6 56
Dominican Republic 2021-10-08 2 404
Mongolia 2021-03-08 84 392
Ghana 2021-05-12 89 992
Algeria 2021-05-10 16 39
Uganda 2021-04-20 27 410
Senegal 2021-06-09 15 681
Morocco 2021-04-22 11 221
Ecuador 2021-08-17 23 1198
Angola 2021-04-18 23 258
Republic Of Serbia 2021-07-13 6 126
Cameroon 2021-06-23 28 267
Benin 2021-05-27 24 213
Republic Of Congo 2021-06-26 9 136
Afghanistan 2021-05-08 16 47
Myanmar 2021-05-28 9 41
Saudi Arabia 2021-05-12 8 45
Iceland 2021-05-07 71 3796
Ivory Coast 2021-10-12 5 6
Egypt 2021-09-01 27 140
Fiji 2021-04-14 10 470
Papua New Guinea 2021-08-17 15 1152
Burundi 2021-07-28 16 54
Iraq 2021-07-20 10 48
Zimbabwe 2021-07-26 6 233
Cayman Islands 2021-07-23 6 32
Guam 2021-04-26 5 337
Liberia 2021-04-06 5 69
Guinea 2021-06-28 2 14
Mayotte 2021-10-28 4 106
Panama 2021-04-29 1 16
Eswatini 2021-07-08 1 14
Moldova 2021-09-01 3 99
Suriname 2021-12-02 1 48
Albania 2021-06-16 1 22
Syria 2021-12-01 1 21
Kosovo 2021-04-30 23 904
Guyana 2021-09-06 16 49
East Timor 2021-04-22 1 226
Tunisia 2021-08-13 2 136
Brunei 2021-12-08 9 80
Lebanon 2021-07-14 1 5
Venezuela 2021-07-07 1 34
North Macedonia 2021-07-30 3 58
Taiwan 2021-07-12 1 9

Data source and processing

The data on this page is recent as of 2022-01-22, 20:37 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 3.1.3, pangoLEARN version 2021-06-15.

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.