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 77
Sequence count 71056
Countries United Kingdom 55193, India 5727, United States of America 3336, Germany 1274, Singapore 823, Spain 468, Italy 383, Belgium 359, Portugal 320, Russia 283, France 240, Indonesia 212, Ireland 186, Australia 183, Japan 181, Sweden 167, Switzerland 142, Canada 132, Netherlands 129, Finland 126, Israel 96, Thailand 94, Mexico 93, Denmark 93, Norway 89, Bangladesh 89, Poland 79, Austria 62, Vietnam 54, Luxembourg 48, Kenya 34, Czech Republic 26, Romania 25, New Zealand 21, Malaysia 21, Bahrain 21, South Africa 21, Nepal 20, South Korea 20, Qatar 19, Hong Kong 15, Cambodia 13, Brazil 12, Botswana 12, Iran 11, Philippines 11, Greece 10, Pakistan 9, China 7, Sri Lanka 6, Malawi 6, Lithuania 4, Georgia 4, Slovenia 4, Myanmar 4, Uganda 4, Guadeloupe 3, Aruba 3, Angola 3, Democratic Republic of the Congo 3, Reunion 2, Peru 2, Turkey 2, Ghana 2, Barbados 2, Mauritius 2, Jordan 1, Morocco 1, Kuwait 1, Argentina 1, Malta 1, Sint Maarten 1, Bulgaria 1, Senegal 1, Guam 1, Usa 1, Slovakia 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
United States Of America 2021-02-05 3337 332536
Germany 2021-03-18 1274 86152
Italy 2021-04-02 383 11171
India 2020-09-07 5727 18320
Spain 2021-04-22 468 6063
Portugal 2021-04-18 320 1670
United Kingdom 2021-02-14 55193 211753
Ireland 2021-04-07 186 6049
Belgium 2021-04-06 359 10239
Finland 2021-04-18 126 1112
Greece 2021-03-23 10 3657
Poland 2021-04-22 79 5731
Switzerland 2021-04-07 142 11884
Indonesia 2021-01-07 212 1504
Thailand 2021-05-02 94 618
Russia 2021-04-07 283 929
Guadeloupe 2021-05-25 3 18
France 2021-04-13 240 13316
Austria 2021-04-17 62 1196
Mexico 2021-04-21 93 3381
Denmark 2021-03-29 93 31873
Sweden 2021-04-01 167 18219
Norway 2021-04-15 89 2814
New Zealand 2021-03-30 21 82
Bangladesh 2021-04-27 89 174
Jordan 2021-04-26 1 4
Australia 2021-03-18 183 657
Morocco 2021-04-22 1 3
Singapore 2021-02-06 823 1420
Kenya 2021-04-07 34 272
Lithuania 2021-05-26 4 457
Kuwait 2021-06-03 1 11
Cambodia 2021-05-25 13 89
Pakistan 2021-05-16 9 22
Reunion 2021-05-04 2 167
Czech Republic 2021-04-22 26 637
Brazil 2021-04-26 12 4037
Japan 2021-03-28 181 14052
Netherlands 2021-04-13 129 11641
Argentina 2021-04-24 1 159
Aruba 2021-04-16 3 412
Georgia 2021-05-11 4 9
Iran 2021-04-26 11 13
Malaysia 2021-04-28 21 134
Philippines 2021-04-15 11 11
Peru 2021-05-15 2 4
Malta 2021-05-19 1 13
Luxembourg 2021-04-14 48 1947
Turkey 2021-05-07 2 145
Nepal 2021-04-12 20 22
Vietnam 2021-04-21 54 62
Sri Lanka 2021-04-07 6 157
Canada 2021-03-21 132 9902
Ghana 2021-04-20 2 14
Israel 2021-04-08 96 979
Bahrain 2021-04-05 21 51
Slovenia 2021-04-20 4 3120
China 2021-04-21 7 30
Romania 2021-03-28 25 400
Qatar 2021-04-17 19 148
Malawi 2021-04-22 6 13
Bulgaria 2021-04-05 1 724
Myanmar 2021-06-01 4 6
Hong Kong 2021-04-22 15 50
South Africa 2021-04-24 21 377
Botswana 2021-05-09 12 87
Uganda 2021-04-20 4 7
Angola 2021-05-03 3 4
Senegal 2021-05-05 1 1
Barbados 2021-04-25 2 2
Guam 2021-04-26 1 2
South Korea 2021-04-11 20 809
Democratic Republic Of The Congo 2021-04-20 3 4
Slovakia 2021-06-15 1 1

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.