A.23.1 2021-05-19



Description

International lineage with variants of biological significance F157L, V367F, Q613H and P681R, described fully in the preprent: Bugembe et al 2021. Q613H is predicted to be functionally equivalent to the D614G mutation that arose early in 2020.
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.

Table 1 | Summary of A.23.1 data

Statistic Information
Countries with sequences 48
Sequence count 1126
Countries Canada 415, United Kingdom 177, Uganda 157, Rwanda 118, United States of America 76, Kenya 39, Belgium 21, Sweden 13, Cambodia 10, South Sudan 9, Latvia 8, Denmark 7, India 7, Indonesia 6, Vietnam 5, France 4, Philippines 4, Zambia 4, Italy 4, Germany 3, Democratic Republic of the Congo 3, Netherlands 3, Switzerland 3, Zimbabwe 3, South Korea 2, Qatar 2, Ghana 2, Republic of the Congo 1, Finland 1, Ireland 1, United Arab Emirates 1, Israel 1, Iran 1, Norway 1, Benin 1, Central African Republic 1, Australia 1, Russia 1, Estonia 1, Poland 1, Malaysia 1, Cameroon 1, Greece 1, Iceland 1, Togo 1, Malawi 1, South Africa 1, New Zealand 1
First detected Uganda
Earliest sample date 2020-10-21
Defining SNPs aa:S:F157L
aa:S:V367F
aa:S:Q613H
aa:S:P681R

Figure 1 | Cumulative sequence count over time A.23.1

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_A.23.1 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 A.23.1 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 A.23.1

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 A.23.1 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 | A.23.1 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 A.23.1 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 2020-12-28 76 820373
Indonesia 2021-01-08 6 5284
Uganda 2020-10-28 157 439
Republic Of Congo 2021-02-09 1 120
Finland 2021-02-22 1 12556
Canada 2020-12-02 415 76231
United Kingdom 2020-11-27 177 726224
Belgium 2021-01-10 21 40996
Latvia 2021-02-02 8 4715
France 2021-01-12 4 73039
Denmark 2021-01-04 7 128071
Kenya 2020-10-22 39 1742
South Korea 2020-12-28 2 7483
Ireland 2021-03-01 1 22797
United Arab Emirates 2020-12-29 1 47
Sweden 2021-01-25 13 96719
Israel 2021-01-22 1 10252
Iran 2020-12-12 1 148
India 2020-12-26 7 32848
Norway 2021-02-02 1 20260
Benin 2021-02-03 1 27
South Sudan 2021-01-08 9 87
Germany 2021-02-24 3 155495
Central African Republic 2020-12-15 1 44
Australia 2021-01-02 1 10666
Democratic Republic Of The Congo 2021-02-19 3 34
Vietnam 2021-02-07 5 67
Russia 2021-03-20 1 3271
Rwanda 2020-10-21 118 342
Philippines 2021-01-08 4 3402
Qatar 2021-02-19 2 794
Estonia 2020-12-29 1 5280
Zambia 2021-01-24 4 179
Poland 2021-02-24 1 16911
Malaysia 2021-03-06 1 1500
Netherlands 2021-01-09 3 51804
Cameroon 2021-02-08 1 39
Greece 2021-02-18 1 7140
Iceland 2021-01-13 1 4301
Switzerland 2021-01-01 3 46854
Italy 2021-02-08 4 43157
Cambodia 2020-11-28 10 990
Togo 2020-12-11 1 301
Malawi 2020-12-28 1 329
South Africa 2021-01-11 1 9285
Ghana 2021-01-06 2 869
Zimbabwe 2020-12-22 3 355
New Zealand 2021-02-08 1 1192

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.

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.