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 50
Sequence count 1191
Countries Canada 421, United Kingdom 178, Uganda 157, Rwanda 129, United States of America 78, Kenya 47, United Arab Emirates 31, Belgium 21, Cambodia 14, Sweden 13, South Sudan 9, Latvia 8, Denmark 7, India 7, Indonesia 6, Philippines 5, Vietnam 5, France 4, Italy 4, Zambia 4, Switzerland 3, Democratic Republic of the Congo 3, Germany 3, Zimbabwe 3, Netherlands 3, South Korea 2, Qatar 2, Ghana 2, Malawi 1, New Zealand 1, Slovenia 1, Cameroon 1, Greece 1, Central African Republic 1, Poland 1, Togo 1, Malaysia 1, Iran 1, Australia 1, Russia 1, Benin 1, Ireland 1, Republic of the Congo 1, Finland 1, Israel 1, Norway 1, Iceland 1, Estonia 1, South Africa 1, East Timor 1
First detected Uganda
Earliest sample date 2020-09-21
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 78 1457550
Canada 2020-12-02 421 128685
Kenya 2020-10-22 47 2734
Malawi 2020-12-28 1 404
United Kingdom 2020-11-27 178 1094468
Denmark 2021-01-04 7 177073
South Korea 2020-12-28 2 11200
New Zealand 2021-02-08 1 2654
France 2021-01-12 4 99915
Switzerland 2021-01-01 3 66958
Slovenia 2021-01-06 1 27420
Sweden 2021-01-25 13 119766
Rwanda 2020-10-21 129 490
Qatar 2021-02-19 2 1953
Cameroon 2021-02-08 1 303
Greece 2021-02-18 1 9114
Belgium 2021-01-10 21 59135
Uganda 2020-10-28 157 568
Democratic Republic Of The Congo 2021-02-19 3 35
Central African Republic 2020-12-15 1 46
United Arab Emirates 2020-09-21 31 1062
Poland 2021-02-24 1 26284
India 2020-12-26 7 52033
Togo 2020-12-11 1 311
Malaysia 2021-03-06 1 4328
Philippines 2021-01-08 5 10440
Germany 2021-02-24 3 227487
Iran 2020-12-12 1 239
Indonesia 2021-01-08 6 7628
Australia 2021-01-02 1 21642
Italy 2021-02-08 4 57197
Zambia 2021-01-24 4 406
Russia 2021-03-20 1 5066
Vietnam 2021-02-07 5 1272
Benin 2021-02-03 1 169
Zimbabwe 2020-12-22 3 400
Latvia 2021-02-02 8 4819
Ireland 2021-03-01 1 31905
Republic Of Congo 2021-02-09 1 190
Finland 2021-02-22 1 15720
Ghana 2021-01-06 2 1073
Netherlands 2021-01-09 3 63465
Israel 2021-01-22 1 18733
Norway 2021-02-02 1 27940
Iceland 2021-01-13 1 4301
Estonia 2020-12-29 1 6994
South Sudan 2021-01-08 9 87
South Africa 2021-01-11 1 13178
East Timor 2020-11-29 1 306
Cambodia 2020-11-28 14 1584

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.