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 43
Sequence count 1061
Countries Canada 405, United Kingdom 174, Uganda 147, Rwanda 109, United States of America 73, Belgium 21, Kenya 16, Cambodia 14, Sweden 13, South Sudan 9, Latvia 8, Denmark 7, India 7, Indonesia 6, Vietnam 5, Italy 4, Philippines 4, France 3, Democratic Republic of the Congo 3, Germany 3, Zimbabwe 3, Netherlands 3, Switzerland 3, Ghana 2, Russia 1, Ireland 1, Qatar 1, Cameroon 1, Greece 1, Togo 1, Norway 1, United Arab Emirates 1, Poland 1, Estonia 1, Malawi 1, South Korea 1, New Zealand 1, Malaysia 1, Australia 1, Republic of the Congo 1, Finland 1, South Africa 1, Israel 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
Rwanda 2020-10-21 109 225
Belgium 2021-01-10 21 23314
United Kingdom 2020-11-27 174 338448
Russia 2021-03-20 1 1153
United States Of America 2020-12-28 73 399715
Kenya 2020-10-22 16 683
Canada 2020-12-02 405 27915
Ireland 2021-03-01 1 9841
Uganda 2020-10-28 147 241
Qatar 2021-02-19 1 491
Cameroon 2021-02-08 1 34
Greece 2021-02-18 1 5827
Indonesia 2021-01-08 6 1472
Togo 2020-12-11 1 84
France 2021-02-23 3 30100
Norway 2021-02-02 1 8263
Latvia 2021-02-02 8 2557
Sweden 2021-01-25 13 62394
Democratic Republic Of The Congo 2021-02-19 3 11
Germany 2021-02-24 3 106119
Vietnam 2021-02-07 5 67
Denmark 2021-01-04 7 68104
United Arab Emirates 2020-12-29 1 24
Poland 2021-02-24 1 14035
South Sudan 2021-01-08 9 45
Zimbabwe 2020-12-22 3 270
Ghana 2021-01-06 2 413
Italy 2021-02-08 4 22705
Estonia 2020-12-29 1 3581
India 2020-12-26 7 14878
Netherlands 2021-01-09 3 31162
Malawi 2020-12-28 1 253
Switzerland 2021-01-01 3 28874
Philippines 2021-01-08 4 2508
South Korea 2020-12-28 1 2523
New Zealand 2021-02-08 1 158
Malaysia 2021-03-06 1 451
Australia 2021-01-02 1 1027
Cambodia 2020-11-28 14 346
Republic Of Congo 2021-02-09 1 56
Finland 2021-02-22 1 5879
South Africa 2021-01-11 1 1844
Israel 2021-01-22 1 7033

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.