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 46
Sequence count 1107
Countries Canada 413, United Kingdom 177, Uganda 155, Rwanda 118, United States of America 74, Kenya 28, Belgium 21, Sweden 13, Cambodia 10, South Sudan 9, Latvia 8, Denmark 7, India 7, Indonesia 6, Vietnam 5, France 4, Philippines 4, Italy 4, Zambia 4, Switzerland 3, Zimbabwe 3, Netherlands 3, Democratic Republic of the Congo 3, Germany 3, Qatar 2, South Korea 2, Ghana 2, Cameroon 1, Greece 1, Iran 1, New Zealand 1, Ireland 1, Russia 1, Togo 1, South Africa 1, Poland 1, Australia 1, Benin 1, United Arab Emirates 1, Malaysia 1, Republic of the Congo 1, Finland 1, Estonia 1, Norway 1, Israel 1, Malawi 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
Qatar 2021-02-19 2 790
Cameroon 2021-02-08 1 35
Greece 2021-02-18 1 6176
Rwanda 2020-10-21 118 342
Canada 2020-12-02 413 42737
United Kingdom 2020-11-27 177 440357
Switzerland 2021-01-01 3 30847
France 2021-02-23 4 32289
United States Of America 2020-12-28 74 468725
Philippines 2021-01-08 4 3402
South Korea 2020-12-28 2 4426
Uganda 2020-10-28 155 309
Vietnam 2021-02-07 5 68
Belgium 2021-01-10 21 29724
Iran 2020-12-13 1 129
New Zealand 2021-02-08 1 192
Ireland 2021-03-01 1 13324
Zimbabwe 2020-12-22 3 270
Sweden 2021-01-25 13 70082
Kenya 2020-10-22 28 1157
Russia 2021-03-20 1 1950
Indonesia 2021-01-08 6 2461
Cambodia 2020-11-28 10 557
Netherlands 2021-01-09 3 36723
Ghana 2021-01-06 2 593
Denmark 2021-01-04 7 87567
India 2020-12-26 7 24172
Togo 2020-12-11 1 84
South Africa 2021-01-11 1 4027
Poland 2021-02-24 1 14818
Australia 2021-01-02 1 1686
Italy 2021-02-08 4 28996
Benin 2021-02-03 1 27
South Sudan 2021-01-08 9 58
United Arab Emirates 2020-12-29 1 27
Malaysia 2021-03-06 1 573
Republic Of Congo 2021-02-09 1 113
Finland 2021-02-22 1 6936
Zambia 2021-01-24 4 179
Estonia 2020-12-29 1 3820
Democratic Republic Of The Congo 2021-02-19 3 30
Latvia 2021-02-02 8 4712
Germany 2021-02-24 3 112753
Norway 2021-02-02 1 9716
Israel 2021-01-22 1 8816
Malawi 2020-12-28 1 267

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.