A.23.1 2021-04-08



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 reported 2
Countries with sequences 34
Sequence count 597
Countries United Kingdom 169, Uganda 136, Rwanda 91, Canada 46, United States of America 37, Belgium 21, Cambodia 14, Sweden 13, Kenya 11, Latvia 8, Denmark 6, Indonesia 6, Vietnam 5, Italy 3, Democratic Republic of the Congo 3, Switzerland 3, Germany 3, Netherlands 3, France 2, Zimbabwe 2, India 2, South Africa 1, United Arab Emirates 1, Ireland 1, New Zealand 1, Norway 1, Australia 1, Mauritius 1, Israel 1, Malaysia 1, Togo 1, Poland 1, Ghana 1, Botswana 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
South Africa 2021-01-11 1 761
United Kingdom 2020-11-27 169 242997
Vietnam 2021-02-07 5 5
Italy 2021-02-08 3 13420
United States Of America 2020-12-28 37 197358
Canada 2020-12-31 46 1508
Rwanda 2020-10-21 91 178
Denmark 2021-01-04 6 19655
United Arab Emirates 2020-12-29 1 24
Uganda 2020-10-28 136 181
Kenya 2020-12-31 11 244
Belgium 2021-01-10 21 11649
Latvia 2021-02-02 8 2066
Ireland 2021-03-01 1 3701
Sweden 2021-01-22 13 19806
Democratic Republic Of The Congo 2021-01-16 3 6
Switzerland 2021-01-01 3 16800
France 2021-02-23 2 7618
Indonesia 2021-01-08 6 551
New Zealand 2021-02-08 1 118
Norway 2021-02-02 1 3282
Australia 2021-01-02 1 594
Zimbabwe 2020-12-27 2 205
Cambodia 2020-11-28 14 64
India 2021-01-20 2 1880
Germany 2021-02-24 3 38342
Israel 2021-01-22 1 1583
Malaysia 2021-03-06 1 7
Togo 2020-12-11 1 59
Netherlands 2021-01-09 3 14538
Poland 2021-02-24 1 4054
Ghana 2021-01-06 1 160
Botswana 2021-01-21 1 68

Data source and processing

The data on this page is recent as of 2021-04-08, 07:39 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 2.3.8, pangoLEARN version 2021-04-01.

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.