BA.1 2021-12-09
Description
Table 1 | Summary of BA.1 data
| Statistic | Information |
|---|---|
| Countries with sequences | |
| Sequence count | |
| Countries | |
| First detected | South Africa and Botswana |
| Earliest sample date | |
| Defining SNPs | del:6513:3 del:11283:9 nuc:C241T ORF1A:K856R nuc:C3037T nuc:T5386G ORF1A:A2710T ORF1A:T3255I ORF1A:P3395H ORF1A:I3758V nuc:T13195C ORF1B:P314L nuc:C15240T ORF1B:I1566V S:A67V S:T95I S:G339D S:S371L S:S373P S:K417N S:N440K S:G446S S:S477N S:T478K S:E484A S:Q493R S:G496S S:Q498R S:N501Y S:T547K S:D614G S:H655Y S:N679K S:P681H S:N764K S:D796Y S:N856K S:Q954H S:N969K nuc:C25000T E:T9I M:D3G M:Q19E M:A63T nuc:A27259C nuc:C27807T N:RG203KR |
Figure 1 | Cumulative sequence count over time BA.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_BA.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 BA.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 BA.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 BA.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 | BA.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 BA.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 2 | Reported BA.1 imports | Country count: 0
| Country | Earliest report | Date local transmission | Local transmission | Method of surveillance | Source |
|---|
Table 3 | Raw data for figures
| Country | Earliest sequence | Number of variant sequences | Total sequences since first variant sequence |
|---|
Data source and processing
The data on this page is recent as of 2021-12-09, 14:37 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 3.1.16, pangoLEARN version 2021-11-18.
Pangolin assigns BA.1 to sequences with at least 32 of the 47 defining BA.1 SNPs – defined here.
Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.
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 publication in Wellcome Open Research here describing this web tracker.