289,487 publicly available German SARS-CoV-2 genomes and their metadata were used for the general German maps, excluding data from Thuringia. For Thuringia, we always used 7394 genomes and their …
R-script to generate Figure 1, Figure 1—figure supplement 1.
Total number of reported SARS-CoV-2 samples and number of reported Alpha lineage samples for each German federal state per month.
The respective proportions of Alpha and non-Alpha samples are calculated.
Total number of reported SARS-CoV-2 samples and number of reported Alpha lineage samples for each Thuringian district per month.
The respective proportions of Alpha and non-Alpha samples are calculated.
289,487 publicly available German SARS-CoV-2 genomes and their metadata were used for the general German maps excluding data from Thuringia. For Thuringia, we always used 7394 genomes and their …
The tree includes 64,131 German (non-Thuringian; blue) and 6298 Thuringian (red) Alpha genomes. Two genomes of the original Wuhan lineage are included as origin.
(a) Accumulated number of sequenced samples for each subcluster per district and per month. (b) Combined visualization of each district’s ‘inbound mobility’ from other districts (color intensity) …
R-script to generate Figure 2, Figure 2—figure supplements 1 and 2.
Accumulated sample count for each Thuringian district per Alpha subcluster and month.
Total number of incoming trips and numbers of trips coming from all cluster-affiliated districts to each Thuringian district per Alpha subcluster and per month.
The proportion of trips from cluster-affiliated districts among the total incoming trips is calculated.
The inbound mobility of each district (color intensity) is shown as a proportion of incoming mobility from other districts with or without an identified sample. The darker the color (red and blue) …
The randomized surveillance results in November 2022 (c) have been added to highlight the spreading progress of BQ.1.1. Dots reflect the location of each sample (based on residents’ zip codes). …
R-script to generate Figure 3.
Overview of all Thuringian samples collected for the mobility-guided pilot experiment between October 5 and November 25, 2022.
Mobility data and sampling counts of communities sampled for the mobility-guided pilot experiment between October 5 and November 25, 2022.
For each community, the incoming one-way trips from the community of BQ.1.1 origin in Thuringia based on the October 2020 and June 2021 datasets, the number of guided and randomized samples per community, and an indication of found BQ.1.1 samples are provided.
The mutation used to define the subcluster is highlighted in bold.
Designation | Mutations | Number of samples | Time period | Remarks |
---|---|---|---|---|
1 | S:H49Y, ORF1a:I841V | 44 | Feb-May 2021 | S:H49Y eases cell entry in S-pseudotyped lentiviral system (Ozono et al., 2021) |
2 | S:N354K | 63 | Feb-May 2021 | S:N354K slightly impaired mAb h11B11 (Du et al., 2021) |
3 | S:G496S, ORF1a:E1013K | 12 | Mar-May 2021 | S:G496S: compromises BA.1 replication fitness and changed mAb sensitivities, reduces ACE2 binding affinity, and increases immune evasion (Liang et al., 2022; Kimura et al., 2022; Asif et al., 2022) |
4 | S:N703D, ORF1a:D1228G, ORF1a:A2123V | 51 | Mar-May 2021 | – |
5 | S:T716V, N:G204P, ORF1a:D1600N | 22 | Apr-May 2021 | – |
6 | S:S939F | 206 | Feb-May 2021 | S:S939F: modulates T-cell propensity (Donzelli et al., 2022) |
6.1† | S:V90F, S:S939F | 55 | Feb-May 2021 | – |
7 | ORF1b:A520V | 811 | Feb-Jun 2021* | – |
7.1 ‡ | S:N185D, ORF1b:A520V, ORF1b:L1504F | 40 | Feb-May 2021 | – |
Only one sample for June.
Branch from subcluster 6.
Branch from subcluster 7.
'microreact’-file summarizing all data presented in the microreact project.
The project can be found at here.
Description of supplementary method ‘Phylogenetic time tree construction’.
'xz’-packed fasta-file, containing all SARS-CoV-2 Alpha lineage genomes used in the Nextstrain analysis.
Metadata tsv-file containing the information for all SARS-CoV-2 Alpha lineage genomes used in the Nextstrain analysis.
'yaml’-file containing the build-instructions for the Nextstrain analysis.
'xz’-packed fasta-file containing the resulting, subsampled genomes of the Nextstrain analysis.
Nextstrain ‘tree.nwk’-file used to visualize the phylogenetic time tree.
Contains 64,131 German (non-Thuringian) and 6298 Thuringian Alpha lineage genomes.
Metadata tsv-file for the Alpha lineage genomes contained in the phylogenetic time tree.
GeoData used in Figure 1—source code 1, Figure 2—source code 1, Figure 3—source code 1.