Total number of all sequenced SARS-CoV-2 samples (purple) and the proportion of the Alpha lineage for all sequenced samples (yellow-red) for each state of Germany and each district of Thuringia.

257,721 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 7,404 genomes and their metadata from our database for both the German and the Thuringian maps. Please note that for all states except Thuringia, we used the postal code of the sending laboratory as a proxy for the geographic location of a sample. Thuringia is highlighted by a grey border on the maps of Germany.

Overview of nine Alpha subclusters in Thuringia, their sample count, their time period, and their specific mutations that are shared across all members of the subcluster (excluding characteristic Alpha mutations that are shared across all subclusters).

The mutation used to define the subcluster is highlighted in bold.

Overview of the subclusters “S:N185D” and “S:S939F” in Thuringian districts.

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) and the occurrence of a subcluster sample (red = sample found, blue = no sample found). 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 blue color of a district, the higher the proportion of inbound mobility from other districts with an identified subcluster sample (red districts). The light blue color describes that most of the inbound mobility of a district comes from other districts without an identified subcluster sample (blue districts). Numbers refer to district types 1, 2, and 3, as further defined in the main text.

Overview of the mobility-guided sampling of the Omicron sublineage BQ.1.1 in Thuringia compared to the default randomized sampling (surveillance) in October 2022.

For clarity, the surveillance results in November 2022 were added to highlight the spreading progress of BQ.1.1. Circles reflect the location of each sample (based on residents’ zip codes). Orange circle: First identified BQ.1.1 sample; Red circle: Additionally identified BQ.1.1 sample; Grey: Sample of another lineage. Purple arrows show the eight residential movements with the most participants from the originating community of the first identified BQ.1.1 sample (orange circle). The mobile service data were extracted from 2020/21.