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.

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 7,394 genomes and their metadata from our database for the German and 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. A gray border on the maps of Germany highlights Thuringia.

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:S939F” and “ORF1b:A520V” 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 (blue 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. The last month of subcluster “ORF1b:A520V” is not visualized, as affected districts were unchanged.

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

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). Orange dot: First identified BQ.1.1 sample; Red dot: Additionally identified BQ.1.1 sample; Blue dot: Another SARS-CoV-2 lineage. Purple triangles represent the number of one-way trips a community received from the community of the first BQ.1.1 occurrence (orange dot) based on mobility data from October 2020 and June 2021. The same mobility data from mobility-guided sampling (a) were added in grayscales to the randomized surveillance (b and c) as a visual reference only. Sampling dots are slightly scattered to improve visibility.