Fig. 2. Tracking Variants of Concern (VOCs) across time.

For every wastewater sample, fragments deriving from SARS-CoV-2 were analyzed for mutations corresponding to COVID variants of concern (VOC), and the Variant Allele Frequency (VAF) was estimated per mutation per sample. Unique mutations refer to point mutations that are unique to a given VOC, while recurrent mutations are present in more than one VOC. The annotation track on top reflects which VOC corresponds to which mutation (columns). This annotation track has unique colors in each line, and the colors are present only to assist in delineating between each subsequent row. Each cell in the dated rows represents the VAF for a given mutation for a given sample at a given time point, with dark red reflecting all RNA fragments having a given mutation, lighter red reflecting a mixture of presence and absence for a mutation, blue representing the presence of the wild type (i.e. not deriving from a given VOC), and gray representing no coverage of that genomic context in the sequence data. Source data are provided as a Source Data file.