PRJEB44932 SARS-CoV-2 Wastewater Sequences Processed

The frequency is calculated as the counts divided by the coverage. The mutation pre-processing pipeline is available at \url{github.com/DASL-Lab/data-treatment-plant}, and heavily relies on the GromStole pipeline (\url{github.com/PoonLab/gromstole}). After being processed into counts and coverage, the data were filtered to only include mutations that are relevant to analysis.

There were many mutations with either consistently low counts (possibly due to sequencing errors) or low coverage. After filtering the data for sampling dates that were common to all locations, there are 1,061 unique mutations at each location on each sampling date. We found all mutations that had both a frequency of at least 0.1 and a frequency below 0.9 (with a coverage at least 40) at at least two time points during the study in any location.

This ensures that we have all of the mutations that were potentially part of a circulating lineage without relying on lineage definitions. Jahn, Katharina, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier Fernandez-Cassi, Carola Bänziger, et al. 2022. “Early Detection and Surveillance of SARS- CoV-2 Genomic Variants in Wastewater Using COJAC.” Nature Microbiology 7 (8): 1151–60. doi.org/10.1038/s41564-022-01185-x.