FIG 2.

SARS-CoV-2 SNVs in wastewater samples. (a) Allele frequencies of SARS-CoV-2 in wastewater metatranscriptomes for each sample. Each point is a SNV by location on the SARS-CoV-2 genome (x axis), and the height of the bar (y axis) is the frequency of the alternative allele (relative to the reference genome EPI_ISL_402124) at that position. Wastewater SNVs are colored based on whether they have previously been observed in clinical samples from California, the United States, or neither. (b) Wastewater SARS-CoV-2 frequencies grouped by whether they have been observed in clinical samples from different regions. Most highly abundant SNVs have been observed previously in California or elsewhere in the United States. (c) SARS-CoV-2 SNVs grouped by the number of wastewater samples observed in (out of seven high-quality samples). Most SNVs that were observed in two or more samples have been observed clinically in California. (d) Multiple hypothesis adjusted (Bonferroni correction) P value distribution of hypergeometric tests for overlap between all wastewater SNVs observed and the variants clinically observed and reported in each location (a county level designation in the United States). Alameda County was the most significant comparison.