Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater

SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 74-day time course. We show that changes in SARS-CoV-2 RNA concentrations follow symptom onset gathered by retrospective interview of patients but precedes clinical test results. Additionally, we determine a near complete (98.5%) SARS-CoV-2 genome sequence from the wastewater and use phylogenic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for high-resolution genotyping of the predominant strains circulating in a community.

Deposited files include the following original data generated in the study:

1) Basecalled Nanopore reads for the SARS-CoV-2 genome from municipal wastewater. Date of sampling - 3/27/2020
2) Output of bioinformatic pipeline used for genome assembly and variant calling
3) Data generated in the phylogenetic analysis.