Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater

Cell Rep Med. 2020 Sep 22;1(6):100098. doi: 10.1016/j.xcrm.2020.100098. Epub 2020 Aug 31.


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. In addition, we determine a nearly complete (98.5%) SARS-CoV-2 genome sequence from wastewater and use phylogenetic 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 genotyping viral strains circulating in a community.

Keywords: COVID-19; SARS-CoV-2; genome sequencing; wastewater-based epidemiology.