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

• Published in: Cell reports. Medicine Vol. 1; no. 6; p. 100098
• Main Authors: Nemudryi, Artem, Nemudraia, Anna, Wiegand, Tanner, Surya, Kevin, Buyukyoruk, Murat, Cicha, Calvin, Vanderwood, Karl K., Wilkinson, Royce, Wiedenheft, Blake
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22.09.2020; Elsevier
• Subjects: Advanced Basic Science; COVID-19; genome sequencing; SARS-CoV-2; wastewater-based epidemiology; COVID-19; genome sequencing; SARS-CoV-2; wastewater-based epidemiology
• ISSN: 2666-3791; 2666-3791
• DOI: 10.1016/j.xcrm.2020.100098

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. [Display omitted] SARS-CoV-2 RNA concentrations in wastewater correlate with COVID-19 epidemiologySARS-CoV-2 RNA levels in wastewater follow symptom onset by 5–8 daysSARS-CoV-2 RNA levels in wastewater precede clinical PCR test results by 2–4 daysSARS-CoV-2 genome from wastewater can trace phylogenetic origin Nemudryi et al. demonstrate that wastewater can be used to monitor the progression and abatement of SARS-CoV-2 spread at the community level. The authors show a correlation between epidemiological indicators and viral concentrations measured in wastewater. In addition, they infer viral ancestry using a phylogenetic analysis of sequenced SARS-CoV-2 genome(s) from wastewater.