Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance

Abstract

ABSTRACTWastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-generation sequencing can provide deeper insights via genomic analyses of multiple diverse pathogens. We conducted a year-long sequencing surveillance of 1,408 composite wastewater samples collected from 12 neighborhood-level access points in the Greater Tempe area, Arizona, USA, and show that variation in wastewater viromes is driven by seasonal time and location. Wastewater virome temporal dynamics were influenced in a cyclical manner, with the most dissimilarity between samples 23 weeks apart (i.e., winter vs summer, spring vs fall). We identified diverse urinary and enteric viruses including polyomaviruses, astroviruses and noroviruses, and showed that their genotypes/subtypes shifted across season. We show that while wastewater data of certain respiratory viruses like SARS-CoV-2 strongly correlate with clinical case rates, laboratory-reported case incidences were discordant with surges of high viral load in wastewater for other viruses like human coronavirus 229E. These results demonstrate the utility of wastewater sequencing for informing decision making in public health.IMPORTANCEWastewater genomic sequencing surveillance can provide insights into the spread of pathogens in communities. Advances in next-generation sequencing methodologies allow for more precise detection of viruses in wastewater. Long-term wastewater genomic sequencing surveillance is an important tool for public health preparedness. This system can act as a public health observatory that gives real-time early warning for infectious disease outbreaks and improved response times.