Dataset from Bioinformatics Framework for Wastewater-based Surveillance of Infectious Diseases

Background: The purpose of this study was to implement and evaluate a near real-time wastewater-based epidemiology (WBE) framework for SARS-CoV-2 surveillance across the United States. COVID-19 was projected to become one of the largest mass casualty events in U.S. history, highlighting the need for accurate population-level assessment to guide prevention and mitigation strategies. Traditional diagnostic testing through swabs, saliva, or serum had limited reach, while WBE provided a cost-effective alternative capable of screening up to 70% of the U.S. population weekly at less than 0.01% of the cost of individual clinical testing. This study aimed to complement existing surveillance methods, assess the true disease burden, identify geographic disparities, and provide timely data to inform public health decision-making.

Materials/Methods: The study developed a WBE bioinformatics framework for SARS-CoV-2 at national, city, and neighborhood (intra-sewershed) levels to generate RT-qPCR and RNA sequencing data that tracked viral distribution and genetic variations in wastewater samples. Weekly wastewater samples were analyzed to estimate community viral loads, which were then compared with reported infection, hospitalization, and mortality data from local health systems. The team also optimized pipelines for high throughput sequencing analysis to detect SARS-CoV-2 variants and implemented a robust data communication platform, expanding their existing public online dashboard in collaboration with the City of Tempe, Arizona.

Outcome/Impact: The study successfully established a scalable, real-time wastewater surveillance system capable of detecting and tracking SARS-CoV-2 across multiple geographic levels. The WBE framework increased testing coverage, enhanced temporal and spatial resolution of community surveillance, and provided an early warning system for identifying outbreaks before clinical cases surged. The approach enabled continuous variant monitoring, improved public health responsiveness, and demonstrated the utility of wastewater surveillance as a sustainable tool for managing current and future infectious disease outbreaks. Sequencing data from this study are available in the Sequence Read Archive (SRA) repository and can be accessed via https://www.ncbi.nlm.nih.gov/bioproject/847239 https://www.ncbi.nlm.nih.gov/bioproject/847239 and https://www.ncbi.nlm.nih.gov/bioproject/662596.