City-Scale Wastewater Metagenomics as an Early-Warning System for Seasonal Influenza and SARS-CoV-2: A Prospective Time-Series Study
DOI:
https://doi.org/10.64229/534nks33Keywords:
Wastewater-Based Epidemiology, Metagenomics, Influenza, SARS-CoV-2, Early Warning, SurveillanceAbstract
We conducted a year-long city-wide wastewater surveillance study using metagenomic sequencing to detect and quantify seasonal influenza and SARS-CoV-2 viruses. Weekly composite sewage samples were collected from the main treatment plant serving ~1.5 million residents. Samples were concentrated and subjected to targeted hybrid-capture metagenomic sequencing for respiratory viruses. Viral read counts for SARS-CoV-2 and influenza A were quantified and compared with clinical case data (confirmed COVID-19 and influenza cases) on a weekly basis. We observed clear seasonal peaks of each virus in wastewater that closely mirrored reported case trends. SARS-CoV-2 signal peaks preceded clinical case peaks by ~1–2 weeks on average, while influenza A peaks led flu case peaks by ~5 days. Pearson correlation analysis showed strong association between wastewater viral loads and clinical data (SARS-CoV-2: r≈0.85, influenza A: r≈0.70) at these lead times. Figure 1 illustrates how a targeted metagenomic enrichment panel can recover a broad range of respiratory viruses from sewage. Our findings demonstrate that city-scale wastewater metagenomics can serve as an early-warning system for community transmission of both seasonal influenza and SARS-CoV-2. The noninvasive approach provides timely surveillance of viral trends that can inform public health interventions.
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