First seen in local wastewater – Novel virus variants observed weeks prior to routine surveillance underscore the potential of wastewater-based epidemiology

<h2>Abstract</h2> Wastewater-based epidemiology (WBE) is a valuable surveillance method for the early detection and monitoring of infectious diseases at the population level. By rapidly sequencing genetic material extracted from wastewater, local and regional virus surveillance can be enhanced, enabling earlier identification of emerging variants than routine clinical testing typically allows. This provides a critical advantage for immune-evasive pathogens. In this study, a cost-effective sequencing and sensitive analysis strategy has been employed to monitor SARS-CoV-2 variants in the metropolitan Ruhr area of Germany. Pathogen-specific tiled amplification was combined with both established analytical tools and a customized method for enhanced sensitivity utilizing unique single nucleotide variants (SNVs) in different lineages. Samples were collected twice weekly over six weeks, resulting in 55 samples from five sampling sites. Consistent with prior knowledge, the findings demonstrated earlier detection of emerging variants of concern (VOCs) in wastewater compared to patient-based genomic surveillance, which, at the national level, sequenced approximately 2.4 % of detected SARS-CoV-2 cases by April 2023. Particularly notable is that XBB.1.5 was identified in local wastewater from intra-urban sewersheds two weeks before its appearance in patient samples and XBB.1.9 several months prior to its local clinical manifestation. Furthermore, this study corroborates own and other prior reports that local sampling sites can extend the early-warning horizon for novel variants when compared to wastewater treatment plants (WWTPs), likely due to lower dilution and closer proximity to infection sources. Overall, these results underscore the utility of sequencing-based WBE in delivering timely, actionable insights to healthcare providers and authorities. Such methodologies represent a promising expansion of current surveillance infrastructures and quantitative frameworks, offering practical benefits for optimizing environmental viral monitoring and supporting improved public health responses.