SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.

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SARS-CoV-2 surveillance is crucial to identify variants with altered epidemiological properties. Wastewater-based epidemiology (WBE) provides an unbiased and complementary approach to sequencing individual cases. Yet, national WBE surveillance programs have not been widely implemented and data analyses remain challenging. We deep-sequenced 2,093 wastewater samples representing 95 municipal catchments, covering >57% of Austria's population, from December 2020 to September 2021. Our Variant Quantification in Sewage pipeline designed for Robustness (VaQuERo) enabled us to deduce variant abundance from complex wastewater samples and delineate the spatiotemporal dynamics of the dominant Alpha and Delta variants as well as regional clusters of other variants of concern. These results were cross validated by epidemiological records of >130,000 individual cases. Finally, we provide a framework to predict emerging variants de novo and infer variant-specific reproduction numbers from wastewater. This study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without dense individual monitoring.

Given the availability of technological solutions and guidelines for safe drinking water, direct potable reuse of reclaimed water has become a promising option to overcome severe lack of potable water in arid regions. However, the growing awareness of the presence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) in corresponding raw wastes has led to new safety concerns. This study investigated the fate of ARB and intracellular and extracellular ARG after each treatment step of an advanced water treatment facility in Windhoek, Namibia. The New Goreangab Water Reclamation Plant (NGWRP) produces drinking water from domestic secondary wastewater treatment plant effluent and directly provides for roughly a quarter of Windhoek's potable water demand. Procedures to study resistance determinants were based on both, molecular biology and culture-based microbiological methods. TaqMan real-time PCR was employed to detect and quantify intracellular resistance genes sul1, ermB, vanA, nptII and nptIII as well as extracellular resistance gene sul1. The NGWRP reduced the amount of both culturable bacterial indicators as well as the resistance genes to levels below the limit of detection in the final product. The main ozonation and the ultrafiltration had the highest removal efficiencies on both resistance determinants.