Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

Wastewater surveillance of SARS-CoV-2 at the national scale tracks emerging variants. 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.

Automated summary

Wastewater surveillance of SARS-CoV-2 at the national scale is effective in tracking emerging variants. The study developed a system called VaQuERo, which allows for accurate quantification of predefined variants in complex wastewater samples. The research also identified increased viral genetic diversity during the Delta variant period and proposed a framework for predicting emerging variants and measuring the reproductive advantage of variants of concern using wastewater data.