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

Abstract

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.

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

“…Wastewater monitoring is an invaluable tool for SARS-CoV-2 surveillance [1][2][3][4][5][6][7][8] . Despite multiple recent successes in VoC monitoring and detection from wastewater sequencing data [9][10][11][12][13][14][15] , there are multiple challenges associated with the nature of the environmental data. Since wastewater represents a pooled sample of multiple hosts, it harbors a diversity of SARS-CoV-2 variants that are currently circulating in the population 1,2,10,13 , including potentially previously unreported genotypes 16 .…”

Wastewater surveillance of pathogens can inform public health responses

“…As a result, wastewater surveillance has played an important part in the polio-eradication campaign 2 . Building from the work on poliovirus, data from wastewater have complemented clinical surveillance during the COVID-19 pandemic by offering a comprehensive view of infection burden and transmission -both symptomatic and asymptomatic -and information on which SARS-CoV-2 variants are circulating in a community 3,4 (including so-called cryptic variants that have never been detected in clinical samples 5 ). Yet despite the established value of wastewater surveillance for monitoring poliovirus and its emerging importance during the COVID-19 pandemic, most global public health surveillance systems still rely heavily on medically attended case data 6 .…”

The World of Organoids: Gastrointestinal Disease Modelling in the Age of 3R and One Health with Specific Relevance to Dogs and Cats

“…COVID-19, for instance, is a very prominent and current example. SARS-CoV-2 infections are diagnosed in humans as well as many different species of animals [ 2 ], and viral particles can be found in wastewater [ 3 ]. Referring to the global problem of SARS-CoV-2 infections for humans, animals, and environmental contamination, one can appreciate the importance of One Health in a global context.…”