National-scale surveillance of emerging SARS-CoV-2 variants in wastewater
Preprint
- 14 January 2022
- preprint
- research article
- Published by Cold Spring Harbor Laboratory
Abstract
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.GraphicalKeywords
This publication has 77 references indexed in Scilit:
- LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasetsNucleic Acids Research, 2012
- A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEffFly, 2012
- Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSiftFrontiers in Genetics, 2012
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Supplemental Material for A Better Lemon Squeezer? Maximum-Likelihood Regression With Beta-Distributed Dependent VariablesPsychological Methods, 2006
- Generalized Additive Models for Location, Scale and ShapeJournal of the Royal Statistical Society Series C: Applied Statistics, 2005
- Scattered data interpolation with multilevel B-splinesIEEE Transactions on Visualization and Computer Graphics, 1997
- Some parametric models on the simplexJournal of Multivariate Analysis, 1991
- Some Statistical Models for Limited Dependent Variables with Application to the Demand for Durable GoodsEconometrica, 1971