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City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants

Lookup NU author(s): Dr Mathew Brown, Dr Matthew WadeORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


© 2022 The AuthorsGenomic surveillance of SARS-CoV-2 has provided a critical evidence base for public health decisions throughout the pandemic. Sequencing data from clinical cases has helped to understand disease transmission and the spread of novel variants. Genomic wastewater surveillance can offer important, complementary information by providing frequency estimates of all variants circulating in a population without sampling biases. Here we show that genomic SARS-CoV-2 wastewater surveillance can detect fine-scale differences within urban centres, specifically within the city of Liverpool, UK, during the emergence of Alpha and Delta variants between November 2020 and June 2021. Furthermore, wastewater and clinical sequencing match well in the estimated timing of new variant rises and the first detection of a new variant in a given area may occur in either clinical or wastewater samples. The study's main limitation was sample quality when infection prevalence was low in spring 2021, resulting in a lower resolution of the rise of the Delta variant compared to the rise of the Alpha variant in the previous winter. The correspondence between wastewater and clinical variant frequencies demonstrates the reliability of wastewater surveillance. However, discrepancies in the first detection of the Alpha variant between the two approaches highlight that wastewater monitoring can also capture missing information, possibly resulting from asymptomatic cases or communities less engaged with testing programmes, as found by a simultaneous surge testing effort across the city.

Publication metadata

Author(s): Brunner FS, Brown MR, Bassano I, Denise H, Khalifa MS, Wade MJ, van Aerle R, Kevill JL, Jones DL, Farkas K, Jeffries AR, Cairns E, Wierzbicki C, Paterson S

Publication type: Article

Publication status: Published

Journal: Water Research

Year: 2022

Volume: 226

Print publication date: 01/11/2022

Online publication date: 28/10/2022

Acceptance date: 26/10/2022

Date deposited: 26/06/2023

ISSN (print): 0043-1354

ISSN (electronic): 1879-2448

Publisher: Elsevier Ltd


DOI: 10.1016/j.watres.2022.119306


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Funder referenceFunder name
Department of Health and Social Care
Genome Research Limited