Wastewater sequencing of SARS-CoV2 in Liverpool, UK

Background: Genomic 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. However, it is so far unclear how much spatial and temporal resolution of variant dynamics it can offer. Methods: We sampled 8 network locations and the main wastewater treatment plant in the city of Liverpool (500,000 inhabitants, UK) at least twice a week between November 2020 and June 2021. By using amplicon-based sequencing of SARS-CoV-2 virions, we reconstruct frequencies of the circulating variants in small areas of the city (8,600-111,800 inhabitants). Findings: We found fine-scale differences within the city during the emergence of Alpha and Delta variants. We further noted that wastewater and clinical sequencing match well in the estimated timing of new variant rises and that first detection of a new variant in a given area may occur in either clinical or wastewater samples. Interpretation: 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.