Wastewater monitoring of COVID in UK. Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England

Here we use the arrival and spread of Omicron in England to test the utility of WBE in tracking SARS-CoV-2 variants at a national level. We use genome sequencing of SARS-CoV-2 from >20,000 longitudinal samples that cover >70% of the English population and obtained from 524 sites, including sewage treatment works and finer scale sampling from the sewer networks in cities. We use these data to test how quickly WBE is able to detect the arrival of Omicron in England and its ability to then give insight into Omicron’s geographical spread and rise in frequency through time, verifying results against data from individual testing efforts in clinical and non-clinical settings. Data were generated using an amplicon approach covering the whole SARS-CoV2 genome, as described in: https://www.protocols.io/view/wastewater-sequencing-using-the-easyseq-rc-pcr-sar-81wgb7bx3vpk/v2