Optimised protocol for monitoring SARS-CoV-2 in wastewater using RC-PCR

This study presents an optimised protocol for quantification and sequencing of SARS-CoV-2 in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. We present sequencing data from optimisation of the protocol for wastewater sequencing. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method.