The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater

Wastewater based surveillance has gained attention in the four years following the start of the COVID-19 pandemic. Accurate pathogen detection, quantification and characterisation rely on the selection of appropriate methodologies. Using samples collected in England (UK) by the Environmental Monitoring for Health Protection programme we investigated the impact of viral concentration method on long amplicon sequencing. Two long amplicon methods were assessed, the first for dual-typing norovirus genogroups I and II (GI and GII) and the second for whole genome sequencing of SARS-CoV-2. In addition, this project also explored the impact of viral concentration method on RT-qPCR inhibition and the quantification of norovirus GI and GII, CrAssphage, Phi6 and SARS-CoV-2.