Detection, quantification, and typing of enteroviruses in wastewater

Abstract Wastewater analysis serves as a complementary tool to clinical data in monitoring both the quantity and diversity of circulating enteroviruses among the population. While enterovirus infections typically result in asymptomatic or mild disease, certain types can lead to severe symptoms, highlighting the importance of tracking their prevalence and distribution. Here we present both a RTqPCR assay targeting a conserved region in the 5’ end of the enterovirus genome to detect and quantify its presence in sewage along with a sequencing pipeline based in MinION platform (Oxford Nanopore Technologies) to characterize circulating enterovirus types in samples with sufficient virus load (Cq≤33). Two sequencing approaches are possible: one targeting all enterovirus types (1), and the other specifically focusing on Cluster C enterovirus (2), including poliovirus. The obtained data are processed using a designed pipeline to quantify the proportions of different enterovirus types, providing valuable insights into the spread of potentially severe types.