Monitoring of enterovirus diversity in wastewater by ultra-deep sequencing: An effective complementary tool for clinical enterovirus surveillance

Abstract In a one-year (October 2014–October 2015) pilot study, we assessed wastewater monitoring with sustained sampling for analysis of global enterovirus (EV) infections in an urban community. Wastewater was analysed by ultra-deep sequencing (UDS) after PCR amplification of the partial VP1 capsid protein gene. The nucleotide sequence analysis showed an unprecedented diversity of 48 EV types within the community, which were assigned to the taxonomic species A (n = 13), B (n = 23), and C (n = 12). During the same period, 26 EV types, of which 22 were detected in wastewater, were identified in patients referred to the teaching hospital serving the same urban population. Wastewater surveillance detected a silent circulation of 26 EV types including viruses reported in clinically rare respiratory diseases. Wastewater monitoring as a supplementary procedure can complement clinical surveillance of severe diseases related to non-polio EVs and contribute to the final stages of poliomyelitis eradication.