Environmental tracking of viral pathogens in surface waters around Paris using high-throughput PCR

Surface waters that receive discharges from wastewater treatment plants and other sources of pollution are therefore highly susceptible to microbiological contamination. They can be contaminated by a wide variety of viruses, some of which are known to persist in the environment for extended periods. In this study, we assessed the viral contamination of the Seine and Marne rivers in the Paris area by analyzing 42 water samples collected in both winter and summer 2023. Norovirus GI and GII were quantified by RT-qPCR, and a high-throughput PCR array was used for the qualitative detection of 30 viruses, including enteric viruses, respiratory viruses, and indicators of fecal contamination. Noroviruses were detected in 10-82% of the samples tested, depending on the river and season, at concentrations ranging between 5.8 × 10¹ and 1.1 × 10³ genome copies/L. Across the entire sampling campaign, the most prevalent human viruses detected using the PCR array were aichivirus, adenovirus, and bocavirus (74-83%), followed by enterovirus, astrovirus, norovirus, and cosavirus (12-26%). Some other viruses were sporadically detected (sapovirus, hepatitis A and E viruses, OC43, measles virus). The PCR array enables the simultaneous detection of diverse viruses in a single assay, making it a powerful tool for environmental surveillance of multiple pathogens. Its adaptability allows for the detection of a broad range of targets, delivering results within a short timeframe, typically within the same day.