Wastewater Surveillance to Estimate and Characterize Hepatitis E Virus Circulation

Hepatitis E virus (HEV) is a cause of enterically transmitted hepatitis around the world. Because of the high frequency of asymptomatic infections, the magnitude of HEV infection is underestimated. Wastewater monitoring could be useful to improve our knowledge on HEV epidemiology. In this study, we analyzed the capacity of wastewater surveillance to give an insight into the circulation and the diversity of HEV in two French cities. HEV RNA was detected and quantified by digital PCR in 115 untreated composite wastewater samples collected weekly at the inlet of wastewater treatment plants (WWTPs), 58 at Toulouse WWTP and 57 at Dunkerque WWTP. Plasma HEV RNA in blood donors was detected by a commercial assay (Roche Cobas) over the same period in the same area. HEV diversity was analyzed using long-read single-molecule real-time sequencing (Pacific Biosciences). HEV RNA was detected in 88% and 95% wastewater samples collected at Toulouse (Occitanie region, Southern France) and Dunkerque (Hauts-de-France region, Northern France) WWTPs, respectively. HEV RNA concentration ranged between 4.1 and 5.7 log copies/L and was almost similar between the two sites. A long orf2 fragment of HEV genome (1030 nucleotides) was obtained and sequenced in 45% and 70% of positive HEV RNA wastewater samples collected at Toulouse site and Dunkerque site, respectively. Out of 31 strains identified in Toulouse wastewater, 24 were HEV-3c (77%), 6 were HEV-3f (19%), and 1 was HEV-3h (3%). Out of 55 strains identified in Dunkerque, 30 were HEV-3c (55%) and 25 were HEV-3f (45%). All HEV RNA-positive samples from blood donors that could be genotyped during the study period contained HEV-3. Subtype distribution in 51 blood donors living in Toulouse did not differ from that in Toulouse wastewater. The HEV-3 subtype distribution in 51 Hauts-de-France region blood donors and in Dunkerque wastewater were different, but the predominant subtype was the same (HEV-3c). Lastly, we explored the link between the measurement of viral loads in wastewater and the extent of infection in the served population. Although a good correlation between the peaks of positive HEV RNA estimated in wastewater samples and that observed in blood donors was observed with a lag of + 3 weeks for Toulouse, the correlation was weaker for Dunkerque. Wastewater surveillance system applied locally could be very useful for assessing the HEV infection status of a population.