Persistence of respiratory, enteric, and fecal indicator viruses in fecal sludge from on-site sanitation in Dakar, Senegal

As wastewater-based epidemiology (WBE) broadens its focus to include prevalent diseases with significant global health impact, existing surveillance systems concentrate on sewer-based infrastructure, which excludes the 2.7 billion people using non-sewered systems. To address this gap, our study explores the potential of fecal sludge treatment plants (FSTPs) for WBE, emphasizing the stability of virus RNA targets within pooled fecal sludge. We screened fecal sludge from a centralized treatment facility in Dakar, Senegal for SARS-CoV-2, human norovirus (HuNoV), and microbial source trackers (MSTs) pepper mild mottle virus (PMMoV) and tomato brown rugose fruit virus (ToBRFV). Decay kinetics of genomic RNA markers from these viruses were examined at 4 °C, 15 °C, and 30 °C over 70 days. Results indicate high persistence of viral targets in fecal sludge (T90 value of 3.3 months for exogenous SARS-CoV-2 N1 and N2, 6.2 months for ToBRFV), with all targets detected throughout the 70-day experiment under various temperatures with limited decay (<1 log10 reduction). This study addresses a crucial gap in understanding virus persistence in on-site sanitation systems by providing essential decay rate constants for effective target detection. Our results indicate that sampling at centralized facilities treating fecal sludge from on-site sanitation could facilitate localized pathogen surveillance in low-income settings. Highlights Investigation of the persistence of SARS-CoV-2, HuNoV, PMMoV, and ToBRFV genomic RNA in pooled fecal sludge derived from on-site sanitation systems. Novel microbial source tracker (MST), ToBRFV, exhibited comparable abundance to PMMoV, a well-established MST, in fecal sludge. No significant decay observed for HuNoV and PMMoV over 70 days at all temperature conditions (4, 15, and 30 °C). SARS-CoV-2 N1 and N2 showed T 90 values of 3.3 months at 30 °C. Fecal sludge treatment plants offer a centralized sampling location for wastewater-based epidemiology, providing a strategic approach for monitoring public health. Graphical Abstract