Evaluation of CrAssphage Marker for Tracking Fecal Contamination in River Water in Nepal

Enteric viruses in the aquatic environment are a concern due to the potential for waterborne disease transmission to humans. In Nepal, the Bagmati River serves as a source of drinking and irrigation water; therefore, the detection of waterborne enteric pathogens is integral to maintaining human health. The objective of this study was to quantify the crAssphage marker in surface water samples from the Bagmati River between November 2015 and September 2016. Concentrations of crAssphage were then compared to those of other enteric viruses and indicator organisms found in the samples in order to examine the potential of crAssphage as a marker for fecal contamination. CrAssphage was detected in 17% (1/6) of samples from Sundarijal, 100% (6/6) of samples from Thapathali, and 100% (6/6) samples from Chovar, with the highest average concentrations recorded in May 2016 and the lowest average concentrations recorded in September 2016. Overall, crAssphage was present in 72% (13/18) of samples and was strongly correlated with the presence of fecal indicator bacteria Escherichia coli (r = 0.89) and Enterococcus (r = 0.92) and several enteric viruses. The strongest viral correlations were to salivirus (r = 0.84), pepper mild mottle virus (r = 0.77), Aichi virus 1 (r = 0.75), enteroviruses (r = 0.76), and tobacco mosaic virus (r = 0.71). These results provide evidence for the potential use of crAssphage as a marker for human fecal contamination in river water.