Cross-assembly phage and pepper mild mottle virus as viral water quality monitoring tools-potential, research gaps, and way forward

Microbial water quality is currently assessed by fecal indicator bacteria that are poor representatives of viral pathogens in the environment. Viruses are predicted to account for the majority of infectious risk from exposure to sewage contaminated water. Previously developed viral indicators suffer from a lack of human specificity, low concentrations in sewage, or both. In this commentary review, we discuss recent advances in developing cross-assembly phage (crAssphage) and pepper mild mottle virus (PMMoV) as viral water quality indicators. CrAssphage and PMMoV are abundant in and highly associated with human sewage, correlate with viral pathogens in sewage contaminated environments and globally present. Future work is necessary to describe crAssphage and PMMoV fate in the environment, local variation in abundance and genetic makeup, and relationship between molecular detections and pathogen viability, among other areas. These developments will allow the integration of crAssphage and PMMoV into quantitative microbial risk assessment and water quality regulation.