Wastewater surveillance of influenza activity: Early detection, surveillance, and subtyping in city and neighbourhood communities

Abstract

AbstractRecurrent epidemics of influenza infection and its pandemic potential present a significant risk to global population health. To mitigate hospitalizations and death, local public health relies on clinical surveillance to locate and monitor influenza-like illnesses and/or influenza cases and outbreaks. At an international level, the global integration of clinical surveillance networks is the only reliable method to report influenza types and subtypes and warn of an emergent pandemic strain. During the COVID-19 pandemic, the demonstrated utility of wastewater surveillance (WWS) in complementing or even replacing clinical surveillance, the latter a resource-intensive enterprise, was predicated on the presence of stable viral fragments in wastewater. We show that influenza virus targets are stable in wastewaters and partitions to the solids fraction. We subsequently quantify, type, and subtype influenza virus in municipal wastewater and primary sludge throughout the course of a community outbreak. This research demonstrates the feasibility of applying influenza virus WWS to city and neighbourhood levels; showing a 17-day lead time in forecasting a citywide flu outbreak and providing population-level viral subtyping in near real-time using minimal resources and infrastructure.