Wastewater based infectious disease surveillance and epidemiology

Background

Surveillance of pathogens spreading through a population is an essential tool in epidemic response and public health resource planning. Historically programes have used reported cases, hospitalisations and various sentinel systems to track infection prevalence and transmission in the population. For many infections, virus is shed in feces. In recent years protocols have been developed to quantify the concentration of viral RNA within sewage for a growing number of pathogens. By monitoring municipal wastewater systems it is possible to track fluctuations in prevalence of disease in the population served by the system.

Context

We are part of a collaboration in Switzerland that monitors wastewater from treatment plants across Switzerland. Samples are collected between 5 and 7 days a week, viral concentrations of SARS-CoV-2, Influenza A and B and RSV are quantified using digital deoplet PCR. Amplicons are also sequenced using illumina next generation sequncing.

Research

The focus of my research has been on how to optimise the collection of data and estimation of concentration to provide public health insights.

Firstly, with collaborators at Eawag, UniSante and FOPH we have evaluated the ability of different sampling strategies to inform trends in SARS-CoV-2 prevalence across switzerland and how this translates to reported cases and hospitalisations.

Secondly, with collaborators from Eawag we investigate degredation of viral samples between sampling and testing - which can affect the quality of concentration estimates, highlighting the importance of testing samples promptly - especially when concentrations are low.