Environmental sampling as a tool to monitor enteric virus epidemiology

Our knowledge of the epidemiology of enteric viruses widely relies on testing capacity of clinics and clinical characteristics of infections. However, for only a few enteric viruses (e.g., poliovirus) environmental surveillance (soil and wastewater) is being used to track their existence among a population which leads to many important enteric viruses such as norovirus, rotavirus, and astrovirus being overlooked. In our project, we will use longitudinal wastewater samples from the wastewater treatment plant (WWTP) Leuven of the company Aquafin and air samples from UZ Leuven Daycare Center. To identify the virome of the samples, we will utilize The Novel Enrichment Technique of Viromes (NetoVIR) and use our metagenomics pipeline. Additionally, the COVID-19 pandemic and especially the actions taken to prevent SARS-CoV-2 spread (lockdowns, mask-wearing, and social distancing) have also impacted the spread of other pathogens including rotavirus. We believe that this lack of rotavirus circulation in the seasons 2019-2020 and 2020-2021 could result in a larger pool of infants susceptible to rotavirus infections, and hence we hypothesize a strong rebound of the number of rotavirus cases in Belgium in the subsequent years. Taken together, we hypothesize that the epidemiology of enteric viruses is reflected in environmental samples (sewage and air) and such data can be used as an early warning system for epidemics of enteric viruses. Therefore, this PhD project will be conducted in four main work packages, answering the following questions: 1. What are the long-term effects of the COVID-pandemic on rotavirus epidemiology? 2. Can longitudinal sewage sample analyses be used as a proxy for virus epidemiology or even as an early warning system? 3. Can unbiased analyses of air samples be used to study the epidemiology of enteric viruses? 4. What is the relationship between virus detection in environmental samples and epidemiological surveillance data?