Environmental-based epidemiology for preparedness and early detection of viral epidemics

The risk of viral epidemics and pandemics has undeniably increased in the recent decades due to global changes affecting inter-connectivity, climate and human-animal interface. Notably, several epidemics or pandemics marked the last 20 years, such as those caused by SARS-CoV-1, MERS-CoV, several influenza, Ebola, Zika and lastly SARS-CoV-2. All these viruses originated in animals, before favorable environmental conditions were created to promote species jump and further human-to-human transmission. While many viruses may circulate silently in the population until breaking out, traditional infectious disease surveillance systems detect outbreaks on the basis of clinical symptoms and thus fail to timely identify the critical places and critical times of viral disease emergence. Innovative surveillance and early warning tools are thus urgently needed to more efficiently control and prevent viral threat spread. In this context, the main objective of the VIRALERT project is to set up the initial phase of the epidemic preparedness program at the national scale, through the implementation of an enhanced environmental surveillance allowing early detection of viral epidemics. The originality of the system proposed relies on the integration of two complementary environmental compartments characteristic of human and animal populations, by combining the monitoring of wastewater and surface water. While wastewater-based epidemiology has long proven its feasibility and usefulness for enteric virus surveillance, mounting evidence suggests a much wider applicability to provide essential public health data on non-enteric viruses: wastewater monitoring showed good correlation but also interestingly increasing SARS-CoV-2 transmission in the population ahead of population screening data. The current pandemic has also altered health-seeking behavior and promoted telemedicine, likely durably affecting traditional sentinel surveillance. Non-pharmaceutical interventions have disturbed the spread of endemic viruses, resulting in lower herd immunity, larger pools of susceptible and more severe epidemics in the near future. In complement freshwater-based epidemiology will be explored as a pioneering tool to reflect the viral diversity of major animal reservoirs and epidemic prevention. We therefore propose to take environmental surveillance to the next level by (i) broadening the spectra of viral species monitored beyond human enteric viruses, (ii) monitoring the post-COVID-19 effect on endemic viral populations as an early warning system for future epidemics and (iii) extending it to more reservoirs in an integrated manner to cover human and animal populations. To that purpose, viral populations in wastewater and aquatic environment will be characterized using three complementary molecular techniques to cover the spectrum from a highly targeted approach with little information on virus diversity (RT-qPCR) to a targeted approach with sequence data to unbiased metagenomics for viral communities. Focus will be made on virus families with high epidemic or pandemic potential, i.e. Coronaviridae, Orthomyxoviridae, Flaviviridae, Caliciviridae, Picornaviridae and Hepeviridae. The results emerging from this state-of-the art project will decrease disease burden, improve public health and the well-being of the Luxembourg population by paving the way to a strategic cost effective national prevention resource for viral disease surveillance and possibly beyond.