iPAVE: Innovative Phylodynamic Approaches for Effective Viral Epidemic Management

"The proposed PhD project, iPAVE, seeks to deepen the understanding of epidemiological dynamics and transmission patterns of major Acute Respiratory Infections (ARIs) - Influenza, RSV, and SARS-CoV-2 - in France. By utilizing large-scale genomic datasets from surveillance networks (RELAB and Sentinelles) and cutting-edge phylodynamic methods, the project aims to answer two critical questions : i) How can current phylodynamic methods be extended to cope with large-scale and near real-time molecular surveillance datasets? and ii) What are the key factors driving the spread of circulating Respiratory virus, and how do these factors vary across different populations, geographical regions, and time-periods? While phylodynamic methods, developed over the past two decades, have been instrumental in tracking epidemics using molecular data, they currently struggle with large datasets and real-time analysis. To address these limitations, iPAVE will develop and integrate advanced phylodynamic models into a comprehensive monitoring framework, enabling precise tracking of viral evolution and spread. The project will leverage the RELAB dataset, expected to generate around 10,000 sequences per year, providing a detailed view of ARIs in France. The methodology is divided into three main tasks: data validation and preparation, extending and benchmarking of phylodynamic methods, and large-scale application and analysis. Expected outcomes include a detailed understanding of viral epidemiological dynamics and the establishment of a benchmark for current phylodynamic techniques, which will be applicable for global surveillance. The project will be carried out within the ""Mécanismes moléculaires de la multiplication des Pneumovirus"" unit with a tight collaboration with the National Reference Center for Respiratory virus at Institut Pasteur, leveraging their expertise and high-performance computing infrastructure. It will also beneficit from collaboration with the EID group at Institut Pasteur. This research is poised to make significant contributions to the global surveillance and management of Respiratory virus."