Research axes

CARVI has three main research axes:

Axis 1. Characterization of viral determinants

This area focuses on identifying and characterizing viral traits that drive pathogenicity and tracking their evolution over time. For instance, the team is developing innovative methods, such as bilayer interferometry, to study the HA/NA functional balance in influenza viruses from human and animal reservoirs. These tools will support projects like PEPR PREZODE ZOOFLU (2024–2028). Similarly, the team investigates how viral genome mutations impact fitness and antiviral susceptibility in viruses like influenza, RSV, and SARS-CoV-2, as well as within-host and between-host evolution (Destras et al., Lancet Microbe 2022). This work is closely integrated with the respiratory virus surveillance activities of the National Reference Center (NRC) for respiratory viruses and benefits from the Genepii genomics platform (Hospices Civils de Lyon).

Axis 2. Interactions of respiratory viruses with host/other pathogens 

This axis explores the interactions between respiratory viruses, other pathogens, and host cells at multiple levels. In recent years, the team has established various experimental primary models to study virus-bacteria and virus-virus co-infections (Ruffin et al., Front Immunol 2021; Pizzorno et al., JID 2022). Current projects aim to better understand pathogen-host interactions using diverse approaches, including cell biology, transcriptional and metabolomic profiling, and mathematical modeling, as part of funded initiatives (ANR PRCI MORIARTY 2023–2026; ANR PRME NAReCO 2024–2027). The PEPR-MIE 3D-LUNGO (2024–2028) project supports the development of physiologically relevant models. The team also investigates host responses, such as alterations in antiviral immunity during respiratory co-infections, and explores the spatial and seasonal determinants of RSV transmission through multidisciplinary studies (RSV study group).

Axis 3. Translational Research 

This axis leverages insights from Axis 1 (virus characterization) and Axis 2 (pathogen interactions) to enhance infection control. Two key projects exemplify this approach. The PEPR-MIE VORTEX project (2024–2028) aims to develop a tool for detecting respiratory infections using volatile organic compound signatures in exhaled air. The ANR REVIDA industrial chair project (2024–2027) takes a bedside-to-bench and bench-to-bedside approach, focusing on host responses rather than pathogens to develop diagnostic and prognostic tools (Mommert-Tripon et al., EBioMedicine 2024) and new prognosis marker of severity of viral respiratory diseases