Global burden of respiratory viruses with interest for vaccine development – VIRESP

To achieve this, we are proposing to develop methodologies, techniques and tools
to analyse the infection risk and disease burden in different populations and the benefit of immunization
programs. This Chair will support a dedicated team of researchers and train highly qualified scientists to
provide evidence-based and data-driven strategic direction and enhanced research capacity around respiratory
infectious diseases relevant to the pipeline of vaccine products and the optimal use of vaccinations in France
and globally. This program will leverage on data, infrastructures, and expertise available from several existing
partners at local, national, and global level to deliver:
1. Research publications such as scientific evidence manuscripts and policy papers, as well as conference
outputs.
2. Analytical tools to better understand the burden of respiratory viruses, vaccine performance against those,
and insights for the development of improved or new vaccines.
3. Approaches on how to improve current passive and active surveillance systems with the aim to enhance
pandemic preparedness, and increase industrial preparedness and resilience.
4. Ways to identify better respiratory viruses’ targets for research and development (R&D) to develop
improved vaccines tailored to the need of the populations at risk.
5. An algorithm to identify new viral threads to society and monitor known recurring viruses.
6. A dissemination and capacity-building program focusing on epidemiology, modelling, advanced analytics,
and bioinformatics.

Under Objective 1, that is focused on the burden of respiratory viruses, different projects will make use of a large hospital dataset from the HCL (FIRESP dataset). i) The first set of data was received by the VIRESP team at the end of Nov 2024; ii) initial analyses started in May 2025. Another large dataset being used is the Global Influenza Hospitalization Surveillance Network (GIHSN). i) a Master-2 project on managing binary missing data in epidemiological research was carried out in Q1 of 2024 and a manuscript was submitted in Apr 2025; ii) a PhD project (Aung Pone Myint) looking at the association of influenza virus genetic information with severity markers in hospitalized patients, has the analysis completed. The student presented at the GIHSN annual meeting (Nov 2024), manuscript submission by Aug 2025; iii) the CIFRE PhD project (Angelica Revilla) is conducting an analysis on hospitalizations associated with respiratory viruses beyond influenza, SARS-CoV-2 and RSV. Both of the PhD students had their work accepted for presentation at ESWI Influenza Conference (Valencia, 20-23 Oct 2025).
The objective 2 is to investigate the evolution of respiratory viruses. In collaboration with a team at Institut de Physique des 2 Infinis, Lyon and the Univ of Napoli, Italy, the PhD student AP Myint used available sequences of the SARS-CoV-2 to identify the distances between two consecutive sequences and the distances of these with the vaccine strains. He built a machine learning model with these distances to predict the number of hospitalizations due to each viral chain. Manuscript submission by Aug 2025. In collaboration with the National Influenza Center, Lyon, AP Myint wrote a protocol to: i) identify mutations in the influenza genome from infected patients admitted to HCL from 2018 to 2025; ii) assess the association between viral genetic mutations and disease severity by linking viral sequencing data to clinical data. The protocol was submitted to the ethics committee of the HCL, analysis will start in Aug 2025.
Objective 3 is focused on vaccine performance. For the aim of describing the influenza vaccine-modified disease effect among influenza cases, the protocol was developed in Dec 2024 and data abstraction (with the support of the CRO HEVA) will start in Jul 2025. The PhD student Brice Mastrovito started his PhD under this objective in Dec 2024.
For Objective 4, 3 PhD students are enrolled at UCBL-1 under the Chaire Industrielle (including 1 CIFRE PhD student), 2 Master students have been already trained. The Chaire VIRESP organized a workshop on “Surveillance Dashboards for Respiratory Viruses” in Lyon 31 Mar and 1 Apr, 2025, with speakers coming from the public and private sector, from national or international institutions. A report will be published to highlight the exchanges and discussions that occurred.

The FIRESP dataset will be explored to answer different research questions under Objective 1. A manuscript will be developed by the end of 2025.
Two of the PhD students will present at the ESWI Influenza Conference (Valencia, 20-23 Oct 2025). Aung Pone Myint, will have an oral presentation on “Association of influenza viral genetic information with disease severity markers in hospitalized patients”; and Angelica Revilla will have a poster presentation on “Predictors of severity among rhinovirus/enterovirus associated respiratory hospitalizations: A global perspective from the Global Influenza Hospital Surveillance Network 2017-2024”.
Under objective 2, Aung Pone Myint, will submit a manuscript describing his work on “From Sequences to Strategies: Early Detection of SARS-CoV-2 Variants and Leveraging Genetic Distance for Timely Responses to Reduce Hospitalizations by Emerging Variants” by Aug 2025. He will also start a new project to identify mutations in the influenza genome from infected patients admitted to HCL from 2018 to 2025, by Sep 2025.
The analyses of the project “Describe the influenza vaccine-modified disease effect among influenza cases” under objective 3, will be conducted in the second half of 2025 and a publication is planned for early 2026.

1. Nov, 2024- GIHSN Global Annual Meeting. Oral presentation by Aung Pone Myint: “Association of influenza viral genetic information with severity markers in hospitalized patients”. Nans-les-Pins, France.
2. Dec, CIRI Virology Specialty Day 2024. Oral presentation: by Aung Pone Myint : “Association of influenza viral genetic information with severity markers in hospitalized patients”. Lyon.