Description of the thesis topic

Influenza viruses (IAV) pose a major threat to global health, causing annual epidemics that result in 3 to 5 million cases of severe illness and up to 650,000 deaths worldwide. The ever-present risk of a pandemic underscores the critical need for a better understanding and management of influenza infections. Defective viral genomes (DVG) are naturally occurring viral products with internal deletions that have emerged as promising antiviral candidates due to their ability to interfere with viral replication and modulate immune responses. Although DVGs have demonstrated therapeutic potential against IAV, they have also been implicated in excessive immune activation in highly pathogenic avian influenza (HPAIV) strains. Despite their importance, the molecular mechanisms underlying DVG formation and their interaction with the host immune system remain poorly understood. The objective of this ANR-DFG-funded PhD project is to elucidate the mechanisms of DVG formation in influenza viruses and to characterize their packaging and interaction with the immune system. Using a multidisciplinary approach, incorporating established and novel methodologies from virology, immunology, and RNA biology, we will analyze the VG landscapes of several influenza viruses and determine how differences relate to viral RNA sequence, RNA structure, and viral RNA polymerase activity. In addition, we will determine which DVGs are packaged into viral particles and examine how DVGs stimulate the immune system. Finally, we will use human lung explants and organoids to explore the formation and therapeutic potential of selected DVG.

Work Context

The selected candidate (M/F) will work at the interface of RNA biology, virology, and bioinformatics. The main responsibilities include:

High-throughput sequencing: Applying long-read sequencing technologies (Oxford Nanopore) to quantify DVG populations in cells and virions without PCR bias (Direct RNA sequencing).

RNA structural probing: Implementing the Nano-DMS-MaP method, developed in the host laboratory, to map the secondary structure of full-length viral RNAs and DVGs at single-nucleotide resolution.

Bioinformatics: Analyzing complex long-read sequencing datasets to identify viral isoforms, detect mutations, and model RNA structures using established and custom pipelines.

Molecular virology: Performing infection experiments with human-adapted IAV strains (BSL-2) and preparing samples for analysis.

International collaboration: Translating results into biological insights in collaboration with the German partner, including a planned 6-month scientific exchange in the Brunotte laboratory (Münster).

Requirements:

Education: Master's degree (or equivalent) in molecular biology, biochemistry, virology, or a related field.

Scientific knowledge: Strong background in RNA biology. Knowledge of virology or innate immunity is an asset.

Technical skills: Experience with standard molecular biology techniques (cloning, PCR, RNA extraction). Experience in library preparation for next-generation sequencing (NGS) is highly desirable.

Computational skills: An interest in bioinformatics is essential. Basic knowledge of command-line tools, Python, or R for data analysis is a significant advantage.

Language: Proficiency in English (written and spoken) is mandatory, as this is an international collaboration project. French is not required but helpful for daily life.

Constraints and risks

The selected candidate (M/F) must have experience working with RNA and in culturing eukaryotic cells. High precision and strong organizational skills will be necessary for library preparation and handling Nanopore technology. He/she will be required to work with infectious viruses in BSL-2/BSL-3 conditions and to handle CMR substances (Carcinogenic, Mutagenic, and Reprotoxic) under a chemical fume hood. Appropriate personal protective equipment and biosafety training will be provided.