Viral Codon Usage: A Novel Readout of Virus Evolution and Host Interaction
Supervisors
Juana Díez
UPF, 1st supervisor
Manuel Irimia
CRG, 2nd supervisor
Objectives
To determine how viral codon usage shapes host-cell responses and viral adaptation through a systematic analysis across all known human viruses. The project will test whether viral codon biases predict dependence on shared host tRNA modification pathways and how these features influence virus-induced stress responses and translation efficiency. It aims to uncover general principles of virus–host interaction, anticipate viral evolution, and identify new opportunities for broad-spectrum antiviral strategies.
Methodology
The student will perform a large-scale computational analysis of codon usage across all human virus genomes. This will involve comparative analyses integrating genomics transcriptomics and translatomics data, including the calculation of standard codon usage metrics and the evaluation of compositional features such as dinucleotide frequencies. These signatures will be analyzed within a phylogenetic framework to identify evolutionary patterns and shifts. Depending on the candidate’s interests, there will be opportunities to complement computational predictions with experimental validation in cell culture systems.
Required Skills
A background in virology, RNA biology, or evolutionary biology is required. Substantial experience in computational methods is recommended, including familiarity with command line tools and at least one programming language (e.g., Python). Some familiarity with phylogenetic methods is encouraged. We are particularly interested in candidates with a creative and open scientific mindset who value a collaborative approach to research.
Expected Results
The project is expected to advance our understanding of virus evolution by defining codon usage signatures associated with viral adaptation and identifying convergent patterns across virus families. It will contribute to the development of predictive frameworks linking codon bias to host responses and may reveal novel targets for broad-spectrum antiviral strategies.
Planned Secondments
GIMM (Morais) in year 2 (2 months) to receive training on software for high-level transcriptomic analyses and
statistical methods.
CNRS (Walczak) in year 3 (1 month) to build models on DC’s data.
UCD (Teeling) in year 3 (1 week) to learn about bat immune research, and bat’s exceptional viral responses.
Enrolment in doctoral programs
PhD in Biomedicine from Universitat Pompeu Fabra
References
Muscolino E, Puig-Torrents M, Buigues Bisquert J, Correa Mendonca D, Talló-Parra M, Perez-Vilaro G, Caño-Prades O, Meehan GR, Kerr K, Herder V, Chillón M, Castello A, Sanjuan R, Patel AH, Díez J. Nat Commun. 2026 Feb 19;17(1):2944. doi: 10.1038/s41467-026-69700-w.
Muscolino, E and Díez J. Viral Codon Usage and the Host Transfer RNA. Annu Rev Virol. 2025. doi: 10.1146/annurev-virology-092623-105418. Epub 2025 Apr 23.