Dynamics of RNA Virus Diversity and Host Transcriptomic Responses Across Time Scales: From Single Infection to Experimental Evolution

Viruses are obligate intracellular symbionts that rely entirely on host cellular machinery to complete their life cycles. Despite their simplicity, they are among the most genetically diverse and evolutionarily successful biological entities on Earth. They infect all forms of life—from bacteria and archaea to plants and animals—and play pivotal roles in ecosystem dynamics, evolution, and global health. Among viruses, those with RNA genomes stand out due to their high mutation rates and e ective population sizes, which enable rapid adaptation to new hosts and environments. These traits also make RNA viruses powerful model systems for studying evolution, population genetics, and host-pathogen interactions. RNA viruses typically encode a small number of proteins, often using compact genomes of 1.8-30 kb. This minimalism forces them to rely on multifunctional proteins and extensive host manipulation. Their high error rates, resulting from the lack of proofreading capabilities in most of the RdRPs, generate a swarm of genetic variants during each infection cycle. This heterogeneous collection, known as a viral quasispecies, allows viruses to explore vast areas of sequence space and quickly respond to selective pressures. A particularly intriguing component of viral quasispecies are defective viral genomes (DVGs). DVGs arise during replication. Although they are typically replication-deficient on their own, DVGs can be replicated in trans by co-infecting helper viruses. Understanding how these populations evolve and adapt in di erent host contexts is central to virology, with implications for antiviral strategies, vaccine design, and our understanding of molecular evolution. RNA viruses, despite their small genome sizes, behave as complex, evolving populations subject to mutation, recombination, selection, and drift. Their dynamics are influenced by within-host processes as well as between-host transmission. Di erent replication strategies, like stamping machine versus geometric replication, influence how mutations accumulate and spread. These factors collectively shape the evolutionary trajectory and phenotypic outcomes of infection. Equally important are the responses mounted by host organisms. Over time, hosts have developed mechanisms to detect and eliminate viruses. Innate immunity provides a rapid antiviral defense. Despite taxonomic di erences, many antiviral responses are conserved, especially RNA interference (RNAi). The study of host responses in model organisms provides valuable insights into the universal principles of antiviral defense. In this thesis, I present a systems biology approach to investigate the dynamic interplay between viral evolution and host transcriptomic responses. Drawing on four published articles, this work integrates the analysis of RNA sequencing data across multiple host-virus systems and evolutionary timescales to explore how viral populations adapt, and how hosts respond at the phenotypic and molecular levels. The thesis addresses two di erent scale times: (1) the long-term evolutionary trajectories of three (+)ssRNA viruses: TuMV in A. thaliana, and the betacoronaviruses MHV and HCoV-OC43 in mammalian cells— and (2) the short-term infection dynamics of the OrV in C. elegans. The chapters are also organized into two main axes: one focused on viral diversity; the other on host responses to infection. This integrative and computational approach seeks an understanding of how viral populations evolve in di erent biological contexts, and how hosts reshape their transcriptomes in response to infection.