Genotype networks drive oscillating endemicity and epidemic trajectories in viral evolution
Journal:
arXiv
Published Date:
Jun 3, 2025
Abstract
Rapidly evolving viruses use antigenic drift as a key mechanism to evade host
immunity and persist in real populations. While traditional models of antigenic
drift and epidemic spread rely on low-dimensional antigenic spaces, genomic
surveillance data reveal that viral evolution produces complex antigenic
genotype networks with hierarchical modular structures. In this study, we
present an eco-evolutionary framework in which viral evolution and population
immunity dynamics are shaped by the structure of antigenic genotype networks.
Using synthetic networks, we demonstrate that network topology alone can drive
transitions between stable endemic states and recurrent seasonal epidemics.
Furthermore, our results show how the integration of the genotype network of
the H3N2 influenza in our model allows for estimating the emergence times of
various haplotypes resulting from its evolution. Our findings underscore the
critical role of the topology of genotype networks in shaping epidemic behavior
and, besides, provide a robust framework for integrating real-world genomic
data into predictive epidemic models.
