Post-Emergent Structural Persistence in the SARS-CoV-2 Genome Under Long-Term Evolutionary Forcing

Viral genomic evolution is typically modeled as a stochastic process dominated by mutation, recombination, and selection. While such models successfully describe short-term variation, they provide limited insight into whether viral genomes exhibit persistent large-scale organization once established. In this study, we analyze the post-emergent structural behavior of the SARS-CoV-2 genome using a comparative, structure-aware framework spanning more than two decades of related coronavirus evolution. Across extensive perturbation controls—including noise sweeps, symmetry breaking, and null-structure tests—we observe convergence to a stable, low-dimensional genomic regime characterized by invariant topology, intermediate causal density, and high self-similarity. These results indicate that SARS-CoV-2 evolution operates within a tightly constrained structural regime rather than undergoing unconstrained stochastic drift. The findings provide a system-level explanation for recurrent mutation patterns, constrained variant emergence, and long-term genome stability, with implications for viral evolution, predictability, and intervention strategies. This work explicitly addresses post-emergent behavior and does not consider questions of viral origin.