Icosahedral virus capsids are closed shells built up with a hexagonal lattice of proteins, which incorporate pentamers at their fivefold vertices. Human adenovirus particles lose pentamers (pentons) during infection under a variety of physicochemical cues, including mechanical pulling of molecular motors and the viscous drag of the cytoplasm. By combining atomic force microscopy experiments with survival analysis and Markovian transition state theory, we investigate the sequence of adenovirus penton disassembly that reveals the aging of the virus structure. We show evidence that the lifetime of pentons gradually decreases, accompanied by capsid softening as neighboring pentons are lost. This cooperative dismantling process, which involves first-neighbor penton-penton distances of at least 45 nm, leads to a 50% increase in the virus disassembling rate of the virus particle. Theory and experiments fit remarkably well, allowing us to obtain the spontaneous escape rate and the energy barrier of penton disassembly ($\sim 30k_{B}T$). The observed increase in the penton’s loss rate reveals long-range structural correlations within the capsid. Our estimations suggest that the mechanical cues arising from the strokes of protein motors carrying the virus to the nucleus could help penton disassembly and warrant the timely delivery of weak-enough capsids for adenovirus infection.

Bacteriophage fitness is determined by factors influencing both their replication within bacteria and their ability to maintain infectivity between infections. The latter becomes particularly crucial under adverse environmental conditions or when host density is low. In such scenarios, the damage experienced by viral particles could lead to the loss of infectivity, which might be mitigated if the virus undergoes evolutionary optimization through replication. In this study, we conducted an evolution experiment involving bacteriophage Qβ, wherein it underwent 30 serial transfers, each involving a cycle of freezing and thawing followed by replication of the surviving viruses. Our findings show that Qβ was capable of enhancing its resistance to this selective pressure through various adaptive pathways that did not impair the virus replicative capacity. Notably, these adaptations predominantly involved mutations located within genes encoding capsid proteins. The adapted populations exhibited higher resistance levels than individual viruses isolated from them, and the latter surpassed those observed in single mutants generated via site-directed mutagenesis. This suggests potential interactions among mutants and mutations. In conclusion, our study highlights the significant role of extracellular selective pressures in driving the evolution of phages, influencing both the genetic composition of their populations and their phenotypic properties.

Understanding how ecological factors shape viral evolution is essential for predicting adaptation in RNA viruses. In this study, we investigated the evolutionary dynamics of bacteriophage Qβ under varying host densities, focusing on two nonsynonymous mutations—A1930G and C2011A—located in the A1 protein. Using experimental evolution, phenotypic assays, and competition experiments, we found that C2011A is consistently selected at low bacterial densities, enhancing viral entry but reducing burst size. In contrast, A1930G is fixed at high densities, despite similar phenotypic effects, suggesting its advantage arises from interactions with additional mutations. Clonal analysis revealed that compensatory or beneficial mutations modulate the fitness of A1930G, enabling its fixation. The absence of both mutations in the same genome points to negative epistasis, confirmed by the poor performance of the double mutant generated by site-directed mutagenesis. Sequencing of intermediate transfers showed early emergence of A1930G, but its fixation was prevented by clonal interference with C2011A. These findings highlight how host availability, fitness trade-offs, epistasis, and competition among variants shape the adaptive landscape of RNA viruses.