Different mechanisms for human rhinovirus survival in the presence of deleterious amino acid substitutions at virion protein-protein or RNA-protein interfaces.

A combination of structure-function and genetic analyses of viruses is unveiling a wide repertoire of adaptive mechanisms for restoring biological function in the face of negative selection pressures. The fixation of second-site compensatory mutations in highly heterogeneous RNA virus populations constitutes a frequent and versatile response to recover infectivity in the presence of deleterious mutations. In this study, we explored the following: (i) survival mechanisms of human rhinovirus (RV) when infectivity-impairing amino acid substitutions were introduced at either capsid protein-protein interfaces or capsid protein-RNA interfaces involved in virion assembly and viral RNA uncoating, and (ii) whether recovery of infectivity through compensatory amino acid substitutions in different functional elements in the same virion may be constrained to different extents. Specific interactions between capsid subunits or between the capsid and the genomic RNA in the RV virion were disrupted by replacement of individual amino acid residues with alanine, and the resulting crippled viruses were left to recover normal infectivity during serial infections of human cells. Identification of compensatory amino acid substitutions acquired during virus multiplication revealed that RV can use different genetic mechanisms to recover infectivity, depending on whether the deleterious substitution was localized at either pentamer-pentamer or capsid-RNA interfaces. Moreover, severe constraints to restore infectivity were found when deleterious substitutions were introduced at capsid-RNA interfaces instead of inter-pentamer interfaces. Because of those constraints, the capsid-RNA interface may constitute a preferential target for the design of anti-RV drugs that can interfere with viral assembly and uncoating, while minimizing opportunities for virus escape.IMPORTANCEHuman rhinoviruses cause most common colds and originate serious socioeconomic problems every year. In addition, they are associated with or exacerbate severe respiratory diseases, including chronic obstructive pulmonary disease, a major cause of death worldwide. No vaccines or drugs against rhinovirus infection are currently available. This study shows that when deleterious amino acid substitutions are introduced at interfaces between rhinovirus capsid subunits, infectivity is readily recovered through the fixation of second-site compensatory mutations that restore virion assembly and conformational stability. In contrast, severe difficulties were encountered for the recovery of infectivity when similar deleterious substitutions that impair virion assembly and stability and disregulate genome uncoating are introduced at capsid-viral RNA interfaces. The results suggest that the capsid-RNA interface may constitute a promising target for the design of anti-rhinoviral drugs that impair virus assembly and uncoating, while restraining the emergence of drug-resistant variant viruses.