High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions

Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates including aseptic meningitis, encephalitis, neonatal sepsis and inflammatory muscle disease, among others. Over 100 serotypes have been described to date but except for the EV-A71, there are no available vaccines or therapeutics against NPEVs. Efforts towards rationally designed pan-NPEV vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses. Towards this goal, we tested if electron-microscopy-based polyclonal epitope mapping (EMPEM), a method where structural analysis is performed using serum-derived polyclonal antibodies (pAbs), can be applied to an NPEV. EMPEM was performed on immune complexes featuring CV-A21 viral particles and CV-A21-specific pAbs isolated from mice. Notably, this is the first example of structural analysis of polyclonal immune complexes comprising whole virions. We introduce a data processing workflow that allows reconstruction of different pAbs at near-atomic resolution. The analysis resulted in identification of several antibodies targeting two immunodominant epitopes, near the 3-fold and 5-fold axis of symmetry; the latter overlapping with the receptor binding site. These results demonstrate that EMPEM can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes.