Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis

Abstract

The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA–protein interactions and dissection of virus assembly on the basis of RNA nucleation.

Structure of deformed wing virus, a major honey bee pathogen

“…3B) (40). Reminiscent of the RNAprotein interactions in DWV are structured RNA oligonucleotides that have been recently described in the parechoviruses HPeV-1, HPeV-3, and Ljungan virus, where they also mediate contacts among capsid proteins from different protomers (21,41,42). The conservation of the RNA-binding residues among some of the honey bee iflaviruses, together with the near-complete occupancy of the RNA, indicates that the RNA-capsid binding might play a role in virion stability.…”

2.8 Å resolution cryo-EM structure of human parechovirus 3 in complex with Fab from a neutralizing antibody

“…The HPeV3 virion contains ∼7.4 kb of mostly unstructured single-stranded RNA genome. In the assembled particle, roughly 25% of the RNA adopts a defined conformation near the inner capsid surface, lining symmetry-related sites directly beneath the icosahedral five-fold vertices (19). For parechoviruses, detailed structural analysis of genome-capsid interactions has only been carried out for HPeV1 (21).…”

“…To date, no effective treatments for HPeV3 infection are available, highlighting the urgent need for a greater understanding of the structural and molecular basis for HPeV3 neutralization, especially as epidemics are likely to continue (2, 16-18). The HPeV3 virion is composed of 60 copies of the three structural proteins (VP0, VP1, and VP3) that fit together to form a 28-nm-diameter icosahedral shell around the ∼7.3 kb single-stranded RNA viral genome (19). The genome encodes a single polyprotein that during infection is subsequently cleaved into all the essential capsid components and replication proteins (2A, 2B, 2C, 3A, 3B, 3C and 3D) (20).…”

Human picornaviruses associated with neurological diseases and their neutralization by antibodies

“…There are three HPeV structural proteins: VP0, VP1 and VP3. In parechoviruses VP0 is not processed to VP2 and VP4 [170,171]. Three neutralizing epitopes are known on HPeV-1.…”

“…Whereas antisera generated against the HPeV-1 VP0 peptide were not tested for HPeV-3 neutralization, two other monoclonal antibodies did not cross-react with HPeV-3 [169,174]. Only a non-neutralizing epitope has been described for HPeV-3 [170].…”