Evidence of a novel viral membrane fusion mechanism shared by the Hepaci, Pegi and Pestiviruses

Abstract Enveloped viruses encode specialised glycoproteins that mediate fusion of viral and host membranes. Discovery and understanding of the molecular mechanisms of fusion has been achieved through structural analyses of glycoproteins from many different viruses, and yet the fusion mechanisms of some viral genera remain unknown. We have employed systematic genome annotation and AlphaFold modelling to predict the structures of the E1E2 glycoproteins from sixty viral species in the Hepaci, Pegi and Pestivirus genera. Whilst the predicted structure of E2 varied widely, E1 exhibited a very consistent fold across genera, despite little or no homology at the sequence level. Critically, the structure of E1 is unlike any other known viral glycoprotein. This is the first evidence that the Hepaci, Pegi and Pestiviruses possess a common and novel membrane fusion mechanism. Comparison of E1E2 models from various species reveals recurrent features that are likely to be mechanistically important and sheds light on the evolution of membrane fusion in these viral genera. These findings provide new fundamental understanding of viral membrane fusion and are relevant to structure-guided vaccinology.