The role of conformational epitopes in the evolutionary divergence of enterovirus D68 clades: A bioinformatics-based study

Enterovirus D68 (EV-D68), as one of the major pathogens of paediatric respiratory disease, has been widely spread in the population in recent years. As the basis of virus antigenicity, antigenic epitopes are essential to monitoring the transformation of virus antigenicity. However, there is a lack of systematic studies on the antigenic epitopes of EV-D68. In this study, a bioinformatics-based prediction algorithm for human enteroviruses was used to predict the conformational epitopes of EV-D68. The prediction results showed that the conformational epitopes of EV-D68 were clustered into three sites: site 1, site 2, and site 3. Site 1 was located in the "north rim" region of the canyon near the fivefold axis; site 2 was located in the "puff" region near the twofold axis; and site 3 consisted of two parts, one in the "knob" region on the south rim of the canyon and the other in the threefold axis region. The predicted epitopes overlapped highly with the binding regions of four reported monoclonal antibodies (mAbs), indicating that the predictions were highly reliable. Phylogenetic analysis showed that amino acid mutations in the epitopes of the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop played a crucial role in the evolutionary divergence of EV-D68 clades/subclades and epidemics. This finding indicated that the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop were the most important epitopes of EV-D68. Research on the epitopes of EV-D68 will contribute to outbreak surveillance and to the development of diagnostic reagents and recombinant vaccines.