Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites

Dengue virus (DENV) challenges vaccine design due to antibody-dependent enhancement (ADE) and evidence suggests that Zika virus (ZIKV) experiences ADE with DENV and West Nile virus (WNV) antibodies. Thus, multiple flaviviruses must be considered when developing novel therapies against ZIKV. We analyzed 42 flavivirus polyproteins in their evolutionary context to identify motifs conserved in sequence with low real-time and evolutionary conformational flexibility, thought to be fitness-critical sites. We also analyzed evolutionary rate-shifts between clades for insight on vector specificity. For mosquito-borne flaviviruses, two conserved motifs were identified within the RNA-dependent RNA polymerase (RdRP), critical for flavivirus genome replication. Clade-specific motifs were identified for the ZIKV+DENV and WNV clades, many of which were also in RdRP. Six sites in motifs for WNV experienced significant evolutionary rate-shifts, suggesting their importance for functional divergence. Overall, some of these motifs are prime candidates as broadly neutralizing antiviral drug targets across different mosquito-borne flaviviruses.