Dengue antigenic relationships predict evolutionary dynamics

Abstract

Dengue virus (DENV) exists as four genetically distinct serotypes, each of which is historically assumed to be antigenically uniform. However, recent analyses suggest that antigenic heterogeneity may exist within each serotype, but its source, extent and impact remain unclear. Here, we construct a sequence-based model to directly map antigenic change to underlying genetic divergence. We identify 49 specific substitutions and four colinear substitution clusters that contribute to dengue antigenic diversity. We report moderate antigenic diversity within each serotype, resulting in variation in genotype-specific patterns of heterotypic cross-neutralization. We also quantify the impact of this antigenic heterogeneity on real-world DENV population dynamics. We find that antigenic fitness mediates fluctuations in DENV clade frequencies, although this appears to be primarily explained by coarser serotype-level antigenic differences. These results provide a more nuanced understanding of dengue antigenic evolution, with important ramifications for vaccine design and epidemic preparedness. Author SummaryDengue virus (DENV), the causative agent of dengue hemorrhagic fever, exists as four genetically distinct serotypes, DENV1 to DENV4. These serotypes are antigenically distinct: symptomatic reinfection with a homotypic virus is very rare, while reinfection with a heterotypic virus is sometimes associated with severe disease. Until recently, it has been assumed that viruses within each serotype are antigenically uniform. However, specific genotypes within each serotype have been anecdotally associated with varying severity of patient outcomes and epidemic magnitude. One hypothesis is that each serotype contains overlooked, meaningful antigenic diversity. While antigenic cartography conducted on neutralization titers suggests that heterogeneity may exist within each serotype, its source, extent and impact is unclear. Here, we analyze a previously published titer dataset to quantify and characterize the extent of DENV intraserotype antigenic diversity. We map antigenic changes to specific mutations in E, the dengue envelope protein, and interpolate across the alignment to estimate the antigenic distance between pairs of viruses based on their genetic differences. We identify 49 specific substitutions and four colinear substitution clusters that contribute to dengue antigenic evolution. We find that DENV antigenic divergence is tightly coupled to DENV genetic divergence, and is likely a gradual, ongoing process. We report modest but significant antigenic diversity within each serotype of DENV, which may have important ramifications for vaccine design. To understand the impact of this antigenic heterogeneity on real-world DENV population dynamics, we also quantify the extent to which population immunity-accumulated through recent circulation of antigenically similar genotypes-determines the success and decline of DENV clades in a hyperendemic population. We find that antigenic fitness is a key determinant of DENV population turno...