Extreme Genetic Diversity and Signatures of Balancing Selection in Plasmodium vivax Blood-Stage Antigens

Abstract

BACKGROUND: Knowledge of the genetic diversity of Plasmodium vivax antigen vaccine candidates can offer valuable insights into antigens targeted by host immunity and their utility as vaccine candidates. We previously catalogued the genetic diversity of DBP, MSP1 and members of the RBP family. Here we report the diversity of 14 additional P. vivax vaccine candidates to identify polymorphic domains and immune selection, to guide selection of alleles for vaccine development. METHODS: A total of 289 of 353 publicly available P. vivax whole genome sequences (WGS) from Asia, the Americas, and Oceania passed a stringent variant-calling pipeline. Measures of diversity and balancing selection were calculated both across linear gene sequences and three-dimensional (3D) proteins. RESULTS: Blood-stage antigens AMA1, CyRPA, RBP1A, and P41, exhibited high genetic diversity and signatures of balancing selection on both linear and 3D structures. These signatures were consistent across all endemic regions, suggesting these polymorphic loci are under immune selection. In contrast, CSP, TRAP, MSP4, MSP9, MSP10, GAMA, S12, ARP, S25, and S28 antigens showed low to intermediate genetic diversity and variable patterns among countries. Haplotype networks identified common variants that may represent antigenically distinct clusters. Importantly, sequences from the vaccine strain Sal-1 have extremely low global frequencies. CONCLUSIONS: AMA1, CyRPA, RBP1A and P41 are under strong immune selection, whilst other antigens show limited diversity. Current vaccine formulations based on Sal-1 may have limited efficacy. Our results provide a framework for vaccine developers to select more common variants.