Unlocking the Global Antigenic Diversity and Balancing Selection ofPlasmodium falciparum

AbstractInvestigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies onPlasmodium falciparumantigen diversity have focused on well-known vaccine candidates while the diversity of several others has never been studied. Here we provide an overview of the diversity and population structure of leading vaccine candidate antigens ofP. falciparumusing the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. We developed a stringent variant calling pipeline to extract high quality antigen gene sequences from the global dataset and a new R-package namedVaxPackto streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens includingcsp,trap,eba175,ama1,rh5, andCelTOS. We found that current malaria vaccine formulations are based on rare variants and thus may have limited efficacy. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptations to different human host or mosquito vector populations. This study provides an essential framework for the diversity ofP. falciparumantigens for inclusion in the design of the next generation of malaria vaccines.Author SummaryHighly effective malaria vaccines are important for the sustainable elimination of malaria. However, the diversity of parasite antigens targeted by malaria vaccines has been largely overlooked, with most vaccine formulations based only on a single antigen variant. Failure to accommodate this diversity may result in vaccines only being effective against vaccine-like variants, resulting in limited protective efficacy. Investigation of the diversity of genes encoding parasite antigens can help prioritize and validate them as vaccine candidates as well as to identify the most common variants for inclusion in the next generation of malaria vaccines. Here we measure the diversity of 23 vaccine antigens ofPlasmodium falciparum, using the publicly available MalariaGEN Pf3K (version 5.1) resource comprising more than 2600 genomes from 15 malaria endemic countries. We found that variants found in current vaccine formulations are rare and thus may target only a small proportion of circulating malaria parasite strains. Variation in intensity of immune selection in parasites from different geographic areas suggests adaptation to different human host or vector populations. This study provides an essential framework for the design of the next generation of malaria vaccines, in addition to providing novel insights into malaria biology.