Genomic Epidemiology of the Malaria Parasite Plasmodium falciparum: Implications for Whole-Organism Malaria Vaccine Development

Abstract

Whole-organism malaria vaccines have shown great promise in initial clinical trials against controlled human malaria infections (CHMI) with homologous P. falciparum strains. However, efficacy against heterologous CHMI and against natural infection is somewhat lower. While the reason for lower efficacy against non-vaccine strains is unknown, several knowledge gaps, if addressed, would assist in developing highly-efficacious whole-organism malaria vaccines. First, regions of the parasite genome responsible for protection have not been identified. Such identification could be achieved by comparing breakthrough P. falciparum infections in vaccinated individuals with the vaccine strain; however, it is not clear how best to genetically characterize breakthrough infections, in vaccinated individuals. Second, vaccine and challenge strains have not been characterized and compared at the genomic level to circulating strains from parasite populations in malaria endemic regions. Finally, a rigorous investigation of allele frequency fluctuations between temporally isolated parasite populations would help predict if such changes would affect vaccine efficacy. Using next- and third-generation sequencing technologies, new reference assemblies for whole-organism malaria vaccine and CHMI strains were generated, along with reference assemblies for 19 clinical isolates to use for improved read mapping and characterization of clinical P. falciparum isolates. Using a geographic-specific reference assembly improved the ability to characterize clinical isolates through increased read coverage, and so these references may be helpful to characterize breakthrough infections (particularly for studies in Southeast Asian populations). In addition, assemblies for vaccine and CHMI strains reveal thousands of variants between these parasites. CHMI strains also have variants which convey differences in immunological potential, thus confirming their appropriateness as heterologous CHMI strains. Vaccine and CHMI strains were also shown to representative of their respective geographic origins when compared to extant parasite populations from malaria endemic regions. Finally, we show that while there were fluctuations in allele frequencies between West and East African parasite populations over almost a decade, none affected the frequency of vaccine candidate alleles in a way that would meaningfully impact vaccine efficacy. These results will greatly assist in the interpretation of whole-organism malaria vaccine trials, and will pave the way for the design of next-generation whole-organism malaria vaccines.