Designing Next Generation Genomics and Serological Tools for Surveillance of Plasmodium vivax Malaria to Guide Elimination Efforts in Southeast Asia

Abstract

Malaria is a major global health problem caused by mosquito-borne, protozoan parasites belonging to the genus Plasmodium. Plasmodium vivax, the human malaria parasite with the widest global distribution, accounts for majority of the total malaria cases outside sub-Saharan Africa. The inability to establish long term in vitro culture system and low parasite densities, combined with high levels of human genomic DNA isolated from patient samples with P. vivax infections, makes it difficult to obtain sufficient amounts of parasite DNA for whole genome sequencing (WGS). New, reliable, highly sensitive and specific methods are needed to produce high quality P. vivax WGS data. Genome-wide analyses of the parasite, using WGS, have the potential to improve our understanding of parasite population dynamics and help identifying locations that serve as possible transmission sources and sinks. Additionally, protein microarrays that can simultaneously measure human antibody responses to a large number of Plasmodium antigens have the potential to identify P. vivax specific biomarkers to detect not only current but also past malaria infections, providing a more sensitive surveillance tool for identifying human populations at risk. To address these needs, using Roche/NimbleGen SeqCap EZ whole genome capture technology, high quality WGS data was generated from P. vivax clinical samples collected from the China-Myanmar border. This new genome-wide data along with publicly available WGS from circulating isolates in Southeast Asia were utilized to characterize parasite genetic diversity and relatedness, population structure, complexity of infection, and distinguish locally transmitted infections from imported P. vivax infections revealing clonal parasite population on the China-Myanmar border. Using protein microarray analyses, several P. vivax specific serologic markers during active infection were identified that may serve as useful biomarkers of current or recent P. vivax infection supporting the possibility of serology as a tool for estimating species-specific malaria exposure to P. vivax in heterogeneous malaria transmission settings. The combination of next generation tools attempted to be designed as part of this dissertation will help improve the understanding of the genomic epidemiology and estimates of transmission patterns of this human malaria parasite, thus, guiding rational P. vivax malaria control and elimination policies in Southeast Asia.