Molecular epidemiology and population genomics of Plasmodium knowlesi

Genomic complexity of parasites and vectors challenges malaria control in Southeast Asia

Southeast Asia is a uniquely complex region of malaria transmission that maintains an astounding level of species diversity among potential malaria vectors and also generates drug-resistant and quickly diverging populations of malaria parasites. All five human malaria species circulate in Southeast Asia with over 50 Anopheles species that vary in their ability to transmit these pathogens. The intricate relationships of these parasites and vectors are not well-understood. Human activity in Southeast Asian countries has created an increasingly fragmented landscape, bringing humans and mosquitoes into more frequent contact, sustaining malaria transmission in a region where few control tools are effective. Genomic shifts at the species, population, and individual level in parasites and vectors introduce variation that has produced drug- and insecticide resistance. The goal of this review is to highlight genomic studies of Southeast Asian malaria parasites and vectors that demonstrate how diversity in these organisms presents unique challenges and opportunities for global malaria control and eradication efforts.

Population genomics in neglected malaria parasites

Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.