PvGAP: Development of a globally-applicable, highly-multiplexed microhaplotype amplicon panel for Plasmodium vivax

Plasmodium vivax malaria research has yet to fully benefit from the advances in genomic surveillance that have revolutionized P. falciparum epidemiology. Closing this gap is critical because genomic tools are necessary to achieve certain malaria control program objectives: 1) they allow monitoring of the spread of drug resistance and thus selection of therapeutic drugs based on local prevalence of resistance; 2) they permit classification of infections as local or imported, enabling more precise targeting of control resources; and 3) they can distinguish reinfection, recrudescence, and relapse, a necessity for conducting therapeutic efficacy studies. To achieve these objectives, microhaplotype marker panels that allow powerful genotyping of polyclonal infections are needed. A handful of such panels have been published for P. vivax , but they may be limited to certain geographic areas. We here present a Globally-applicable Amplicon Panel for P. vivax (PvGAP) designed to maximize discriminatory capability between geographic regions. PvGAP has 80 high diversity targets suitable for population genomics and eight targets of specific epidemiological interest, such as putative markers of drug resistance. We demonstrate PvGAP achieves robust amplification with field data and that it clearly distinguishes samples from different locations both at a regional and global scale. PvGAP is ready for broad application that can support powerful and comprehensive studies of malaria genomic epidemiology.