PvGAP: Development of a Globally Applicable, Highly Multiplexed Microhaplotype Amplicon Panel for Plasmodium vivax

Plasmodium vivax malaria research has yet to fully benefit from advances in genomic surveillance that have revolutionized P. falciparum epidemiology. Closing this gap will enable monitoring the spread of drug resistance, classifying infections as local or imported, and distinguishing reinfection, recrudescence, and relapse. To achieve these objectives, microhaplotype marker panels that allow powerful genotyping of polyclonal infections are needed.

We designed a globally applicable amplicon panel for P. vivax (PvGAP), selecting targets based on both genetic diversity and distance to maximize discriminatory capability between geographic regions. We evaluated this panel with field samples from Ethiopia and in silico using whole genomes from the MalariaGEN Pv4 database.

PvGAP has 80 high-diversity targets suitable for population genomics and 8 targets of epidemiological interest, such as putative markers of drug resistance. We demonstrate robust amplification with field data and competitive accuracy for relatedness inference in 3 disparate geographic regions.

PvGAP joins existing P. vivax panels as a cost-effective and practical option for genomic epidemiology of this neglected disease. It will support drug resistance surveillance and discrimination of local and imported cases, and it may aid in separating reinfection, recrudescence, and relapse in therapeutic efficacy studies, all critical needs of National Malaria Control Programs.