Plasmodium vivax within-country SNP panel for Vietnam

Genetic surveillance tools are increasingly recognized for their potential to address specific elimination challenges for the malaria parasite Plasmodium vivax. To better support national malaria control program priorities, use cases have been defined creating scenarios where genetic epidemiology can help inform decision-making, aligning multiple scientific fields to develop and best implement new technologies.Genetic surveillance of malaria parasites has traditionally been approached with microsatellite markers that are not under evolutionary pressure. These have been popular markers to study connectivity and transmission intensity, but they are difficult to standardize and compare between datasets. SNP barcodes designed for finger printing parasite isolates, connectivity analysis and characterizing border malaria and imported infections have been designed.However, these barcodes were often designed at a global level and not suited to study subtle patterns on a smaller geographical scale such as within-country, which is the level these tools would normally be implemented. Therefore, we developed a within-country SNP barcode for routine Plasmodium vivax population analysis in Vietnam using P. vivax genomes. We have 2 sets of genomes, the first was used to design the within-country barcode, and the second to validate the barcode (in addition to online available genomes) and the assay.The designed 42-SNP barcode was incorporated in a highly multiplexed NGS protocol, Pv AmpliSeq, and validated using isolates from travelers and migrants and surveillance sites in Vietnam, the data of which is deposited as a separate study.