P. vivax microhaplotype deep sequencing assays v1

This SOP is adapted from a high throughput rhAmpSeq library preparation protocol by integrated DNA technologies (IDT) and has been optimized at the Australian Genomic Research Facility. The SOP describes the laboratory procedures for amplifying a panel of 98 Plasmodium vivax markers, using high-throughput multiplex PCR, for downstream genotyping by sequencing on the Illumina platform. The 98 markers include a panel of 93 microhaplotype loci (loci comprising of 3 or more globally high diversity SNPs) distributed across the P. vivax genome, as well as one Plasmodium species confirmation marker and 4 putative drug resistance markers. Further information on potential use cases for P. vivax microhaplotype genotyping, including recurrence classification, characterization of infection diversity, and spatiotemporal monitoring, can be found in Siegel et al [1].