Understanding Plasmodium vivax recurrent infections using an amplicon deep sequencing assay, PvAmpSeq, identity-by-descent and model-based classification.

Plasmodium vivax infections are characterised by recurrent bouts of blood-stage parasitaemia. Understanding the genetic relatedness of recurrences can distinguish whether these are caused by relapse, reinfection, or recrudescence, which is critical to understand treatment efficacy and transmission dynamics. We developed PvAmpseq, an amplicon sequencing assay targeting 11 SNP-rich regions of the P. vivax genome. PvAmpSeq was validated on field isolates from a clinical trial in the Solomon Islands and a longitudinal observational cohort in Peru, and statistical models were applied for genetic classification of infection pairs. In the Solomon Islands trial, where participants received antimalarials at baseline, half of the recurrent infections were caused by parasites with >50% relatedness to the baseline infection, with statistical models classifying 25% and 25% as probable relapses and recrudescences, respectively. In the Peruvian cohort, 26% of recurrences were likely relapses. PvAmpSeq provides high-resolution genotyping to characterise P. vivax recurrences, offering insights into transmission and treatment outcomes.