Applying novel tools to parse Plasmodium vivax relapses in clinical trials

About This Grant

ABSTRACT Relapsing malaria species, such as Plasmodium vivax (Pv), remain major challenges to malaria elimination due to their propensity to form hypnozoites that cause chronic latent infection in the liver and give rise to frequent relapses. Pv relapses cause significant morbidity and mortality worldwide. Despite advances, genotyping to distinguish relapses from re-infections remains fraught, limiting the evaluation of anti-relapse interventions like primaquine and tafenoquine. This study applies novel genomic and bioinformatic tools to clinical trial data in Southeast Asia and introduces innovative approaches to parse Pv relapse outcomes. Our approach leverages molecular inversion probes (MIPs) to deeply sequence Pv infections, capturing the diversity across the vivax genome and complexity within infected individuals. We will use Tapestry, a new bioinformatics tool, to enable haplotype reconstruction and identity-by-descent (IBD) analysis within and across multiclonal infections. Finally, Bayesian statistical models will refine relapse predictions by integrating genetic complexity, IBD relatedness, and clinical factors. Aim 1 investigates primaquine failures observed in a Thai Pv relapse trial (NCT04228315). Suspected relapses occurred in four individuals despite chloroquine and primaquine treatment; host CYP2D6 polymorphisms were ruled out. We hypothesize that high initial hypnozoite burden drove these relapses. We will generate evidence for this via genomic analyses that enhance detection of circulating parasite variants and assess infection complexity as a proxy for liver-stage hypnozoite burden. Aim 2 evaluates malaria elimination interventions in a Cambodian military cohort. Aim 2A tests whether rebound infections after cessation of monthly prophylaxis (MMP with dihydroartemisinin - piperaquine and weekly primaquine) represent relapses due to high hypnozoite burden, as reflected by genetic complexity. Aim 2B classifies Pv recurrences in soldiers wearing permethrin-treated uniforms to estimate vector-prevention efficacy. Results will differentiate relapse from reinfection and recalibrate protective efficacy estimates. In summary, this proposal seeks to address a fundamental gap in our ability to use genotyping to evaluate anti-relapse and other interventions that are needed to decrease the global burden of Plasmodium vivax. Expected outcomes include refined relapse classification, improved understanding of hypnozoite dynamics, and insights into anti-vivax interventions across diverse settings. Future directions include scaling our approach to larger cohort studies across diverse settings to improve classification of relapse outcomes.