Genomic Analyses Reveal the Common Occurrence and Complexity of Plasmodium vivax Relapses in Cambodia

Abstract

Plasmodium vivax parasites have a unique dormant stage that can cause relapses weeks or months after the initial infection. These dormant parasites are among the main challenges of vivax malaria control as they constitute a reservoir that is difficult to eliminate. Since field studies are confounded by reinfections and possible recrudescence of drug-resistant parasites, most analyses of P. vivax relapses have focused on travelers returning from regions of malaria endemicity. However, it is not clear whether these individuals accurately recapitulate the relapse patterns of repeatedly infected individuals residing in areas of endemicity. Here, we present analyses of vivax malaria patients enrolled in a tightly controlled field study in Cambodia. After antimalarial drug treatment was administered, we relocated 20 individuals to a nontransmission area and followed them for 60 days, with blood collection performed every second day. Our analyses reveal that 60% of the patients relapsed during the monitoring period. Using whole-genome sequencing and high-throughput genotyping, we showed that relapses in Cambodia are often polyclonal and that the relapsing parasites harbor various degrees of relatedness to the parasites present in the initial infection. Our analyses also showed that clone populations differed dynamically, with new clones emerging during the course of the relapsing infections. Overall, our study data show that it is possible to investigate the patterns, dynamics, and diversity of P. vivax relapses of individuals living in a region of malaria endemicity and reveal that P. vivax relapses are much more pervasive and complex than previously considered. (This study has been registered at ClinicalTrials.gov under registration no. NCT02118090.)

Genetic diversity in twoPlasmodium vivaxprotein ligands for reticulocyte invasion

“…One of the limitations in this work is that the majority of patients likely carry multiple clones of P. vivax [45,46]. By using a qPCR approach as we did, we are aware that the PvDBP and PvEBP estimated gene copy number reflects the major clone contained in each isolate Next generation sequencing such as single cell DNA sequencing or even droplet PCR approach should be able to overcome this issue and assess CNV for each clone.…”

Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

“…To provide a worldwide comparative study of the P. vivax genetic diversity, population structure and evolution, we performed a large literature search to identify previously published genomic data set. We identified and collected fastq files from 1,134 P. vivax isolates obtained from the following 12 different bioprojects: PRJEB10888 ( 14 ), PRJEB2140 ( 12 ), PRJNA175266 ( 54 ), PRJNA240356 ( 13 ), PRJNA240452, PRJNA240531, PRJNA271480 ( 13 ), PRJNA284437 ( 55 ), PRJNA350554 ( 56 ), PRJNA432819 ( 57 ), PRJNA432819 ( 58 ), PRJNA65119 ( 59 ). In addition, 17 P. vivax-like sequenced genomes from Cameroon, Ivory Coast and Gabon were collected from two different bioprojects (PRJNA474492 and PRJEB2579) ( 23, 25 ).…”

Whole Genome Sequencing ofPlasmodium vivaxIsolates Reveals Frequent Sequence and Structural Polymorphisms in Erythrocyte Binding Genes

“…High heterozygosity was also observed in P. vivax populations from Qatar, India, and Sudan (average H E = 0.78; 62), with only slight differentiation from P. vivax in Ethiopia ( F ST = 0.19) [102]. Frequent inbreeding among dominant clones [92, 95] and strong selective pressures especially in relapse infections [19, 20, 102, 103] may also contribute to close genetic relatedness between and within populations. Thus, in this study, it is not surprising to detect a high level of parasite gene flow among the study sites at a small geographical scale, despite the limited number of samples.…”