Introduction

The P. vivax Genome Variation project aims to understand genome diversity of this parasite that, because it can remain dormant in the liver for years, is particularly hard to eliminate using conventional malaria control measures.

Objectives & Coordination

Plasmodium vivax is a major cause of illness in many tropical regions, particularly South America and much of Asia. The biology of P. vivax parasites complicates efforts to study its genome: the parasites don’t grow well in culture, hampering in vitro studies, and infections are characterised by a lower density of parasites in the blood, making it difficult to isolate sufficient parasite DNA for sequencing.

The P. vivax Genome Variation project is coordinated by the MalariaGEN Resource Centre and connects multiple research groups which are primarily concerned with understanding the population genetics and identifying the genetic causes of antimalarial drug resistance in P. vivax — a major public health concern.

Our work is focused on three related objectives:

Building a catalogue of P. vivax genome variation

We aim to create a genome-wide catalogue of P. vivax polymorphisms generated by sequencing clinical samples from endemic countries, which we will then use to construct a high-resolution map of genome variation and population genetics. This resource will provide a foundation for genomic surveillance of P. vivax to guide malaria elimination.

Providing researchers with standardised genotype data on their samples

Our sequence data analysis pipeline provides researchers with high-quality genotype calls on their samples in a standardised format which enables reliable comparisons to be made with data from other studies and geographical locations.

Publishing global analyses of genome variation, population genetics and evolutionary selection

The data resources generated through this project will be valuable in addressing a range of scientific questions in addition to drug resistance. Although P. vivax causes much less mortality than P. falciparum, there is growing recognition that it can sometimes cause severe complications, raising the question of whether there are parasite genetic factors that cause some strains of P. vivax to be more virulent than others. There is also much interest in whether there are genetic types of parasite that can overcome the resistance to P. vivax infection possessed by African populations due to the Duffy negative blood group.

Sampling locations

Afghanistan, Bhutan, Brazil, Cambodia, China, India, Indonesia, Iran, Laos, Madagascar, Malaysia, Myanmar, Papua New Guinea, Sri Lanka, Thailand, Vietnam.

Data

The following data have been released by the P. vivax Genome Variation project:

Current

For partners

Resources for partners working on parasites

Partner studies

We work with investigators who are pursuing independent partner studies in a number of malaria-endemic countries. Click a link below to learn more about their work.

Publications

• An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
  MalariaGEN et. al
  Wellcome Open Research, 2022; 7 136
  10.12688/wellcomeopenres.17795.1
• Using deep learning to identify recent positive selection in malaria parasite sequence data
  Deelder et al.
  Malaria Journal, 2021; 20(1) 270
  10.1186/s12936-021-03788-x
• Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa
  Benavente et al.
  Nature Communications, 2021; 12(1) 3160
  10.1038/s41467-021-23422-3
• Population genomic evidence of Plasmodium vivax Southeast Asian origin
  Daron et al.
  Science Advances, 2021; 7(18) eabc3713
  10.1126/sciadv.abc3713
• Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia
  Abera D et al
  Malaria Journal, 2021; 20 129
  10.1186/s12936-021-03660-y
• Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes
  Ford et al.
  PLoS Neglected Tropical Diseases, 2020; 14(10) e0008234
  10.1371/journal.pntd.0008234
• Genetic diversity and neutral selection in Plasmodium vivax erythrocyte binding protein correlates with patient antigenicity
  Han et al.
  PLoS Neglected Tropical Diseases, 2020; 14(7) e0008202
  10.1371/journal.pntd.0008202
• Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain
  van Dorp et al.
  Molecular Biology and Evolution, 2020; 37(3) 773-785
  10.1093/molbev/msz264
• A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria
  Diez Benavente et al.
  PLoS Genetics, 2020; 16(2) e1008576
  10.1371/journal.pgen.1008576
• A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax
  Trimarsanto et al.
  bioRxiv, 2019; 776781
  10.1101/776781
• Genomic analysis of Plasmodium vivax in southern Ethiopia reveals selective pressures in multiple parasite mechanisms.
  Auburn et al.
  The Journal of Infectious Diseases, 2019; 220 1738-1749
  10.1093/infdis/jiz016
• Tafenoquine versus Primaquine to Prevent Relapse of Plasmodium vivax Malaria
  Llanos-Cuentas et al.
  New England Journal of Medicine , 2019; 380(3) 229-241
  10.1056/NEJMoa1802537
• Single-Dose Tafenoquine to Prevent Relapse of Plasmodium vivax Malaria
  Lacerda et al.
  New England Journal of Medicine, 2019; 380(3) 215-228
  10.1056/NEJMoa1710775
• Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics
  Auburn S, Benavente ED, et al.
  Nature Communications, 2018; 9 2585
  10.1038/s41467-018-04965-4
• Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
  Diez Benavente et al.
  PLoS One, 2017; 12(5) e0177134
  10.1371/journal.pone.0177134
• A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes
  Auburn et al.
  Wellcome Open Research, 2016; 1 4
  10.12688/wellcomeopenres.9876.1
• Genomic analysis reveals a common breakpoint in amplifications of the Plasmodium vivax multidrug resistance 1 locus in Thailand
  Auburn et al.
  The Journal of Infectious Diseases, 2016; 214 1235-1242
  10.1093/infdis/jiw323
• Independent origin and global distribution of distinct Plasmodium vivax Duffy Binding Protein gene duplications
  Hostetler et al.
  PLoS Neglected Tropical Diseases, 2016; 10(10) e0005091
  10.1371/journal.pntd.0005091
• Genomic analysis of local variation and recent evolution in Plasmodium vivax
  Pearson et al
  Nature Genetics, 2016; 48 959-964
  10.1038/ng.3599
• Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing
  Auburn et al.
  PLoS One, 2013; 8(1) e53160
  10.1371/journal.pone.0053160