Partner study description

This project describes the genomic component within the broader vivaxGEN initiative. The vivaxGEN network comprises researchers and other key stakeholders from across the globe with a shared aim to develop novel molecular surveillance tools for P. vivax that provide clinically relevant information on emerging parasite adaptations, transmission dynamics, the major routes of parasite spread within and across borders, and the impact of local treatment policies on the dormant liver-stage reservoir. Researchers involved in this collaboration aim to identify markers through several separate genome-wide studies at each of the 14 sites/countries involved. Current studies include a multicenter collaborative effort to detect geographic markers for identifying and mapping imported P. vivax infections. Another study is underway to identify microhaplotype-based markers across the P. vivax genome that can be used as a parsimonious approach to characterize the identity by descent (IBD) between infection pairs. These and other markers will then be applied as a ‘genetic barcode’ that can be used at high sample throughput on a broad range of sample sources including DNA derived from blood spots on filter paper. To find out more about our work, visit the vivaxGEN site (http://menzies.edu.au/vivaxGEN). For interests in collaborating on any of the above projects, contact us at the emails below.

Publications

• 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
• 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
• 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
• Genomic analysis of local variation and recent evolution in Plasmodium vivax
  Pearson et al
  Nature Genetics, 2016; 48 959-964
  10.1038/ng.3599