Partner study description

Ric Price, Rintis Noviyanti and Francois Nosten are the principal investigators in a genome-wide study that aims to characterise the molecular profile of drug resistance-conferring variants in Thai and Indonesian parasite populations. The study entails genome-wide scans to identify novel resistance variants as well as characterising known variants in P. falciparum and P. vivax field isolates with ex vivo-determined drug sensitivity profiles for a range of antimalarial drugs. Samples are contributed by consenting patients attending local health centres and hospitals in Indonesia and Thailand. These studies are coordinated by Sarah Auburn and Jutta Marfurt.

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
• 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
• 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
• 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