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An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples.

null nullIshag AdamMohammad Shafiul AlamSisay AlemuChanaki AmaratungaRoberto AmatoVoahangy AndrianaranjakaNicholas M AnsteyAbraham AseffaElizabeth A AshleyAshenafi AssefaSarah AuburnBridget E BarberAlyssa BarryDhelio Batista PereiraJun CaoNguyen Hoang ChauKesinee ChotivanichCindy S ChuArjen M DondorpEleanor DruryDiego F EcheverryBerhanu ErkoFe Esperanza EspinoRick FairhurstMd Abul FaizMaría Fernanda VillegasQi GaoLemu GolassaSonia GoncalvesMatthew J GriggYaghoob HamediTran Tinh HienYe HtutKimberly J JohnsonNadira Darshani KarunaweeraWasif KhanSrivicha KrudsoodDominic P KwiatkowskiMarcus LacerdaBenedikt LeyPharath LimYaobao LiuAlejandro Llanos-CuentasChanthap LonTatiana Lopera-MesaJutta MarfurtPascal MichonOlivo MiottoRezika MohammedIvo MuellerChayadol Namaik-LarpPaul N NewtonThuy-Nhien NguyenFrancois H NostenRintis NoviyantiZuleima PavaRichard D PearsonBeyene PetrosAung Pyae PhyoRichard N PriceSasithon PukrittayakameeAwab Ghulam RahimMilijaona RandrianarivelojosiaJulian C RaynerAngela RumasebSasha V SiegelVictoria J SimpsonKamala ThriemerAlberto Tobon-CastanoHidayat TrimarsantoMarcelo Urbano FerreiraIvan D VélezSonam WangchukThomas E WellemsNicholas J WhiteTimothy WilliamMaria Fernanda Yasnot-AcostaDaniel Yilma
Published in: Wellcome open research (2022)
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr , dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
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