Richard D. PearsonRoberto AmatoSarah AuburnOlivo MiottoJacob Almagro-GarciaChanaki AmaratungaSeila SuonSivanna MaoRintis NoviyantiHidayat TrimarsantoJutta MarfurtNicholas M. AnsteyTimothy WilliamMacIej F. BoniChristiane DolecekHien Tinh TranNicholas J. WhitePascal MichonPeter SibaLivingstone TavulGabrielle HarrisonAlyssa BarryIvo MuellerMarcelo U. FerreiraNadira KarunaweeraMilijaona RandrianarivelojosiaQi GaoChristina HubbartLee HartBen JefferyEleanor DruryDaniel MeadMihir KekreSusana CampinoMagnus ManskeVictoria J. CorneliusBronwyn MacInnisKirk A. RockettAlistair MilesJulian C. RaynerRick M. FairhurstFrancois NostenRic N. PriceDominic P. KwiatkowskiWellcome Trust Sanger InstituteWellcome Trust Centre for Human GeneticsMenzies School of Health ResearchMahidol UniversityNational Institute of Allergy and Infectious DiseasesNational Centre for Parasitology, Entomology and Malaria ControlSampov Meas Referral HospitalEijkman Institute for Molecular BiologyQueen Elizabeth HospitalOxford University Clinical Research UnitPapua New Guinea Institute of Medical ResearchDivine Word UniversityWalter and Eliza Hall Institute of Medical ResearchUniversity of MelbourneUniversidade de Sao Paulo - USPUniversity of Colombo Faculty of MedicineInstitut Pasteur de MadagascarMinistry of Health of People's Republic of ChinaNuffield Department of Clinical Medicine2018-12-112019-03-142018-12-112019-03-142016-08-01Nature Genetics. Vol.48, No.8 (2016), 959-96415461718106140362-s2.0-84971401229https://repository.li.mahidol.ac.th/handle/20.500.14594/42947© 2016 Nature America, Inc. All rights reserved. The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1038/ng.3599