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

MalariaGEN, Ishag Adam, Mohammad Shafiul Alam, Sisay Alemu, Chanaki Amaratunga, Roberto Amato, Voahangy Andrianaranjaka, Nicholas M. Anstey, Abraham Aseffa, Elizabeth Ashley, Ashenafi Assefa, Sarah Auburn, Bridget E. Barber, Alyssa Barry, Dhelio Batista Pereira, Jun Cao, Nguyen Hoang Chau, Kesinee Chotivanich, Cindy Chu, Arjen M. DondorpEleanor Drury, Diego F. Echeverry, Berhanu Erko, Fe Espino, Rick Fairhurst, Abdul Faiz, María Fernanda Villegas, Qi Gao, Lemu Golassa, Sonia Goncalves, Matthew J. Grigg, Yaghoob Hamedi, Tran Tinh Hien, Ye Htut, Kimberly J. Johnson, Nadira Karunaweera, Wasif Khan, Srivicha Krudsood, Dominic P. Kwiatkowski, Marcus Lacerda, Benedikt Ley, Pharath Lim, Yaobao Liu, Alejandro Llanos-Cuentas, Chanthap Lon, Tatiana Lopera-Mesa, Jutta Marfurt, Pascal Michon, Olivo Miotto, Rezika Mohammed, Ivo Mueller, Chayadol Namaik-larp, Paul N. Newton, Thuy Nhien Nguyen, Francois Nosten, Rintis Noviyanti, Zuleima Pava, Richard D. Pearson, Beyene Petros, Aung P. Phyo, Ric N. Price, Sasithon Pukrittayakamee, Awab Ghulam Rahim, Milijaona Randrianarivelojosia, Julian C. Rayner, Angela Rumaseb, Sasha V. Siegel, Victoria J. Simpson, Kamala Thriemer, Alberto Tobon-Castano, Hidayat Trimarsanto, Marcelo Urbano Ferreira, Ivan D. Vélez, Sonam Wangchuk, Thomas E. Wellems, Nicholas J. White, Timothy William, Maria F. Yasnot, Daniel Yilma

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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.

Original languageEnglish
Article number136
Pages (from-to)1-22
Number of pages22
JournalWellcome Open Research
Publication statusPublished - 2022


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