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

MalariaGEN , Adam I 1 , Alam MS 2 , Alemu S 3 , Amaratunga C 4 , Amato R 5 Show all authors , Andrianaranjaka V 6 , Anstey NM 7 , Aseffa A 3 , Ashley E 8 , Assefa A 9 , Auburn S 7 , Barber BE 10 , Barry A 11 , Batista Pereira D 12 , Cao J 13 , Chau NH 14 , Chotivanich K 15 , Chu C 16 , Dondorp AM 17 , Drury E 5 , Echeverry DF 18 , Erko B 19 , Espino F 20 , Fairhurst R 21 , Faiz A 22 , Fernanda Villegas M 23 , Gao Q 13 , Golassa L 19 , Goncalves S 5 , Grigg MJ 7 , Hamedi Y 24 , Hien TT 14 , Htut Y 25 , Johnson KJ 5 , Karunaweera N 26 , Khan W 2 , Krudsood S 15 , Kwiatkowski DP 5 , Lacerda M 27 , Ley B 7 , Lim P 4 , Liu Y 13 , Llanos-Cuentas A 28 , Lon C 29 , Lopera-Mesa T 30 , Marfurt J 7 , Michon P 31 , Miotto O 5 , Mohammed R 32 , Mueller I 11 , Namaik-Larp C 33 , Newton PN 8 , Nguyen TN 34 , Nosten F 34 , Noviyanti R 35 , Pava Z 36 , Pearson RD 5 , Petros B 37 , Phyo AP 17 , Price RN 7 , Pukrittayakamee S 15 , Rahim AG 38 , Randrianarivelojosia M 39 , Rayner JC 40 , Rumaseb A 7 , Siegel SV 5 , Simpson VJ 5 , Thriemer K 7 , Tobon-Castano A 30 , Trimarsanto H 35 , Urbano Ferreira M 41 , Vélez ID 42 , Wangchuk S 43 , Wellems TE 4 , White NJ 34 , William T 44 , Yasnot MF 45 , Yilma D 46

Affiliations 

  • 1 Faculty of Medicine, University of Khartoum, Khartoum, Sudan
  • 2 Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
  • 3 Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
  • 4 National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
  • 5 Wellcome Sanger Institute, Hinxton, UK
  • 6 Université d'Antananarivo, Antananarivo, Madagascar
  • 7 Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
  • 8 Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
  • 9 Ethiopian Public Health Institute, Addis Ababa, Ethiopia
  • 10 Menzies School of Health Research, Darwin, Australia
  • 11 Walter and Eliza Hall Institute, Parkville, Australia
  • 12 Centro de Pesquisa em Medicina Tropical de Rondônia, Porto Velho, Brazil
  • 13 National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
  • 14 Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
  • 15 Mahidol University, Bangkok, Thailand
  • 16 Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
  • 17 Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
  • 18 Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
  • 19 Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
  • 20 Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
  • 21 National Institutes of Health (NIH), Bethesda, USA
  • 22 Dev Care Foundation, Dhaka, Bangladesh
  • 23 Centro de Investigaciones Clinicas, Cali, Colombia
  • 24 Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
  • 25 Department of Medical Research, Yangon, Myanmar
  • 26 University of Colombo, Colombo, Sri Lanka
  • 27 Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil
  • 28 Cayetano Heredia University, Lima, Peru
  • 29 National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
  • 30 Universidad de Antioquia, Medellin, Colombia
  • 31 National University of Vanuatu, Port-Vila, Vanuatu
  • 32 Department of Internal Medicine, University of Gondar, Gondar, Ethiopia
  • 33 Umphang Hospital, Tak, Thailand
  • 34 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
  • 35 Eijkman Institute for Molecular Biology, Jakarta, Indonesia
  • 36 Centro Internacionale de Entrenamiento e Investigaciones Medicas, Cali, Colombia
  • 37 Addis Ababa University, Addis Ababa, Ethiopia
  • 38 Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan
  • 39 Institut Pasteur de Madagascar, Antananarivo, Madagascar
  • 40 Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
  • 41 Universidade de São Paulo, São Paulo, Brazil
  • 42 University of Antioquia, Medellin, Colombia
  • 43 Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
  • 44 Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
  • 45 Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
  • 46 Jimma University, Jimma, Ethiopia
Wellcome Open Res, 2022;7:136.
PMID: 35651694 DOI: 10.12688/wellcomeopenres.17795.1

Abstract

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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