An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
Issued Date
2022-01-01
Resource Type
eISSN
2398502X
Scopus ID
2-s2.0-85131082443
Journal Title
Wellcome Open Research
Volume
7
Rights Holder(s)
SCOPUS
Bibliographic Citation
Wellcome Open Research Vol.7 (2022)
Suggested Citation
Adam I., Alam M.S., Alemu S., Amaratunga C., Amato R., Andrianaranjaka V., Anstey N.M., Aseffa A., Ashley E., Assefa A., Auburn S., Barber B.E., Barry A., Batista Pereira D., Cao J., Chau N.H., Chotivanich K., Chu C., Dondorp A.M., Drury E., Echeverry D.F., Erko B., Espino F., Fairhurst R., Faiz A., Fernanda Villegas M., Gao Q., Golassa L., Goncalves S., Grigg M.J., Hamedi Y., Hien T.T., Htut Y., Johnson K.J., Karunaweera N., Khan W., Krudsood S., Kwiatkowski D.P., Lacerda M., Ley B., Lim P., Liu Y., Llanos-Cuentas A., Lon C., Lopera-Mesa T., Marfurt J., Michon P., Miotto O., Mohammed R., Mueller I., Namaik-larp C., Newton P.N., Nguyen T.N., Nosten F., Noviyanti R., Pava Z., Pearson R.D., Petros B., Phyo A.P., Price R.N., Pukrittayakamee S., Rahim A.G., Randrianarivelojosia M., Rayner J.C., Rumaseb A., Siegel S.V., Simpson V.J., Thriemer K., Tobon-Castano A., Trimarsanto H., Urbano Ferreira M., Vélez I.D., Wangchuk S., Wellems T.E., White N.J., William T., Yasnot M.F., Yilma D. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples. Wellcome Open Research Vol.7 (2022). doi:10.12688/wellcomeopenres.17795.1 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/83908
Title
An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
Author(s)
Adam I.
Alam M.S.
Alemu S.
Amaratunga C.
Amato R.
Andrianaranjaka V.
Anstey N.M.
Aseffa A.
Ashley E.
Assefa A.
Auburn S.
Barber B.E.
Barry A.
Batista Pereira D.
Cao J.
Chau N.H.
Chotivanich K.
Chu C.
Dondorp A.M.
Drury E.
Echeverry D.F.
Erko B.
Espino F.
Fairhurst R.
Faiz A.
Fernanda Villegas M.
Gao Q.
Golassa L.
Goncalves S.
Grigg M.J.
Hamedi Y.
Hien T.T.
Htut Y.
Johnson K.J.
Karunaweera N.
Khan W.
Krudsood S.
Kwiatkowski D.P.
Lacerda M.
Ley B.
Lim P.
Liu Y.
Llanos-Cuentas A.
Lon C.
Lopera-Mesa T.
Marfurt J.
Michon P.
Miotto O.
Mohammed R.
Mueller I.
Namaik-larp C.
Newton P.N.
Nguyen T.N.
Nosten F.
Noviyanti R.
Pava Z.
Pearson R.D.
Petros B.
Phyo A.P.
Price R.N.
Pukrittayakamee S.
Rahim A.G.
Randrianarivelojosia M.
Rayner J.C.
Rumaseb A.
Siegel S.V.
Simpson V.J.
Thriemer K.
Tobon-Castano A.
Trimarsanto H.
Urbano Ferreira M.
Vélez I.D.
Wangchuk S.
Wellems T.E.
White N.J.
William T.
Yasnot M.F.
Yilma D.
Alam M.S.
Alemu S.
Amaratunga C.
Amato R.
Andrianaranjaka V.
Anstey N.M.
Aseffa A.
Ashley E.
Assefa A.
Auburn S.
Barber B.E.
Barry A.
Batista Pereira D.
Cao J.
Chau N.H.
Chotivanich K.
Chu C.
Dondorp A.M.
Drury E.
Echeverry D.F.
Erko B.
Espino F.
Fairhurst R.
Faiz A.
Fernanda Villegas M.
Gao Q.
Golassa L.
Goncalves S.
Grigg M.J.
Hamedi Y.
Hien T.T.
Htut Y.
Johnson K.J.
Karunaweera N.
Khan W.
Krudsood S.
Kwiatkowski D.P.
Lacerda M.
Ley B.
Lim P.
Liu Y.
Llanos-Cuentas A.
Lon C.
Lopera-Mesa T.
Marfurt J.
Michon P.
Miotto O.
Mohammed R.
Mueller I.
Namaik-larp C.
Newton P.N.
Nguyen T.N.
Nosten F.
Noviyanti R.
Pava Z.
Pearson R.D.
Petros B.
Phyo A.P.
Price R.N.
Pukrittayakamee S.
Rahim A.G.
Randrianarivelojosia M.
Rayner J.C.
Rumaseb A.
Siegel S.V.
Simpson V.J.
Thriemer K.
Tobon-Castano A.
Trimarsanto H.
Urbano Ferreira M.
Vélez I.D.
Wangchuk S.
Wellems T.E.
White N.J.
William T.
Yasnot M.F.
Yilma D.
Author's Affiliation
Faculty of Tropical Medicine, Mahidol University
Ethiopian Public Health Institute
Oxford University Clinical Research Unit
Universidad de Córdoba, Monteria
Cambridge Institute for Medical Research
University of Gondar
Jiangsu Institute of Parasitic Diseases
Ministry of Health Myanmar
Université d'Antananarivo
Institut Pasteur de Madagascar
University of Khartoum Faculty of Medicine
Gokila
Universidad Peruana Cayetano Heredia
Jimma University
Armauer Hansen Research Institute
Addis Ababa University
University of Colombo
Eijkman Institute for Molecular Biology
Universidad del Valle, Cali
Instituto de Higiene e Medicina Tropical
Universidad de Antioquia
Shoklo Malaria Research Unit
Harvard T.H. Chan School of Public Health
Walter and Eliza Hall Institute of Medical Research
Menzies School of Health Research
QIMR Berghofer Medical Research Institute
Parsons Corporation
Fiocruz Amazônia
Deakin University
Nanjing Medical University
National Institute of Allergy and Infectious Diseases (NIAID)
Mahosot Hospital, Lao
Mahidol University
International Centre for Diarrhoeal Disease Research Bangladesh
Nuffield Department of Medicine
Universidade de São Paulo
National Institutes of Health (NIH)
Wellcome Sanger Institute
Burnet Institute
Hormozgan University of Medical Sciences
Nangarhar University
Dev Care Foundation
Ministry of Health
Universités d'Antananarivo et de Mahajanga
Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit
MilliporeSigma
Centro de Investigaciones Clínicas
Umphang Hospital
Fundação de Medicina Tropical Dr. Heitor Vieira Dourado
Centro Internacionale de Entrenamiento e Investigaciones Medicas
Centro de Pesquisa em Medicina Tropical de Rondônia
Government of Vanuatu
Queen Elizabeth Hospital
Ethiopian Public Health Institute
Oxford University Clinical Research Unit
Universidad de Córdoba, Monteria
Cambridge Institute for Medical Research
University of Gondar
Jiangsu Institute of Parasitic Diseases
Ministry of Health Myanmar
Université d'Antananarivo
Institut Pasteur de Madagascar
University of Khartoum Faculty of Medicine
Gokila
Universidad Peruana Cayetano Heredia
Jimma University
Armauer Hansen Research Institute
Addis Ababa University
University of Colombo
Eijkman Institute for Molecular Biology
Universidad del Valle, Cali
Instituto de Higiene e Medicina Tropical
Universidad de Antioquia
Shoklo Malaria Research Unit
Harvard T.H. Chan School of Public Health
Walter and Eliza Hall Institute of Medical Research
Menzies School of Health Research
QIMR Berghofer Medical Research Institute
Parsons Corporation
Fiocruz Amazônia
Deakin University
Nanjing Medical University
National Institute of Allergy and Infectious Diseases (NIAID)
Mahosot Hospital, Lao
Mahidol University
International Centre for Diarrhoeal Disease Research Bangladesh
Nuffield Department of Medicine
Universidade de São Paulo
National Institutes of Health (NIH)
Wellcome Sanger Institute
Burnet Institute
Hormozgan University of Medical Sciences
Nangarhar University
Dev Care Foundation
Ministry of Health
Universités d'Antananarivo et de Mahajanga
Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit
MilliporeSigma
Centro de Investigaciones Clínicas
Umphang Hospital
Fundação de Medicina Tropical Dr. Heitor Vieira Dourado
Centro Internacionale de Entrenamiento e Investigaciones Medicas
Centro de Pesquisa em Medicina Tropical de Rondônia
Government of Vanuatu
Queen Elizabeth Hospital
Other Contributor(s)
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.