Wellcome Open Research (Apr 2022)
An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved]
- Sonia Goncalves,
- Lemu Golassa,
- Wasif Khan,
- Sisay Alemu,
- Mohammad Shafiul Alam,
- Pharath Lim,
- Elizabeth Ashley,
- Nicholas M Anstey,
- Bridget E Barber,
- Jutta Marfurt,
- Ashenafi Assefa,
- Dhelio Batista Pereira,
- Alyssa Barry,
- Nguyen Hoang Chau,
- Jun Cao,
- Fe Espino,
- Cindy Chu,
- Ivo Mueller,
- María Fernanda Villegas,
- Rick Fairhurst,
- Thuy-Nhien Nguyen,
- Yaghoob Hamedi,
- Matthew J Grigg,
- Rintis Noviyanti,
- Ye Htut,
- Tran Tinh Hien,
- Nadira Karunaweera,
- Kimberly J Johnson,
- Dominic P Kwiatkowski,
- Srivicha Krudsood,
- Francois Nosten,
- Benedikt Ley,
- Marcus Lacerda,
- Alejandro Llanos-Cuentas,
- Yaobao Liu,
- Tatiana Lopera-Mesa,
- Milijaona Randrianarivelojosia,
- Chanthap Lon,
- Sasithon Pukrittayakamee,
- Rezika Mohammed,
- Pascal Michon,
- Paul N Newton,
- Chayadol Namaik-larp,
- Richard D Pearson,
- Julian C Rayner,
- Zuleima Pava,
- Aung P Phyo,
- Beyene Petros,
- Awab Ghulam Rahim,
- Ric N Price,
- Sasha V Siegel,
- Angela Rumaseb,
- Kamala Thriemer,
- Victoria J Simpson,
- Marcelo Urbano Ferreira,
- Alberto Tobon-Castano,
- Sonam Wangchuk,
- Ivan D Vélez,
- Nicholas J White,
- Thomas E Wellems,
- Maria F Yasnot,
- Arjen M. Dondorp,
- Timothy William,
- Daniel Yilma,
- Sarah Auburn,
- Hidayat Trimarsanto,
- Abraham Aseffa,
- Qi Gao,
- Roberto Amato,
- Voahangy Andrianaranjaka,
- Ishag Adam,
- Kesinee Chotivanich,
- Olivo Miotto,
- Chanaki Amaratunga,
- Eleanor Drury,
- Diego F. Echeverry,
- Berhanu Erko,
- Abdul Faiz
Affiliations
- Sonia Goncalves
- Wellcome Sanger Institute, Hinxton, UK
- Lemu Golassa
- ORCiD
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Wasif Khan
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
- Sisay Alemu
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
- Mohammad Shafiul Alam
- ORCiD
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
- Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Elizabeth Ashley
- ORCiD
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Bridget E Barber
- ORCiD
- Menzies School of Health Research, Darwin, Australia
- Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Dhelio Batista Pereira
- ORCiD
- Centro de Pesquisa em Medicina Tropical de Rondônia, Porto Velho, Brazil
- Alyssa Barry
- Walter and Eliza Hall Institute, Parkville, Australia
- Nguyen Hoang Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Jun Cao
- 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
- Fe Espino
- ORCiD
- Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
- Cindy Chu
- ORCiD
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Australia
- María Fernanda Villegas
- Centro de Investigaciones Clinicas, Cali, Colombia
- Rick Fairhurst
- National Institutes of Health (NIH), Bethesda, USA
- Thuy-Nhien Nguyen
- ORCiD
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Yaghoob Hamedi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Matthew J Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Ye Htut
- Department of Medical Research, Yangon, Myanmar
- Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nadira Karunaweera
- ORCiD
- University of Colombo, Colombo, Sri Lanka
- Kimberly J Johnson
- Wellcome Sanger Institute, Hinxton, UK
- Dominic P Kwiatkowski
- ORCiD
- Wellcome Sanger Institute, Hinxton, UK
- Srivicha Krudsood
- Mahidol University, Bangkok, Thailand
- Francois Nosten
- ORCiD
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Benedikt Ley
- ORCiD
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Marcus Lacerda
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil
- Alejandro Llanos-Cuentas
- Cayetano Heredia University, Lima, Peru
- Yaobao Liu
- 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
- Tatiana Lopera-Mesa
- Universidad de Antioquia, Medellin, Colombia
- Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
- Sasithon Pukrittayakamee
- Mahidol University, Bangkok, Thailand
- Rezika Mohammed
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia
- Pascal Michon
- National University of Vanuatu, Port-Vila, Vanuatu
- Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Chayadol Namaik-larp
- Umphang Hospital, Tak, Thailand
- Richard D Pearson
- ORCiD
- Wellcome Sanger Institute, Hinxton, UK
- Julian C Rayner
- ORCiD
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Zuleima Pava
- Centro Internacionale de Entrenamiento e Investigaciones Medicas, Cali, Colombia
- Aung P Phyo
- ORCiD
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Beyene Petros
- Addis Ababa University, Addis Ababa, Ethiopia
- Awab Ghulam Rahim
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan
- Ric N Price
- ORCiD
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Sasha V Siegel
- Wellcome Sanger Institute, Hinxton, UK
- Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Victoria J Simpson
- Wellcome Sanger Institute, Hinxton, UK
- Marcelo Urbano Ferreira
- ORCiD
- Universidade de São Paulo, São Paulo, Brazil
- Alberto Tobon-Castano
- Universidad de Antioquia, Medellin, Colombia
- Sonam Wangchuk
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
- Ivan D Vélez
- University of Antioquia, Medellin, Colombia
- Nicholas J White
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Thomas E Wellems
- ORCiD
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Maria F Yasnot
- ORCiD
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
- Arjen M. Dondorp
- ORCiD
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Timothy William
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Daniel Yilma
- ORCiD
- Jimma University, Jimma, Ethiopia
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Abraham Aseffa
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
- Qi Gao
- 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
- Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK
- Voahangy Andrianaranjaka
- Université d'Antananarivo, Antananarivo, Madagascar
- Ishag Adam
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Kesinee Chotivanich
- Mahidol University, Bangkok, Thailand
- Olivo Miotto
- ORCiD
- Wellcome Sanger Institute, Hinxton, UK
- Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Eleanor Drury
- Wellcome Sanger Institute, Hinxton, UK
- Diego F. Echeverry
- ORCiD
- Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
- Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Abdul Faiz
- ORCiD
- Dev Care Foundation, Dhaka, Bangladesh
- Journal volume & issue
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Vol. 7
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.
