ArticleCommunications biology2022
A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.
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Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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0cells of the map it votes in
18citing papers in PubMed
5.4field-weighted citation impact, top 4% of its field
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages.Nature communications · 2025Trial
- Building the toolkit to address malaria resurgence and radical cure of vivax malaria in Ethiopia: a meeting report.Malaria journal · 2026Article
- Spatiotemporal differentiation of Plasmodium vivax populations in the western Greater Mekong Subregion using a 22-SNP barcode.PLoS neglected tropical diseases · 2026Article
- PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax.PLoS neglected tropical diseases · 2026Article
- Genomics in Epidemiology and Disease Surveillance: An Exploratory Analysis.Life (Basel, Switzerland) · 2025Review
- Article
- Genetic characterization ofLancet regional health. Americas · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.bioRxiv : the preprint server for biology · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.GigaScience · 2025Article
- Detecting imported malaria infections in endemic settings using molecular surveillance: current state and challenges.Frontiers in epidemiology · 2025Review
- Geo-classification of drug-resistant travel-associatedAntimicrobial agents and chemotherapy · 2024Article
- High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes.Nature communications · 2024Article
- Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites.Nature communications · 2024Article
- Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay.PLoS neglected tropical diseases · 2024Article
- Imported malaria into Australia: surveillance insights and opportunities.Journal of travel medicine · 2024Article
- Analytic Approaches in Genomic Epidemiological Studies of Parasitic Protozoa.Transboundary and emerging diseases · 2024Review
- Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.Frontiers in genetics · 2024Article
- minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.PeerJ · 2023Article
Corrections and comments
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Authors and funding
62 authors at 20 institutions in 21 countries.
Hidayat TrimarsantoGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
Roberto AmatoWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Richard D PearsonWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0002-7386-3566
Edwin SutantoEijkman Institute for Molecular Biology, Jakarta, Indonesia.ORCID 0000-0002-2997-4648
Rintis NoviyantiEijkman Institute for Molecular Biology, Jakarta, Indonesia.
Leily TriantyEijkman Institute for Molecular Biology, Jakarta, Indonesia.
Jutta MarfurtGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.ORCID 0000-0002-3846-0825
Zuleima PavaGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
Diego F EcheverryInternational Training and Medical Research Center (CIDEIM), Cali, Colombia.ORCID 0000-0003-0301-4478
Tatiana M Lopera-MesaMalaria Group, Universidad de Antioquia, Medellin, Colombia.
Lidia M MontenegroMalaria Group, Universidad de Antioquia, Medellin, Colombia.
Alberto Tobón-CastañoMalaria Group, Universidad de Antioquia, Medellin, Colombia.ORCID 0000-0002-1671-2649
Matthew J GriggGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.ORCID 0000-0001-9914-8352
Bridget BarberGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
Timothy WilliamInfectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia.
Nicholas M AnsteyGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
Sisay GetachewCollege of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
Beyene PetrosCollege of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
Abraham AseffaArmauer Hansen Research Institute, Addis Ababa, Ethiopia.
Ashenafi AssefaEthiopian Public Health Institute, Addis Ababa, Ethiopia.
Awab G RahimMahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
Nguyen H ChauOxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
Tran T HienOxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
Mohammad S AlamInfectious Diseases Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh.ORCID 0000-0001-8330-5499
Wasif A KhanInfectious Diseases Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh.ORCID 0000-0002-7650-8068
Benedikt LeyGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.ORCID 0000-0002-5734-0845
Kamala ThriemerGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
Sonam WangchuckRoyal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan.
Yaghoob HamediInfectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran.
Ishag AdamFaculty of Medicine, University of Khartoum, Khartoum, Sudan.
Yaobao LiuNational 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.
Qi GaoNational 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.
Kanlaya SriprawatShoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
Marcelo U FerreiraDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Moses LamanPapua New Guinea Institute of Medical Research, Madang, Papua New Guinea.
Alyssa BarryDeakin University, Victoria, Australia.
Ivo MuellerPopulation Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.ORCID 0000-0001-6554-6889
Marcus V G LacerdaFundação de Medicina Tropical, Manaus, Brazil.ORCID 0000-0003-3374-9985
Alejandro Llanos-CuentasUniversidad Peruana Cayetano Heredia, Lima, Peru.
Srivicha KrudsoodMahidol University, Bangkok, Thailand.
Chanthap LonArmed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Rezika MohammedUniversity of Gondar, Gondar, Ethiopia.
Daniel YilmaJimma University, Jimma, Ethiopia.
Dhelio B PereiraCentro de Pesquisa em Medicina Tropical, Porto Velho, Brazil.ORCID 0000-0002-7761-5498
Fe E J EspinoResearch Institute for Tropical Medicine, Manilla, Philippines.ORCID 0000-0003-1690-1711
Cindy S ChuMahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
Iván D VélezMalaria Group, Universidad de Antioquia, Medellin, Colombia.
Chayadol Namaik-LarpUmphang Hospital, Tak, Thailand.
Maria F VillegasCentro de Investigaciones Clinicas, Cali, Colombia.
Justin A GreenGlaxoSmithKline, Brentford, UK.
Gavin KohGlaxoSmithKline, Brentford, UK.ORCID 0000-0002-7336-1566
Julian C RaynerWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0002-9835-1014
Eleanor DruryWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0002-9887-6961
Sónia GonçalvesWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Victoria SimpsonWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Olivo MiottoWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0001-8060-6771
Alistair MilesWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Nicholas J WhiteMahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
Francois NostenShoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.ORCID 0000-0002-7951-0745
Dominic P KwiatkowskiWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0002-5023-0176
Ric N PriceGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.ORCID 0000-0003-2000-2874
Sarah AuburnGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia. Sarah.Auburn@Menzies.edu.au.ORCID 0000-0002-4638-536X
Mahidol University · THCharles Darwin University · AUWellcome Sanger Institute · GBEijkman Institute for Molecular Biology · IDUniversidad de Antioquia · COArmauer Hansen Research Institute · ETGlaxoSmithKline (United Kingdom) · GBInternational Centre for Diarrhoeal Disease Research · BDJiangsu Institute of Parasitic Diseases · CNOxford University Clinical Research Unit · VNAddis Ababa University · ETArmed Forces Research Institute of Medical Science · THCentro de Investigación de la Caña de Azúcar de Colombia · COCentro Internacional de Entrenamiento e Investigaciones Medicas · CODeakin University · AUEthiopian Public Health Institute · ETFundação de Medicina Tropical · BRHormozgan University of Medical Sciences · IRInstitut Pasteur · FRJimma University · ET
Funding
Understanding, tracking and eliminating malaria transmission in the Asia - Pacific RegionU19AI129392 · NIAID · WALTER AND ELIZA HALL INST MEDICAL RES · PI Ivo J Mueller · 2017 to 2026
$7.1MMedical Research Council M006212Medical Research Council MR/M006212/1NIAID NIH HHS U19 AI129392Wellcome Trust 200909Wellcome Trust 200909/Z/16/ZWellcome Trust 204911Wellcome Trust 204911/Z/16/ZWellcome Trust 206194/Z/17/Z
Abstract
Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.
Indexed as
MalariaMalaria, VivaxHumansInternetLikelihood FunctionsPlasmodium vivax
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.