ArticleScientific reports2025
Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health.
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Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials.Scientific reports · 2025Trial
- Prevalence of Molecular Markers of Resistance to Antimalarial Drugs Three Years After Perennial Malaria Chemoprevention in Sierra Leone.Gates open research · 2025Trial
- MalDeepSeq panel: A targeted ultra-deep sequencing approach to trace drug resistance markers in Plasmodium falciparum.Cell reports methods · 2026Article
- Sustained high prevalence of multiple antimalarial drug resistance markers in Uganda in 2023-2024.Antimicrobial agents and chemotherapy · 2026Article
- Estimating probabilities of malaria importation in southern Mozambique through modellingeLife · 2026Article
- First TES in Djibouti: A Critical Milestone Amid Rising Regional Threats.Open forum infectious diseases · 2026Article
- Geographical Variation in Antimalarial Drug Resistance Marker Prevalence Across the Southern African Elimination Eight Region.medRxiv : the preprint server for health sciences · 2026Article
- Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing.Nature communications · 2026Article
- Classification of outcomes in antimalarial therapeutic efficacy studies with Aster.Antimicrobial agents and chemotherapy · 2026Article
- PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax.PLoS neglected tropical diseases · 2026Article
- Sustained High Prevalence of Multiple Antimalarial Drug Resistance Markers in Uganda in 2023-24.medRxiv : the preprint server for health sciences · 2026Article
- Accuracy of Plasmodium falciparum genetic data for estimating parasite prevalence and malaria incidence in Uganda.Malaria journal · 2026Article
- Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae.bioRxiv : the preprint server for biology · 2026Article
- SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool.Malaria journal · 2026Article
- Imported malaria predominates in near-elimination settings in Southwestern Uganda.medRxiv : the preprint server for health sciences · 2026Article
- Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites.Genome medicine · 2026Article
- Target product profiles of laboratory and data analytical frameworks for genotyping to monitor antimalarial efficacy.PLOS global public health · 2026Article
- Imported malaria predominates in near-elimination settings in Southwestern Uganda.PLOS global public health · 2026Article
- Mixed malaria infections: A critical review and Detect-Characterise-Act surveillance framework.Current research in parasitology & vector-borne diseases · 2026Review
- The Portable Microhaplotype Object and Tools.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
34 authors.
Andrés Aranda-DíazEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA. andres.aranda@isglobal.org.
Eric Neubauer Vickers *EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Kathryn Murie *EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Brian Palmer *EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Nicholas HathawayEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Inna GerlovinaEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Simone BoeneCentro de Investigação em Saúde de Manhiça, Maputo, Mozambique.
Manuel García-UlloaISGlobal, Barcelona, Spain.
Pau CisteróISGlobal, Barcelona, Spain.
Thomas KatairoInfectious Diseases Research Collaboration, Kampala, Uganda.
Francis Ddumba SemakubaInfectious Diseases Research Collaboration, Kampala, Uganda.
Bienvenu NsengimaanaInfectious Diseases Research Collaboration, Kampala, Uganda.
Hazel GwarindaLaboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre of Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.
Carla García-FernándezISGlobal, Barcelona, Spain.
William LouieEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Endashaw EsayasArmauer Hansen Research Institute, Addis Ababa, Ethiopia.
Clemente Da SilvaCentro de Investigação em Saúde de Manhiça, Maputo, Mozambique.
Debayan DattaISGlobal, Barcelona, Spain.
Shahiid KiyagaInfectious Diseases Research Collaboration, Kampala, Uganda.
Innocent WiringilimaanaInfectious Diseases Research Collaboration, Kampala, Uganda.
Sindew Mekasha FelekeEthiopian Public Health Institute, Addis Ababa, Ethiopia.
Adam BennettPATH, Seattle, WA, USA.
Jennifer L SmithGlobal Health Group, Malaria Elimination Initiative, University of California, San Francisco, USA.
Endalamaw GadisaArmauer Hansen Research Institute, Addis Ababa, Ethiopia.
Jonathan B ParrDivision of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
Melissa D ConradDivision of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Jaishree RamanLaboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre of Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.
Stephen TukwasibweInfectious Diseases Research Collaboration, Kampala, Uganda.
Isaac SsewanyanaInfectious Diseases Research Collaboration, Kampala, Uganda.
Eduard Rovira-VallbonaISGlobal, Barcelona, Spain.
Cristina M TatoChan Zuckerberg Biohub, San Francisco, CA, USA.
Jessica BriggsEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Alfredo MayorCentro de Investigação em Saúde de Manhiça, Maputo, Mozambique.
Bryan GreenhouseEPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.
Funding
Epidemiology and determinants of emerging artemisinin-resistant malaria in EthiopiaR01AI177791 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Jonathan Boyd Parr · 2023 to 2026
$3.2MSurveillance to track and characterize antimalarial resistance trends in Ugandan Plasmodium falciparum parasites (STARTUP)R01AI173557 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Melissa D Conrad · 2023 to 2026
$2.9MMentoring translational scientists in international infectious disease researchK24AI144048 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Bryan R Greenhouse · 2019 to 2026
$1.6MData and analysis ecosystem for eukaryotic pathogen targeted sequencingU01AI184646 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GREENHOUSE, BRYAN R · 2024 to 2025
$1.5MImproving the accuracy of malaria surveillance with serology and parasite genetic dataK23AI166009 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Jessica Briggs · 2022 to 2026
$955kGenetics Modifiers of Anthrax Lethal Toxin Induced PathophysiologyR01AI077791 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BRADLEY, KENNETH ALAN · 2009 to 2010
$765kGenetic and social network analysis to target interventions for malaria eliminationK01AI153555 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SMITH, JENNIFER LINNEA · 2020 to 2024
$725kTranslational Studies of Plasmodium Falciparum Infection DynamicsK23AI076614 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GREENHOUSE, BRYAN R · 2008 to 2012
$609kBill and Melinda Gates Foundation OPP1132226Bill and Melinda Gates Foundation OPP1209843Bill & Melinda Gates Foundation INV-003212Bill & Melinda Gates Foundation INV-019032Bill & Melinda Gates Foundation INV-024346Bill & Melinda Gates Foundation INV-031512Bill & Melinda Gates Foundation INV-037316Departament d'Universitats i Recerca, Generalitat de Catalunya 2017 SGR 664Gates Foundation INV-003212Gates Foundation INV-019032Gates Foundation INV-024346Gates Foundation INV-031512Gates Foundation INV-037316Generalitat de Catalunya CEX2023-0001290-SGlobal Fund EPHI5405Ministerio de Ciencia e Innovación PID2020-118328RB-I00/AEI/10.13039/501100011033National Institute of Allergy and Infectious Diseases 5K01AI153555National Institute of Allergy and Infectious Diseases K23AI166009National Institute of Allergy and Infectious Diseases K24AI144048National Institute of Allergy and Infectious Diseases R01 AI77791NIAID NIH HHS K01 AI153555NIAID NIH HHS K23 AI076614NIAID NIH HHS K23 AI166009NIAID NIH HHS K24 AI144048NIAID NIH HHS R01 AI077791NIAID NIH HHS R01 AI173557NIAID NIH HHS R01 AI177791NIAID NIH HHS U01 AI184646
Abstract
Targeted amplicon sequencing is a powerful and efficient tool for interrogating the Plasmodium falciparum genome, generating actionable data from infections to complement traditional malaria epidemiology. For maximum impact, genomic tools should be multi-purpose, robust, sensitive, and reproducible. We developed, characterized, and implemented MAD
Indexed as
Drug ResistanceGenetic VariationMalaria, FalciparumPlasmodium falciparumAnimalsComputational BiologyGene FrequencyHaplotypesHigh-Throughput Nucleotide SequencingHumansPublic HealthSequence Analysis, DNAAntimalarial resistanceComplexity of infectionCsphrp2 deletionIdentity-by-descentMalariaMicrohaplotypePlasmodium falciparumTargeted amplicon sequencing
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