ArticleScientific reports2019
Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic diversity, population structure, and drug resistance of Plasmodium falciparum in Kenya: a systematic review and meta-analysis.Malaria journal · 2025Pooled it
- Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials.Scientific reports · 2025Trial
- Persistent and multiclonal malaria parasite dynamics despite extended artemether-lumefantrine treatment in children.Nature communications · 2024Trial
- Comparison of techniques and markers to distinguish Plasmodium falciparum recrudescence from new infection in Rwanda.Scientific reports · 2026Article
- UnderstandingiScience · 2026Article
- Classification of outcomes in antimalarial therapeutic efficacy studies with Aster.Antimicrobial agents and chemotherapy · 2026Article
- SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool.Malaria journal · 2026Article
- Target product profiles of laboratory and data analytical frameworks for genotyping to monitor antimalarial efficacy.PLOS global public health · 2026Article
- Classification of outcomes in antimalarial therapeutic efficacy studies with Aster.bioRxiv : the preprint server for biology · 2025Article
- A NovelmedRxiv : the preprint server for health sciences · 2025Article
- UnderstandingmedRxiv : the preprint server for health sciences · 2025Article
- Detection of novelMicrobial genomics · 2025Article
- Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda.Scientific reports · 2025Article
- Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination.The American journal of tropical medicine and hygiene · 2025Review
- Geo-classification of drug-resistant travel-associatedAntimicrobial agents and chemotherapy · 2024Article
- Article
- Additional blood meals increase sporozoite infection in Anopheles mosquitoes but not Plasmodium falciparum genetic diversity.Scientific reports · 2024Article
- Molecular tools are crucial for malaria elimination.Molecular biology reports · 2024Review
- Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing.Malaria journal · 2024Article
- Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures.PLOS global public health · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
Clinical trials monitoring malaria drug resistance require genotyping of recurrent Plasmodium falciparum parasites to distinguish between treatment failure and new infection occurring during the trial follow up period. Because trial participants usually harbour multi-clonal P. falciparum infections, deep amplicon sequencing (AmpSeq) was employed to improve sensitivity and reliability of minority clone detection. Paired samples from 32 drug trial participants were Illumina deep-sequenced for five molecular markers. Reads were analysed by custom-made software HaplotypR and trial outcomes compared to results from the previous standard genotyping method based on length-polymorphic markers. Diversity of AmpSeq markers in pre-treatment samples was comparable or higher than length-polymorphic markers. AmpSeq was highly reproducible with consistent quantification of co-infecting parasite clones within a host. Outcomes of the three best-performing markers, cpmp, cpp and ama1-D3, agreed in 26/32 (81%) of patients. Discordance between the three markers performed per sample was much lower by AmpSeq (six patients) compared to length-polymorphic markers (eleven patients). Using AmpSeq for discrimination of recrudescence and new infection in antimalarial drug trials provides highly reproducible and robust characterization of clone dynamics during trial follow-up. AmpSeq overcomes limitations inherent to length-polymorphic markers. Regulatory clinical trials of antimalarial drugs will greatly benefit from this unbiased typing method.
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Registered trials
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 OpenQuestion graph.