ArticleMalaria journal2017
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity.
Article in Malaria journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 83 citations in OpenAlex.
- 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
- SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool.Malaria journal · 2026Article
- Distinguishing new from persistent infections at the strain level using longitudinal genotyping data.bioRxiv : the preprint server for biology · 2025Article
- Infection length and host environment influence on Plasmodium falciparum dry season reservoir.EMBO molecular medicine · 2024Article
- A retrospective analysis ofAntimicrobial agents and chemotherapy · 2024Article
- Genotyping Plasmodium falciparum gametocytes using amplicon deep sequencing.Malaria journal · 2024Article
- Microsatellites reveal high polymorphism and high potential for use in anti-malarial efficacy studies in areas with different transmission intensities in mainland Tanzania.Malaria journal · 2024Article
- Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing.Nature communications · 2024Article
- Molecular speciation of Plasmodium and multiplicity of P. falciparum infection in the Central region of Ghana.PLOS global public health · 2024Article
- Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures.PLOS global public health · 2024Article
- Amplicon deep sequencing of five highly polymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate population structure in Ethiopia.Malaria journal · 2023Article
- Plasmodium falciparum population structure inferred by msp1 amplicon sequencing of parasites collected from febrile patients in Kenya.Malaria journal · 2023Article
- AmpSeqR: an R package for amplicon deep sequencing data analysis.F1000Research · 2023Article
- East Africa International Center of Excellence for Malaria Research: Summary of Key Research Findings.The American journal of tropical medicine and hygiene · 2022Article
- Article
- Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study.Molecular ecology resources · 2022Article
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome.The Journal of infectious diseases · 2022Article
- Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations.International journal for parasitology. Drugs and drug resistance · 2021Review
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundHumans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali.
resultsA total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali.
conclusionsAmplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection may perform well for understanding COI, they may offer little geographic or temporal discrimination between parasite populations.
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