ArticlePLoS computational biology2023
coiaf: Directly estimating complexity of infection with allele frequencies.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- Molecular surveillance of multiplicity of infection, haplotype frequencies, and prevalence in infectious diseases.PLoS computational biology · 2026Article
- Population genomics of Plasmodium malariae from 4 African countries.JCI insight · 2026Article
- Malaria control and the unexpected spread of diagnostic-resistantbioRxiv : the preprint server for biology · 2026Article
- Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites.Genome medicine · 2026Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Probabilistic classification of late treatment failure in uncomplicated falciparum malaria.Nature communications · 2025Article
- Highly multiplexed molecular inversion probe panel inFrontiers in genetics · 2025Article
- Review of MrsFreqPhase methods: methods designed to estimate statistically malaria parasite multiplicity of infection, relatedness, frequency and phase.Malaria journal · 2024Review
- MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data.Bioinformatics (Oxford, England) · 2024Article
- SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
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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.