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estMOI: estimating multiplicity of infection using parasite deep sequencing data
Samuel A Assefa1, Mark D Preston, Susana Campino
1London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK and Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Box 30096 BT3, Blantyre, Malawia.
Bioinformatics (Oxford, England)
|January 21, 2014
Summary
Multiple parasite infections, or multiplicity of infection (MOI), are common in endemic areas. A new method using sequencing data accurately detects these complex Plasmodium falciparum infections, especially in high-transmission regions.
Area of Science:
- Parasitology
- Genetics
- Infectious Diseases
Background:
- Individuals in endemic areas often have multiple parasite strains, known as multiplicity of infection (MOI).
- MOI influences immune status and transmission intensity, and can confound population genetic analyses assuming clonal isolates.
- Current PCR-based methods for MOI estimation, like genotyping merozoite surface protein (MSP1/2) genes in Plasmodium falciparum, often underestimate true MOI.
Purpose of the Study:
- To develop and present a novel, sensitive method for estimating MOI using genome-wide sequencing data.
- To implement this method in user-friendly software called estMOI.
- To assess the prevalence of multiple infections in clinical Plasmodium falciparum isolates.
Main Methods:
- Utilizing deep coverage sequencing data to detect MOI by analyzing the abundance of heterozygous genotypes across the genome.
- Developing a method that considers unique combinations of polymorphisms from sequence reads to estimate MOI.
- Applying the estMOI software to clinical Plasmodium falciparum isolates from diverse geographical regions.
Main Results:
- The estMOI method accurately estimates MOI by leveraging genome-wide heterozygous genotype data.
- Multiple Plasmodium falciparum infections were found to be prevalent across clinical isolates analyzed.
- High transmission intensity regions showed a particularly high frequency of multiple infections.
Conclusions:
- Genome-wide sequencing data offers a more sensitive approach to detect and estimate MOI compared to traditional methods.
- The estMOI software provides a valuable tool for accurate MOI assessment in Plasmodium falciparum.
- Understanding MOI is crucial for accurate population genetic studies and for assessing malaria transmission dynamics.
