estMOI: estimating multiplicity of infection using parasite deep sequencing data.
Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission.
London 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.
Samuel A
SA
Assefa
Mark D
MD
Preston
Susana
S
Campino
Harold
H
Ocholla
Colin J
CJ
Sutherland
Taane G
TG
Clark
D000465:Algorithms; D000818:Animals; D018503:Genome, Protozoan; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016778:Malaria, Falciparum / Q000453:epidemiology / Q000469:parasitology*; D010963:Plasmodium falciparum / Q000235:genetics* / Q000302:isolation & purification; D011110:Polymorphism, Genetic; D012984:Software